A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and ... View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-03-16

AUTHORS

Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf, Eugene V Koonin

ABSTRACT

BACKGROUND: All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated (cas) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. However, the proximity of CRISPR and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis. RESULTS: The protein sequences of the numerous cas gene products were classified into approximately 25 distinct protein families; several new functional and structural predictions are described. Comparative-genomic analysis of CRISPR and cas genes leads to the hypothesis that the CRISPR-Cas system (CASS) is a mechanism of defense against invading phages and plasmids that functions analogously to the eukaryotic RNA interference (RNAi) systems. Specific functional analogies are drawn between several components of CASS and proteins involved in eukaryotic RNAi, including the double-stranded RNA-specific helicase-nuclease (dicer), the endonuclease cleaving target mRNAs (slicer), and the RNA-dependent RNA polymerase. However, none of the CASS components is orthologous to its apparent eukaryotic functional counterpart. It is proposed that unique inserts of CRISPR, some of which are homologous to fragments of bacteriophage and plasmid genes, function as prokaryotic siRNAs (psiRNA), by base-pairing with the target mRNAs and promoting their degradation or translation shutdown. Specific hypothetical schemes are developed for the functioning of the predicted prokaryotic siRNA system and for the formation of new CRISPR units with unique inserts encoding psiRNA conferring immunity to the respective newly encountered phages or plasmids. The unique inserts in CRISPR show virtually no similarity even between closely related bacterial strains which suggests their rapid turnover, on evolutionary scale. Corollaries of this finding are that, even among closely related prokaryotes, the most commonly encountered phages and plasmids are different and/or that the dominant phages and plasmids turn over rapidly. CONCLUSION: We proposed previously that Cas proteins comprise a novel DNA repair system. The association of the cas genes with CRISPR and, especially, the presence, in CRISPR units, of unique inserts homologous to phage and plasmid genes make us abandon this hypothesis. It appears most likely that CASS is a prokaryotic system of defense against phages and plasmids that functions via the RNAi mechanism. The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. However, it appears that this inheritance is extremely unstable on the evolutionary scale such that the repertoires of unique psiRNAs are completely replaced even in closely related prokaryotes, presumably, in response to rapidly changing repertoires of dominant phages and plasmids. More... »

