CRISPR-Cas adaptive immunity

A reusable prokaryotic module for RNA-guided adaptive immunity against mobile genetic elements. The module has three obligate stages: adaptation, in which a Cas1-Cas2 integrase captures a protospacer from invading DNA and integrates it as a new spacer at the leader-proximal end of a CRISPR array; crRNA biogenesis, in which the transcribed array is processed into mature guides; and interference, in which a crRNA-loaded effector recognises a complementary target and destroys it. Effector architecture is the principal axis of variation and is modelled as alternative implementations rather than as separate modules: multi-subunit class 1 effectors (Cascade-Cas3, Csm/Cmr-Cas10) and single-protein class 2 effectors (Cas9, Cas12a, Cas13a) occupy the same structural slot in the pathway. Phage-encoded suppression of this module is a separate counter-defence module (MODULE:anti_crispr_suppression); host restriction-modification, BREX, retron, and other innate defence systems are outside the boundary, as is the laboratory use of Cas effectors as genome editors.

MODULE:crispr_cas_adaptive_immunityDRAFTCONCRETEBiological Processmodules/crispr_cas_adaptive_immunity.yaml
CRISPR-cas systemGO:0099048
GO:0099048
CRISPR-cas system
GO:0099048 supplies the module boundary and names the same three stages used here as parts: acquisition of foreign DNA into CRISPR loci, crRNA biogenesis, and target interference.
PMID:17379808
CRISPR provides acquired resistance against viruses in prokaryotes.
Establishes the heritable, sequence-specific nature of the system: spacer content determines phage resistance, which is the functional output the module delivers.
PMID:18703739
Small CRISPR RNAs guide antiviral defense in prokaryotes.
Establishes that the array is transcribed and processed into small guide RNAs by a Cas protein complex (Cascade), separating crRNA biogenesis from interference as distinct stages.
PMID:31857715
Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants.
Supplies the class 1 / class 2 effector division and the type-level subdivisions used as the variant axis for the interference part.
PMID:29522745
The Biology of CRISPR-Cas: Backward and Forward.
Review support for treating adaptation, biogenesis, and interference as the three canonical stages shared across all CRISPR-Cas types.

Three design decisions are worth recording. First, the effector variants are variants rather than sibling modules because they are interchangeable realisations of one pathway slot; a genome may carry several systems, so selection is ONE_OR_MORE rather than EXACTLY_ONE. Second, primed acquisition is modelled as a connection from interference back to adaptation rather than as a fourth part, since it reuses the same Cas1-Cas2 machinery. Third, GO has no molecular-function term for crRNA-guided target recognition, so surveillance complexes carry nucleic-acid-binding terms and the gap is recorded in knowledge_gaps rather than papered over with an ill-fitting id. Exemplars are drawn from the two best-characterised concrete systems -- Escherichia coli K-12 type I-E (Cas1 Q46896 through Cas3 P38036) and Pseudomonas aeruginosa PA14 type I-F (the Csy complex) -- plus the reviewed class 2 and type III effectors; they orient the families and are not a claim that the module is confined to those organisms.

11Nodes
3Parts
2Variant Sets
7Variants
13Annotons
3Connections

Derived QC

Recommended-field compliance

76.5% recommended fields populated
  • knowledge_gaps[0] · provenance (0/1)
  • knowledge_gaps[1] · provenance (0/1)
  • knowledge_gaps[2] · provenance (0/1)
  • knowledge_gaps[3] · provenance (0/1)

Module deep research

✗ none found

No MODULE:crispr_cas_adaptive_immunity deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • adaptation → crrna_biogenesis [NOT_CHECKED]
    Informational, not metabolic: the array produced by adaptation is the template transcribed and processed in biogenesis.