PAGES

7-7

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1745-6150-1-7

DOI

http://dx.doi.org/10.1186/1745-6150-1-7

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1011010591

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/16545108


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biochemistry and Cell Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA", 
          "id": "http://www.grid.ac/institutes/grid.419234.9", 
          "name": [
            "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Makarova", 
        "givenName": "Kira S", 
        "id": "sg:person.0676725351.01", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676725351.01"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA", 
          "id": "http://www.grid.ac/institutes/grid.267313.2", 
          "name": [
            "Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Grishin", 
        "givenName": "Nick V", 
        "id": "sg:person.015412226217.60", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015412226217.60"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA", 
          "id": "http://www.grid.ac/institutes/grid.419234.9", 
          "name": [
            "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Shabalina", 
        "givenName": "Svetlana A", 
        "id": "sg:person.0710230733.50", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0710230733.50"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA", 
          "id": "http://www.grid.ac/institutes/grid.419234.9", 
          "name": [
            "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wolf", 
        "givenName": "Yuri I", 
        "id": "sg:person.0634453251.89", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634453251.89"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA", 
          "id": "http://www.grid.ac/institutes/grid.419234.9", 
          "name": [
            "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Koonin", 
        "givenName": "Eugene V", 
        "id": "sg:person.01017015051.78", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01017015051.78"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/nrmicro1163", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017393430", 
          "https://doi.org/10.1038/nrmicro1163"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf02101285", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045563541", 
          "https://doi.org/10.1007/bf02101285"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00239-004-0046-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053505023", 
          "https://doi.org/10.1007/s00239-004-0046-3"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2148-5-57", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043482380", 
          "https://doi.org/10.1186/1471-2148-5-57"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrm1568", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000271628", 
          "https://doi.org/10.1038/nrm1568"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2003-4-12-r81", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016542336", 
          "https://doi.org/10.1186/gb-2003-4-12-r81"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2148-5-33", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012058457", 
          "https://doi.org/10.1186/1471-2148-5-33"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35052098", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031106143", 
          "https://doi.org/10.1038/35052098"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-4-41", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013163036", 
          "https://doi.org/10.1186/1471-2105-4-41"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb936", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030796576", 
          "https://doi.org/10.1038/nsmb936"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsb1101-953", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037147119", 
          "https://doi.org/10.1038/nsb1101-953"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/418244a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035887015", 
          "https://doi.org/10.1038/418244a"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2006-03-16", 
    "datePublishedReg": "2006-03-16", 
    "description": "BACKGROUND: All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated (cas) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. However, the proximity of CRISPR and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis.\nRESULTS: The protein sequences of the numerous cas gene products were classified into approximately 25 distinct protein families; several new functional and structural predictions are described. Comparative-genomic analysis of CRISPR and cas genes leads to the hypothesis that the CRISPR-Cas system (CASS) is a mechanism of defense against invading phages and plasmids that functions analogously to the eukaryotic RNA interference (RNAi) systems. Specific functional analogies are drawn between several components of CASS and proteins involved in eukaryotic RNAi, including the double-stranded RNA-specific helicase-nuclease (dicer), the endonuclease cleaving target mRNAs (slicer), and the RNA-dependent RNA polymerase. However, none of the CASS components is orthologous to its apparent eukaryotic functional counterpart. It is proposed that unique inserts of CRISPR, some of which are homologous to fragments of bacteriophage and plasmid genes, function as prokaryotic siRNAs (psiRNA), by base-pairing with the target mRNAs and promoting their degradation or translation shutdown. Specific hypothetical schemes are developed for the functioning of the predicted prokaryotic siRNA system and for the formation of new CRISPR units with unique inserts encoding psiRNA conferring immunity to the respective newly encountered phages or plasmids. The unique inserts in CRISPR show virtually no similarity even between closely related bacterial strains which suggests their rapid turnover, on evolutionary scale. Corollaries of this finding are that, even among closely related prokaryotes, the most commonly encountered phages and plasmids are different and/or that the dominant phages and plasmids turn over rapidly.