Function consistency and core coverage

16 gene-function check(s) reflected in core functions · 0 conflict(s) · 13 evidence or coverage gap(s) (32 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
cas1_integrase cas1 / ygbT (Escherichia coli K-12)
UniProtKB:Q46896
Family Representative 		DNA endonuclease activity
GO:0004520 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas1_integrase cas1 (Pseudomonas aeruginosa PA14)
UniProtKB:Q02ML7
Family Representative 		DNA endonuclease activity
GO:0004520 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas2_adaptation_subunit cas2 / ygbF (Escherichia coli K-12)
UniProtKB:P45956
Family Representative 		protein-macromolecule adaptor activity
GO:0030674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas6_processing_activity casE / cas6e (Escherichia coli K-12)
UniProtKB:Q46897
Family Representative 		RNA endonuclease activity
GO:0004521 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas6_processing_activity cas6f / csy4 (Pseudomonas aeruginosa PA14)
UniProtKB:Q02MM2
Family Representative 		RNA endonuclease activity
GO:0004521 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas6_processing_activity cas6 (Mycobacterium tuberculosis H37Rv)
UniProtKB:P9WPJ1
Family Representative 		RNA endonuclease activity
GO:0004521 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
rnase_iii_processing_activity rnc (Escherichia coli K-12)
UniProtKB:P0A7Y0
Family Representative 		ribonuclease III activity
GO:0004525 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cascade_surveillance_complex PROTEIN_COMPLEX
Gene 		double-stranded DNA binding
GO:0003690 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
cas3_target_degradation cas3 / ygcB (Escherichia coli K-12)
UniProtKB:P38036
Family Representative 		single-stranded DNA endonuclease activity
GO:0000014 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas3_target_degradation cas3 (Pseudomonas aeruginosa PA14, type I-F)
UniProtKB:Q02ML8
Family Representative 		single-stranded DNA endonuclease activity
GO:0000014 		Function Unreviewed
No retained annotation or core molecular function supports this GO assertion. Missing or broader evidence is a coverage gap, not proof the activity is absent.
cas10_hd_dnase DOMAIN
Gene 		single-stranded DNA endonuclease activity
GO:0000014 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
cas10_coa_synthesis DOMAIN
Gene 		cyclic oligoadenylate synthase activity
No function ID 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
csm6_coa_activated_rnase csm6 (Thermus thermophilus HB8)
UniProtKB:Q53W17
Family Representative 		RNA endonuclease activity
GO:0004521 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
csm6_coa_activated_rnase csm6 (Mycobacterium tuberculosis H37Rv)
UniProtKB:P71635
Family Representative 		RNA endonuclease activity
GO:0004521 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas9_rna_guided_dnase cas9 / csn1 (Streptococcus pyogenes M1)
UniProtKB:Q99ZW2
Family Representative 		DNA endonuclease activity
GO:0004520 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas9_rna_guided_dnase cas9 (Neisseria meningitidis 8013)
UniProtKB:C9X1G5
Family Representative 		DNA endonuclease activity
GO:0004520 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas12a_rna_guided_dnase cas12a / cpf1 (Acidaminococcus sp. BV3L6)
UniProtKB:U2UMQ6
Family Representative 		double-stranded DNA endonuclease activity
GO:1990238 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas12a_rna_guided_dnase cas12a / cpf1 (Francisella tularensis subsp. novicida)
UniProtKB:A0Q7Q2
Family Representative 		double-stranded DNA endonuclease activity
GO:1990238 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas12a_rna_guided_dnase:required_function cas12a / cpf1 (Acidaminococcus sp. BV3L6)
UniProtKB:U2UMQ6
Family Representative 		deoxyribonuclease I activity
GO:0004530 		Review Disagreement
The review removes, modifies, or marks this term over-annotated and provides no retained/core support. Review the rationale; rejection of an evidence row alone is not a biological NOT.
cas12a_rna_guided_dnase:required_function cas12a / cpf1 (Francisella tularensis subsp. novicida)
UniProtKB:A0Q7Q2
Family Representative 		deoxyribonuclease I activity
GO:0004530 		Review Disagreement
The review removes, modifies, or marks this term over-annotated and provides no retained/core support. Review the rationale; rejection of an evidence row alone is not a biological NOT.
cas13a_rna_guided_rnase cas13a / c2c2 (Leptotrichia shahii)
UniProtKB:P0DOC6
Family Representative 		RNA endonuclease activity
GO:0004521 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas13a_rna_guided_rnase cas13a / c2c2 (Leptotrichia buccalis)
UniProtKB:C7NBY4
Family Representative 		RNA endonuclease activity
GO:0004521 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cas1_integrase Cas1 integrase family
InterPro:IPR002729
Family 		DNA endonuclease activity
GO:0004520 		Family Review Missing
No supported structured family review is available for InterPro:IPR002729.
cas2_adaptation_subunit Cas2 family
InterPro:IPR010152
Family 		protein-macromolecule adaptor activity
GO:0030674 		Family Review Missing
No supported structured family review is available for InterPro:IPR010152.
cas6_processing_activity Cas6-family pre-crRNA endoribonuclease
Family 		RNA endonuclease activity
GO:0004521 		Family Id Missing
The family has no identifier linking it to a curated family review.
rnase_iii_processing_activity bacterial RNase III family
Family 		ribonuclease III activity
GO:0004525 		Family Id Missing
The family has no identifier linking it to a curated family review.
cas3_target_degradation Cas3 helicase-nuclease family
InterPro:IPR006474
Family 		single-stranded DNA endonuclease activity
GO:0000014 		Family Review Missing
No supported structured family review is available for InterPro:IPR006474.
csm6_coa_activated_rnase Csm6/Csx1 CARF-domain ribonuclease family
Family 		RNA endonuclease activity
GO:0004521 		Family Id Missing
The family has no identifier linking it to a curated family review.
cas9_rna_guided_dnase Cas9 family
InterPro:IPR028629
Family 		DNA endonuclease activity
GO:0004520 		Family Review Missing
No supported structured family review is available for InterPro:IPR028629.
cas12a_rna_guided_dnase Cas12a (Cpf1) family
InterPro:IPR027620
Family 		double-stranded DNA endonuclease activity
GO:1990238 		Family Review Missing
No supported structured family review is available for InterPro:IPR027620.
cas12a_rna_guided_dnase:required_function Cas12a (Cpf1) family
InterPro:IPR027620
Family 		deoxyribonuclease I activity
GO:0004530 		Family Review Missing
No supported structured family review is available for InterPro:IPR027620.
cas13a_rna_guided_rnase Cas13a (C2c2) family
InterPro:IPR053395
Family 		RNA endonuclease activity
GO:0004521 		Family Review Missing
No supported structured family review is available for InterPro:IPR053395.

Gene-review completeness (26/26 grounded genes reviewed)

25 complete review(s) · 0 with deep research · 0 missing review · 26 reviewed but lacking deep research

Gene Review Complete Deep research
cas1 Q02ML7 ✓ ✓ ✗
cas10 A0A0A7HFE1 ✓ ✓ ✗
cas10 Q53W19 ✓ ✓ ✗
cas12a A0Q7Q2 ✓ ✓ ✗
cas12a U2UMQ6 ✓ ✓ ✗
cas13a C7NBY4 ✓ ✓ ✗
cas13a P0DOC6 ✓ ✓ ✗
cas3 Q02ML8 ✓ ✓ ✗
cas6 P9WPJ1 ✓ ✓ ✗
cas6f Q02MM2 ✓ ✓ ✗
cas9 C9X1G5 ✓ ✓ ✗
cas9 Q99ZW2 ✓ ✓ ✗
casA Q46901 ✓ ✓ ✗
casB P76632 ✓ ✓ ✗
casC Q46899 ✓ ✓ ✗
casD Q46898 ✓ ✓ ✗
casE Q46897 ✓ ✓ ✗
csm6 P71635 ✓ ✓ ✗
csm6 Q53W17 ✓ ✓ ✗
csy1 Q02ML9 ✓ ✓ ✗
csy2 Q02MM0 ✓ ✓ ✗
csy3 Q02MM1 ✓ ✓ ✗
rnc P0A7Y0 ✓ ✓ ✗
ygbF P45956 ✓ ✓ ✗
ygbT Q46896 ✓ 23/24 ✗
ygcB P38036 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2 archaeaNCBITaxon:2157
CRISPR-Cas adaptive immunityBiological Processcrispr_cas_adaptive_immunity
CRISPR-cas systemGO:0099048
Context
bacteriaNCBITaxon:2 archaeaNCBITaxon:2157