\nCONCLUSION: We proposed previously that Cas proteins comprise a novel DNA repair system. The association of the cas genes with CRISPR and, especially, the presence, in CRISPR units, of unique inserts homologous to phage and plasmid genes make us abandon this hypothesis. It appears most likely that CASS is a prokaryotic system of defense against phages and plasmids that functions via the RNAi mechanism. The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. However, it appears that this inheritance is extremely unstable on the evolutionary scale such that the repertoires of unique psiRNAs are completely replaced even in closely related prokaryotes, presumably, in response to rapidly changing repertoires of dominant phages and plasmids.", 
    "genre": "article", 
    "id": "sg:pub.10.1186/1745-6150-1-7", 
    "inLanguage": "en", 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2726032", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2720255", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2726029", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2720267", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1036001", 
        "issn": [
          "1745-6150"
        ], 
        "name": "Biology Direct", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "1"
      }
    ], 
    "keywords": [
      "unique insert", 
      "related prokaryotes", 
      "evolutionary scale", 
      "target mRNAs", 
      "comparative-genomic analysis", 
      "eukaryotic RNA interference system", 
      "novel DNA repair system", 
      "plasmid genes", 
      "dominant phage", 
      "protein product sequences", 
      "RNA-dependent RNA polymerase", 
      "CRISPR-Cas systems", 
      "functional analogy", 
      "distinct protein families", 
      "short palindrome repeats", 
      "RNA interference system", 
      "related bacterial strains", 
      "DNA repair systems", 
      "bacterial genomes", 
      "bacterial chromosome", 
      "cas genes", 
      "palindrome repeats", 
      "RNA polymerase", 
      "RNAi mechanism", 
      "protein family", 
      "DNA repair", 
      "foreign genes", 
      "enzymatic machinery", 
      "prokaryotic system", 
      "heritable immunity", 
      "Clustered Regularly", 
      "gene products", 
      "mechanisms of defense", 
      "protein sequences", 
      "Cas proteins", 
      "CRISPR", 
      "prokaryotes", 
      "functional counterpart", 
      "genes", 
      "repair system", 
      "rapid turnover", 
      "structural predictions", 
      "plasmid", 
      "bacterial strains", 
      "phages", 
      "repair hypothesis", 
      "RNAi", 
      "siRNA system", 
      "hypothetical scheme", 
      "integration of fragments", 
      "protein", 
      "mRNA", 
      "computational analysis", 
      "hypothetical mechanism", 
      "sequence", 
      "interference system", 
      "inserts", 
      "novel form", 
      "product sequence", 
      "defense", 
      "genome", 
      "variable array", 
      "fragments", 
      "CASS components", 
      "chromosomes", 
      "repertoire", 
      "polymerase", 
      "immune system", 
      "repeats", 
      "machinery", 
      "comparative analysis", 
      "RNA", 
      "mechanism", 
      "bacteriophages", 
      "siRNAs", 
      "psiRNA", 
      "inheritance", 
      "Regularly", 
      "hypothesis", 
      "turnover", 
      "immunity", 
      "family", 
      "function", 
      "similarity", 
      "strains", 
      "repair", 
      "degradation", 
      "components", 
      "analysis", 
      "Ca", 
      "functioning", 
      "formation", 
      "response", 
      "proximity", 
      "presence", 
      "basis", 
      "counterparts", 
      "action", 
      "products", 
      "system", 
      "form", 
      "array", 
      "association", 
      "agents", 
      "respective agents", 
      "findings", 
      "scale", 
      "analogy", 
      "CAS", 
      "units", 
      "integration", 
      "prediction", 
      "shutdown", 
      "corollary", 
      "CASS", 
      "scheme", 
      "proximity of CRISPR", 
      "numerous cas gene products", 
      "cas gene products", 
      "Specific functional analogies", 
      "components of CASS", 
      "eukaryotic RNAi", 
      "apparent eukaryotic functional counterpart", 
      "eukaryotic functional counterpart", 
      "fragments of bacteriophage", 
      "prokaryotic siRNAs", 
      "translation shutdown", 
      "Specific hypothetical schemes", 
      "prokaryotic siRNA system", 
      "new CRISPR units", 
      "CRISPR units", 
      "putative RNA-interference-based immune system", 
      "RNA-interference-based immune system"
    ], 
    "name": "A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action", 
    "pagination": "7-7", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1011010591"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1745-6150-1-7"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "16545108"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1745-6150-1-7", 
      "https://app.dimensions.ai/details/publication/pub.1011010591"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-01-01T18:16", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220101/entities/gbq_results/article/article_415.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/1745-6150-1-7"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1745-6150-1-7'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1745-6150-1-7'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1745-6150-1-7'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1745-6150-1-7'