Connections

Spacer integration determines the guide repertoire that biogenesis can produce.
crrna_biogenesis -> interference Provides Input For
Mature crRNA is the guide that loads the effector; an unprocessed array transcript cannot license interference.
interference -> adaptation Positively Regulates
Primed acquisition: partial target recognition by an existing guide stimulates Cas1-Cas2 to acquire further spacers from the same invader, making the module self-reinforcing rather than strictly linear.
Part 1: Adaptation - protospacer capture and spacer integration
spacer acquisitionBiological Processadaptation

Capture of a protospacer from invading DNA and its integration as a new spacer at the leader-proximal end of the CRISPR array, which is what makes the immunity heritable and adaptive.

maintenance of CRISPR repeat elementsGO:0043571

Annotons

Cas1 protospacer integrase
cas1_integrase
Participant: Family: Cas1 integrase family
Family:
Cas1 integrase familyInterPro:IPR002729
Representative Members: cas1 / ygbT (Escherichia coli K-12)UniProtKB:Q46896 cas1 (Pseudomonas aeruginosa PA14)UniProtKB:Q02ML7
Required Function:
DNA endonuclease activityGO:0004520

Function

DNA endonuclease activityGO:0004520
Substrates: protospacer-derived double-stranded DNA fragment CRISPR array leader-repeat junction
Products: CRISPR array carrying a newly integrated spacer

Processes

maintenance of CRISPR repeat elementsGO:0043571

Catalytic subunit of the adaptation complex; cleaves the leader-repeat junction and joins the protospacer ends into the array.

Cas2 adaptation complex subunit
cas2_adaptation_subunit
Participant: Family: Cas2 family
Family:
Cas2 familyInterPro:IPR010152
Representative Members: cas2 / ygbF (Escherichia coli K-12)UniProtKB:P45956

Function

protein-macromolecule adaptor activityGO:0030674 Non-catalytic but not functionless: Cas2 is the element whose removal abolishes acquisition. Deleting the beta6-beta7 hairpin destroys complex assembly, CRISPR-DNA binding and acquisition while leaving the putative active site intact, whereas active-site substitutions (E9Q/E9A/E9R) remain fully functional. DNA binding is a contributes_to claim only, since Cas2 does not bind the substrate alone.
Targets: Cas1 dimers within the adaptation complex protospacer duplex (via the shared arginine clamp)

Processes

maintenance of CRISPR repeat elementsGO:0043571

Dimeric adaptor that bridges two Cas1 dimers and, with Cas1, forms the clamp that measures the protospacer duplex. The bridging is asserted as an adaptor activity; the measuring is not, because GO has no term for it.

PMID:24793649
Cas1-Cas2 complex formation is required for spacer acquisition in vivo, and Cas2 acts as a structural rather than catalytic component of the integration complex.
Part 2: crRNA biogenesis
crRNA biogenesisBiological Processcrrna_biogenesis

Conversion of the primary CRISPR array transcript into mature, repeat-derived guides that license the effector. The processing chemistry differs by system type, which is the variant axis here.

Variant set: pre-crRNA maturation route by processing enzyme architecture (One Or More)

A genome carrying more than one CRISPR-Cas type will run more than one route, so ONE_OR_MORE is used; within a single system the routes are mutually exclusive. The RNase III route also carries a substrate-size bound that the Cas6 route does not: a single-spacer array is matured without it (PMID:23535272).

Cas6-family metal-independent endoribonuclease routeReactioncas6_endoribonuclease_route

The route used by class 1 systems and by type III: a Cas6-family enzyme cleaves within the repeat, either as a standalone enzyme or as an integral Cascade subunit.

Annotons

Cas6-family pre-crRNA endoribonuclease
cas6_processing_activity
Participant: Family: Cas6-family pre-crRNA endoribonuclease
Family:
Cas6-family pre-crRNA endoribonuclease Ferredoxin-fold repeat-specific endoribonucleases. The subtype-specific names Cas6, Cas6e/CasE/Cse3, and Cas6f/Csy4 denote orthologous activities placed differently relative to the surveillance complex.
Representative Members: casE / cas6e (Escherichia coli K-12)UniProtKB:Q46897 cas6f / csy4 (Pseudomonas aeruginosa PA14)UniProtKB:Q02MM2 cas6 (Mycobacterium tuberculosis H37Rv)UniProtKB:P9WPJ1
Required Function:
RNA endonuclease activityGO:0004521

Function

RNA endonuclease activityGO:0004521
Substrates: pre-crRNA (primary CRISPR array transcript)
Products: mature crRNA bearing a repeat-derived 5' handle

Processes

maintenance of CRISPR repeat elementsGO:0043571

Cleaves within each repeat to release single-spacer guides; in type I-E and I-F the enzyme remains bound to the product and nucleates the surveillance complex.

tracrRNA-dependent RNase III routeReactionrnase_iii_tracrrna_route

The type II route: a trans-encoded tracrRNA base-pairs with the repeat portion of pre-crRNA, and the resulting duplex is cut by housekeeping RNase III rather than by a Cas enzyme.

Annotons

RNase III pre-crRNA:tracrRNA duplex processing
rnase_iii_processing_activity
Participant: Family: bacterial RNase III family
Family:
bacterial RNase III family Housekeeping double-strand-specific endoribonuclease recruited by type II systems; it is not a Cas protein and is not encoded in the cas locus.
Representative Members: rnc (Escherichia coli K-12)UniProtKB:P0A7Y0
Required Function:
ribonuclease III activityGO:0004525

Function

ribonuclease III activityGO:0004525
Substrates: pre-crRNA:tracrRNA double-stranded region
Products: mature crRNA:tracrRNA guide duplex

Supplies the processing chemistry that type II systems do not encode themselves; the output is a two-RNA guide rather than a single crRNA.

Part 3: Interference - target recognition and destruction
target interferenceBiological Processinterference

crRNA-guided recognition of a complementary target and its destruction. Effector architecture varies more than any other part of the module and is modelled as a variant set over the same pathway slot.

defense response to virusGO:0051607
Variant set: crRNA-guided effector architecture by effector subunit composition and target chemistry (One Or More)
PMID:31857715
Supplies the class 1 / class 2 division and the type assignments used to name these variants.

Class 1 effectors are multi-subunit surveillance complexes that recruit a separate nuclease; class 2 effectors are single proteins that both recognise and cleave. Genomes frequently carry several systems of different types, hence ONE_OR_MORE.

Class 1 type I Cascade-Cas3 interferenceBiological Processcascade_cas3_variant

A multi-subunit Cascade surveillance complex forms a PAM-licensed R-loop at the target and recruits the processive Cas3 helicase-nuclease, which degrades the target DNA.