 

This table displays all metadata directly associated to this object as RDF triples.

285 TRIPLES      22 PREDICATES      172 URIs      151 LITERALS      7 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1745-6150-1-7 schema:about anzsrc-for:06
2 anzsrc-for:0601
3 anzsrc-for:0604
4 schema:author Nac6b1146c45b42e3b8e2d3fbaddef886
5 schema:citation sg:pub.10.1007/bf02101285
6 sg:pub.10.1007/s00239-004-0046-3
7 sg:pub.10.1038/35052098
8 sg:pub.10.1038/418244a
9 sg:pub.10.1038/nrm1568
10 sg:pub.10.1038/nrmicro1163
11 sg:pub.10.1038/nsb1101-953
12 sg:pub.10.1038/nsmb936
13 sg:pub.10.1186/1471-2105-4-41
14 sg:pub.10.1186/1471-2148-5-33
15 sg:pub.10.1186/1471-2148-5-57
16 sg:pub.10.1186/gb-2003-4-12-r81
17 schema:datePublished 2006-03-16
18 schema:datePublishedReg 2006-03-16
19 schema:description BACKGROUND: All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated (cas) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. However, the proximity of CRISPR and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis. RESULTS: The protein sequences of the numerous cas gene products were classified into approximately 25 distinct protein families; several new functional and structural predictions are described. Comparative-genomic analysis of CRISPR and cas genes leads to the hypothesis that the CRISPR-Cas system (CASS) is a mechanism of defense against invading phages and plasmids that functions analogously to the eukaryotic RNA interference (RNAi) systems. Specific functional analogies are drawn between several components of CASS and proteins involved in eukaryotic RNAi, including the double-stranded RNA-specific helicase-nuclease (dicer), the endonuclease cleaving target mRNAs (slicer), and the RNA-dependent RNA polymerase. However, none of the CASS components is orthologous to its apparent eukaryotic functional counterpart. It is proposed that unique inserts of CRISPR, some of which are homologous to fragments of bacteriophage and plasmid genes, function as prokaryotic siRNAs (psiRNA), by base-pairing with the target mRNAs and promoting their degradation or translation shutdown. Specific hypothetical schemes are developed for the functioning of the predicted prokaryotic siRNA system and for the formation of new CRISPR units with unique inserts encoding psiRNA conferring immunity to the respective newly encountered phages or plasmids. The unique inserts in CRISPR show virtually no similarity even between closely related bacterial strains which suggests their rapid turnover, on evolutionary scale. Corollaries of this finding are that, even among closely related prokaryotes, the most commonly encountered phages and plasmids are different and/or that the dominant phages and plasmids turn over rapidly. CONCLUSION: We proposed previously that Cas proteins comprise a novel DNA repair system. The association of the cas genes with CRISPR and, especially, the presence, in CRISPR units, of unique inserts homologous to phage and plasmid genes make us abandon this hypothesis. It appears most likely that CASS is a prokaryotic system of defense against phages and plasmids that functions via the RNAi mechanism. The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. However, it appears that this inheritance is extremely unstable on the evolutionary scale such that the repertoires of unique psiRNAs are completely replaced even in closely related prokaryotes, presumably, in response to rapidly changing repertoires of dominant phages and plasmids.
20 schema:genre article
21 schema:inLanguage en
22 schema:isAccessibleForFree true
23 schema:isPartOf N6e9c978ee52e4d73884b2791b5e43de7
24 Na7e4157f225b47cf9872e4e6729d0b32
25 sg:journal.1036001
26 schema:keywords CAS
27 CASS
28 CASS components
29 CRISPR
30 CRISPR units
31 CRISPR-Cas systems
32 Ca
33 Cas proteins
34 Clustered Regularly
35 DNA repair
36 DNA repair systems
37 RNA
38 RNA interference system
39 RNA polymerase
40 RNA-dependent RNA polymerase
41 RNA-interference-based immune system
42 RNAi
43 RNAi mechanism
44 Regularly
45 Specific functional analogies
46 Specific hypothetical schemes
47 action
48 agents
49 analogy
50 analysis
51 apparent eukaryotic functional counterpart
52 array
53 association
54 bacterial chromosome
55 bacterial genomes