Annotons

Cascade crRNA-guided surveillance complex
cascade_surveillance_complex
Participant: Protein Complex: Cascade (CRISPR-associated complex for antiviral defence)
Protein Complex:
Cascade (CRISPR-associated complex for antiviral defence)GO:1990904 Multi-subunit class 1 surveillance complex built on a Cas7 backbone around a single crRNA. Named Cascade (CasABCDE) in type I-E and the Csy complex in type I-F. Grounded at GO:1990904 rather than the GO:0032991 root because the complex carries a crRNA; GO has no term for a CRISPR surveillance complex specifically (see knowledge_gaps).
Active units:
Cas8e/Cse1 large subunit
Participant: Gene Product: casA / cse1 (Escherichia coli K-12)
Gene Product:
casA / cse1 (Escherichia coli K-12)UniProtKB:Q46901 Escherichia coli K-12 casA/cse1.
Role: Recognises the PAM and recruits Cas3 to the licensed R-loop.
Cse2/CasB subunit
Participant: Gene Product: casB / cse2 (Escherichia coli K-12)
Gene Product:
casB / cse2 (Escherichia coli K-12)UniProtKB:P76632
Role: Stabilises the R-loop along the displaced strand.
Cas7 backbone subunit
Participant: Gene Product: casC / cas7 (Escherichia coli K-12)
Gene Product:
casC / cas7 (Escherichia coli K-12)UniProtKB:Q46899 The backbone surface targeted by several type I anti-CRISPR proteins.
Role: Oligomerises along the crRNA and presents the guide in segments for base pairing.
Cas5 subunit
Participant: Gene Product: casD / cas5 (Escherichia coli K-12)
Gene Product:
casD / cas5 (Escherichia coli K-12)UniProtKB:Q46898
Role: Caps the crRNA 5' handle and anchors it in the complex.
Cas6e processing subunit
Participant: Gene Product: casE / cas6e (Escherichia coli K-12)
Gene Product:
casE / cas6e (Escherichia coli K-12)UniProtKB:Q46897
Role: Retains the crRNA 3' hairpin after processing it, tying biogenesis to complex assembly.
Cas7f/Csy3 backbone subunit
Participant: Gene Product: csy3 / cas7f (Pseudomonas aeruginosa PA14)
Gene Product:
csy3 / cas7f (Pseudomonas aeruginosa PA14)UniProtKB:Q02MM1
Role: Type I-F backbone equivalent of Cas7; the surface bound by AcrIF8 and related inhibitors.
Cas8f/Csy1 large subunit
Participant: Gene Product: csy1 / cas8f (Pseudomonas aeruginosa PA14)
Gene Product:
csy1 / cas8f (Pseudomonas aeruginosa PA14)UniProtKB:Q02ML9
Role: Type I-F large subunit; PAM recognition and Cas3 recruitment.
Cas5f/Csy2 subunit
Participant: Gene Product: csy2 / cas5f (Pseudomonas aeruginosa PA14)
Gene Product:
csy2 / cas5f (Pseudomonas aeruginosa PA14)UniProtKB:Q02MM0
Role: Type I-F Cas5 equivalent.

Function

double-stranded DNA bindingGO:0003690 Stands in for crRNA-guided, PAM-licensed target recognition and R-loop formation, for which GO has no molecular-function term (see knowledge_gaps).

Processes

CRISPR-cas systemGO:0099048

Finds the target, verifies the PAM, and forms the R-loop that licenses nuclease recruitment; it does not itself degrade the target.

Cas3 helicase-nuclease target degradation
cas3_target_degradation
Participant: Family: Cas3 helicase-nuclease family
Family:
Cas3 helicase-nuclease familyInterPro:IPR006474
Representative Members: cas3 / ygcB (Escherichia coli K-12)UniProtKB:P38036 cas3 (Pseudomonas aeruginosa PA14, type I-F)UniProtKB:Q02ML8

Function

single-stranded DNA endonuclease activityGO:0000014 The committing step, and the one the immunity phenotype tracks: the HD-domain nick on the displaced strand. Degradation that follows is a coupled, separable activity, carried by GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity together with GO:0033677 DNA/RNA helicase activity. The helicase-motif mutant K320N separates them, which is why the nick rather than the exonuclease is asserted here.
Substrates: R-loop-displaced single-stranded target DNA
Products: nicked then processively degraded target DNA

Processes

defense response to virusGO:0051607 CRISPR-cas systemGO:0099048

Recruited by the large Cascade subunit to the licensed R-loop; nicks the displaced strand and then processively unwinds and degrades the target, making it the committed destruction step of type I systems.

Class 1 type III Csm/Cmr-Cas10 interference with cOA signallingBiological Processcas10_csm_variant

Type III effectors are licensed by target RNA rather than DNA. Target-RNA binding activates two separable Cas10 activities: HD-domain degradation of the transcribed DNA, and Palm-domain synthesis of cyclic oligoadenylate second messengers that switch on accessory ribonucleases.

Annotons

Csm/Cmr target-RNA-binding effector complex
csm_effector_complex
Participant: Protein Complex: Csm (type III-A) / Cmr (type III-B) effector complex
Protein Complex:
Csm (type III-A) / Cmr (type III-B) effector complexGO:1990904 Grounded at GO:1990904 rather than the GO:0032991 root because these effectors carry a crRNA; GO has no term for a CRISPR surveillance complex specifically (see knowledge_gaps).
Active units:
Cas10/Csm1 catalytic subunit
Participant: Gene Product: cas10 / csm1 (Thermus thermophilus HB8)
Gene Product:
cas10 / csm1 (Thermus thermophilus HB8)UniProtKB:Q53W19 Thermus thermophilus HB8 cas10/csm1.
Role: Carries both the HD nuclease and the Palm cyclase domains that the complex activates.
Cas10/Csm1 catalytic subunit (cOA exemplar)
Participant: Gene Product: cas10 / csm1 (Streptococcus thermophilus)
Gene Product:
cas10 / csm1 (Streptococcus thermophilus)UniProtKB:A0A0A7HFE1 Streptococcus thermophilus cas10/csm1.
Role: The orthologue in which target-RNA-triggered cyclic oligoadenylate synthesis was demonstrated.

Processes

CRISPR-cas systemGO:0099048

Binds nascent target RNA and thereby licenses the two Cas10 outputs; recognition is transcription-dependent, which is what makes type III immunity tolerant of self-targeting in silent loci.

Cas10 HD-domain single-stranded DNase
cas10_hd_dnase
Participant: Domain: Cas10 HD nuclease domain
Domain:
Cas10 HD nuclease domainInterPro:IPR006674 The metal-dependent nuclease domain of Cas10, as found in Q53W19 and its orthologues.
Required Function:
single-stranded DNA endonuclease activityGO:0000014

Function

single-stranded DNA endonuclease activityGO:0000014 Refined from the generic GO:0004536 after review of the exemplars: the activity is single-strand-restricted, and the enzyme digests circular as well as linear ssDNA, so an exonucleolytic mode (GO:0008297 single-stranded DNA exodeoxyribonuclease activity) accompanies the endonucleolytic one rather than replacing it. The two Cas10 catalytic centres are independent: on the Streptococcus protein D16A abolishes the ssDNase while leaving cyclase output intact, and D575-D576AA does the reverse.
Substrates: single-stranded DNA of the transcribed target locus
Products: degraded target DNA

Degrades the DNA of the locus being transcribed, coupling RNA recognition to DNA destruction.

Cas10 Palm-domain cyclic oligoadenylate synthesis
cas10_coa_synthesis
Participant: Domain: Cas10 Palm (GGDEF-like cyclase) domain
Domain:
Cas10 Palm (GGDEF-like cyclase) domainInterPro:IPR000160 The nucleotidyltransferase Palm domain of Cas10 that makes cyclic oligoadenylates; InterPro annotates it on Q53W19 as a GGDEF domain.

Function

cyclic oligoadenylate synthase activity Deliberately carries no GO id: no term exists for synthesis of cyclic oligoadenylate (cA3-cA6) second messengers from ATP. See knowledge_gaps.
Substrates: ATP
Products: cyclic oligoadenylate (cA3 to cA6)

Converts target detection into a diffusible signal, decoupling the sensing complex from the effector ribonucleases it activates.

cOA-activated Csm6 ribonuclease
csm6_coa_activated_rnase
Participant: Family: Csm6/Csx1 CARF-domain ribonuclease family
Family:
Csm6/Csx1 CARF-domain ribonuclease family Accessory ribonucleases that are not part of the effector complex and are switched on by cOA binding to a CARF domain.
Representative Members: csm6 (Thermus thermophilus HB8)UniProtKB:Q53W17 csm6 (Mycobacterium tuberculosis H37Rv)UniProtKB:P71635
Required Function:
RNA endonuclease activityGO:0004521

Function

RNA endonuclease activityGO:0004521
Substrates: cellular and invader RNA (non-specific)
Products: cleaved RNA

Processes

defense response to virusGO:0051607

Amplifies the response by indiscriminate RNA cleavage once cOA levels rise; the activity is self-limiting because host ring nucleases degrade the signal.