56 bacterial strains
57 bacteriophages
58 basis
59 cas gene products
60 cas genes
61 chromosomes
62 comparative analysis
63 comparative-genomic analysis
64 components
65 components of CASS
66 computational analysis
67 corollary
68 counterparts
69 defense
70 degradation
71 distinct protein families
72 dominant phage
73 enzymatic machinery
74 eukaryotic RNA interference system
75 eukaryotic RNAi
76 eukaryotic functional counterpart
77 evolutionary scale
78 family
79 findings
80 foreign genes
81 form
82 formation
83 fragments
84 fragments of bacteriophage
85 function
86 functional analogy
87 functional counterpart
88 functioning
89 gene products
90 genes
91 genome
92 heritable immunity
93 hypothesis
94 hypothetical mechanism
95 hypothetical scheme
96 immune system
97 immunity
98 inheritance
99 inserts
100 integration
101 integration of fragments
102 interference system
103 mRNA
104 machinery
105 mechanism
106 mechanisms of defense
107 new CRISPR units
108 novel DNA repair system
109 novel form
110 numerous cas gene products
111 palindrome repeats
112 phages
113 plasmid
114 plasmid genes
115 polymerase
116 prediction
117 presence
118 product sequence
119 products
120 prokaryotes
121 prokaryotic siRNA system
122 prokaryotic siRNAs
123 prokaryotic system
124 protein
125 protein family
126 protein product sequences
127 protein sequences
128 proximity
129 proximity of CRISPR
130 psiRNA
131 putative RNA-interference-based immune system
132 rapid turnover
133 related bacterial strains
134 related prokaryotes
135 repair
136 repair hypothesis
137 repair system
138 repeats
139 repertoire
140 respective agents
141 response
142 scale
143 scheme
144 sequence
145 short palindrome repeats
146 shutdown
147 siRNA system
148 siRNAs
149 similarity
150 strains
151 structural predictions
152 system
153 target mRNAs
154 translation shutdown
155 turnover
156 unique insert
157 units
158 variable array
159 schema:name A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
160 schema:pagination 7-7
161 schema:productId N9542d2f1079c48f4a2932b0e77bb3d29
162 Na9a60f12a630474dae96f2440790fe91
163 Ncb4eb8fa89d7453c98f973f7c05fb38a
164 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011010591
165 https://doi.org/10.1186/1745-6150-1-7
166 schema:sdDatePublished 2022-01-01T18:16
167 schema:sdLicense https://scigraph.springernature.com/explorer/license/
168 schema:sdPublisher N30f4cc5d6bd64f42956a3d90202f90c0
169 schema:url https://doi.org/10.1186/1745-6150-1-7
170 sgo:license sg:explorer/license/
171 sgo:sdDataset articles
172 rdf:type schema:ScholarlyArticle
173 N30f4cc5d6bd64f42956a3d90202f90c0 schema:name Springer Nature - SN SciGraph project
174 rdf:type schema:Organization
175 N41c29e71e9e741b69327d6c2c7c7c8e2 rdf:first sg:person.01017015051.78
176 rdf:rest rdf:nil
177 N626ad27b928b4014ab9b6ec83ef39fbe rdf:first sg:person.015412226217.60
178 rdf:rest N62a9e7aa2cb34ca3850e6a6e858f9fee
179 N62a9e7aa2cb34ca3850e6a6e858f9fee rdf:first sg:person.0710230733.50
180 rdf:rest Nd8a25e93b8e643efb3d88b79a8626465
181 N6e9c978ee52e4d73884b2791b5e43de7 schema:issueNumber 1
182 rdf:type schema:PublicationIssue
183 N9542d2f1079c48f4a2932b0e77bb3d29 schema:name doi
184 schema:value 10.1186/1745-6150-1-7
185 rdf:type schema:PropertyValue
186 Na7e4157f225b47cf9872e4e6729d0b32 schema:volumeNumber 1
187 rdf:type schema:PublicationVolume
188 Na9a60f12a630474dae96f2440790fe91 schema:name dimensions_id
189 schema:value pub.1011010591
190 rdf:type schema:PropertyValue
191 Nac6b1146c45b42e3b8e2d3fbaddef886 rdf:first sg:person.0676725351.01
192 rdf:rest N626ad27b928b4014ab9b6ec83ef39fbe
193 Ncb4eb8fa89d7453c98f973f7c05fb38a schema:name pubmed_id
194 schema:value 16545108
195 rdf:type schema:PropertyValue
196 Nd8a25e93b8e643efb3d88b79a8626465 rdf:first sg:person.0634453251.89
197 rdf:rest N41c29e71e9e741b69327d6c2c7c7c8e2
198 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
199 schema:name Biological Sciences
200 rdf:type schema:DefinedTerm
201 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
202 schema:name Biochemistry and Cell Biology
203 rdf:type schema:DefinedTerm
204 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
205 schema:name Genetics
206 rdf:type schema:DefinedTerm