Class 2 type II Cas9 interferenceBiological Processcas9_variant

A single protein loaded with a crRNA:tracrRNA guide recognises a PAM-adjacent target and makes a blunt double-strand break using paired RuvC and HNH nuclease domains.

Annotons

Cas9 guide-RNA-directed DNA endonuclease
cas9_rna_guided_dnase
Participant: Family: Cas9 family
Family:
Cas9 familyInterPro:IPR028629
Representative Members: cas9 / csn1 (Streptococcus pyogenes M1)UniProtKB:Q99ZW2 cas9 (Neisseria meningitidis 8013)UniProtKB:C9X1G5
Required Function:
DNA endonuclease activityGO:0004520

Function

DNA endonuclease activityGO:0004520
Substrates: PAM-adjacent double-stranded target DNA
Products: blunt double-strand break

Processes

defense response to virusGO:0051607

Collapses recognition and destruction into one protein; the HNH and RuvC domains cut the target and non-target strands respectively.

Class 2 type V Cas12a interferenceBiological Processcas12a_variant

A single RuvC-domain effector that uses a crRNA alone, needs no tracrRNA, and leaves staggered ends; target binding also unleashes trans-cleavage of single-stranded DNA.

Annotons

Cas12a crRNA-directed DNA endonuclease
cas12a_rna_guided_dnase
Participant: Family: Cas12a (Cpf1) family
Family:
Cas12a (Cpf1) familyInterPro:IPR027620
Representative Members: cas12a / cpf1 (Acidaminococcus sp. BV3L6)UniProtKB:U2UMQ6 cas12a / cpf1 (Francisella tularensis subsp. novicida)UniProtKB:A0Q7Q2
Required Function:
deoxyribonuclease I activityGO:0004530

Function

double-stranded DNA endonuclease activityGO:1990238 Replaces the GOA GO:0004530 row, which is the EC 3.1.21.1 DNase I reaction: its definition stipulates 5'-phosphodinucleotide end products, a property of the non-specific secreted nuclease and not of Cas12a, and it says nothing about the cleavage being double-stranded or programmed. GO:1990238 is a child of the GO:0004520 that the Cas9 annoton carries, so the two class 2 effectors sit on one branch at appropriate depths. Cas12a also processes its own pre-crRNA at a second, RuvC-independent site by metal-independent intramolecular transesterification (EC 4.6.1.22, leaving a 2',3'-cyclic phosphate), which the gene reviews carry as GO:0004521; it is a separate activity, not another description of this one.
Substrates: crRNA-complementary double-stranded target DNA
Products: staggered double-strand break

Processes

defense response to virusGO:0051607

Single-effector DNA interference with a single-RNA guide. The same RuvC site serves cis- and trans-cleavage, in a target-activated state; pre-crRNA processing is a separate site.

Class 2 type VI Cas13a RNA interferenceBiological Processcas13a_variant

The only effector class whose target is RNA rather than DNA. crRNA-guided recognition of a target transcript activates HEPN ribonuclease sites that then cleave RNA promiscuously.

Annotons

Cas13a crRNA-directed endoribonuclease
cas13a_rna_guided_rnase
Participant: Family: Cas13a (C2c2) family
Family:
Cas13a (C2c2) familyInterPro:IPR053395
Representative Members: cas13a / c2c2 (Leptotrichia shahii)UniProtKB:P0DOC6 cas13a / c2c2 (Leptotrichia buccalis)UniProtKB:C7NBY4
Required Function:
RNA endonuclease activityGO:0004521

Function

RNA endonuclease activityGO:0004521
Substrates: crRNA-complementary target RNA bystander single-stranded RNA
Products: cleaved RNA

Processes

defense response to virusGO:0051607

Targets transcripts rather than genomes, and couples specific recognition to collateral RNA cleavage and growth arrest.