207 sg:grant.2720255 http://pending.schema.org/fundedItem sg:pub.10.1186/1745-6150-1-7
208 rdf:type schema:MonetaryGrant
209 sg:grant.2720267 http://pending.schema.org/fundedItem sg:pub.10.1186/1745-6150-1-7
210 rdf:type schema:MonetaryGrant
211 sg:grant.2726029 http://pending.schema.org/fundedItem sg:pub.10.1186/1745-6150-1-7
212 rdf:type schema:MonetaryGrant
213 sg:grant.2726032 http://pending.schema.org/fundedItem sg:pub.10.1186/1745-6150-1-7
214 rdf:type schema:MonetaryGrant
215 sg:journal.1036001 schema:issn 1745-6150
216 schema:name Biology Direct
217 schema:publisher Springer Nature
218 rdf:type schema:Periodical
219 sg:person.01017015051.78 schema:affiliation grid-institutes:grid.419234.9
220 schema:familyName Koonin
221 schema:givenName Eugene V
222 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01017015051.78
223 rdf:type schema:Person
224 sg:person.015412226217.60 schema:affiliation grid-institutes:grid.267313.2
225 schema:familyName Grishin
226 schema:givenName Nick V
227 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015412226217.60
228 rdf:type schema:Person
229 sg:person.0634453251.89 schema:affiliation grid-institutes:grid.419234.9
230 schema:familyName Wolf
231 schema:givenName Yuri I
232 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634453251.89
233 rdf:type schema:Person
234 sg:person.0676725351.01 schema:affiliation grid-institutes:grid.419234.9
235 schema:familyName Makarova
236 schema:givenName Kira S
237 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676725351.01
238 rdf:type schema:Person
239 sg:person.0710230733.50 schema:affiliation grid-institutes:grid.419234.9
240 schema:familyName Shabalina
241 schema:givenName Svetlana A
242 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0710230733.50
243 rdf:type schema:Person
244 sg:pub.10.1007/bf02101285 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045563541
245 https://doi.org/10.1007/bf02101285
246 rdf:type schema:CreativeWork
247 sg:pub.10.1007/s00239-004-0046-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053505023
248 https://doi.org/10.1007/s00239-004-0046-3
249 rdf:type schema:CreativeWork
250 sg:pub.10.1038/35052098 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031106143
251 https://doi.org/10.1038/35052098
252 rdf:type schema:CreativeWork
253 sg:pub.10.1038/418244a schema:sameAs https://app.dimensions.ai/details/publication/pub.1035887015
254 https://doi.org/10.1038/418244a
255 rdf:type schema:CreativeWork
256 sg:pub.10.1038/nrm1568 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000271628
257 https://doi.org/10.1038/nrm1568
258 rdf:type schema:CreativeWork
259 sg:pub.10.1038/nrmicro1163 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017393430
260 https://doi.org/10.1038/nrmicro1163
261 rdf:type schema:CreativeWork
262 sg:pub.10.1038/nsb1101-953 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037147119
263 https://doi.org/10.1038/nsb1101-953
264 rdf:type schema:CreativeWork
265 sg:pub.10.1038/nsmb936 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030796576
266 https://doi.org/10.1038/nsmb936
267 rdf:type schema:CreativeWork
268 sg:pub.10.1186/1471-2105-4-41 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013163036
269 https://doi.org/10.1186/1471-2105-4-41
270 rdf:type schema:CreativeWork
271 sg:pub.10.1186/1471-2148-5-33 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012058457
272 https://doi.org/10.1186/1471-2148-5-33
273 rdf:type schema:CreativeWork
274 sg:pub.10.1186/1471-2148-5-57 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043482380
275 https://doi.org/10.1186/1471-2148-5-57
276 rdf:type schema:CreativeWork
277 sg:pub.10.1186/gb-2003-4-12-r81 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016542336
278 https://doi.org/10.1186/gb-2003-4-12-r81
279 rdf:type schema:CreativeWork
280 grid-institutes:grid.267313.2 schema:alternateName Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA
281 schema:name Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA
282 rdf:type schema:Organization
283 grid-institutes:grid.419234.9 schema:alternateName National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
284 schema:name National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
285 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...