Bacteriophages inhibit and evade cGAS-like immune function in bacteria

. Author manuscript; available in PMC: 2024 Feb 16.

Published in final edited form as: Cell. 2023 Feb 6;186(4):864–876.e21. doi: 10.1016/j.cell.2022.12.041

KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
P. aeruginosa ATCC 33351 WT	ATCC	NCBI: AWZD00000000.1
P. aeruginosa JD332	Jeremy R. Dettman Lab	NCBI: LJNX01000000.1
P. aeruginosa BWH058	Deborah Hung Lab	NCBI: JIES00000000.1
P. aeruginosa ATCC 27853 WT	ATCC	NCBI: CP015117.1
P. aeruginosa BWHPSA011 (Pa011) WT	Deborah Hung Lab	NCBI: NZ_AXQR00000000 .1
Pa011 ΔCBASS (Removal of 1250436–1254723bp; CapV, CdnA, Cap2, Cap3, DUF2188)	This study	N/A
Pa011 CapV (phospholipase) catalytic mutant S48A	This study	N/A
Pa011 CdnA (cyclase) catalytic mutant D87A/D89A	This study	N/A
Pa011 Cap 2 (E1/E2) catalytic mutant C450A/C453A	This study	N/A
Pa011 Cap3 (JAB) catalytic mutant E38A	This study	N/A
P. aeruginosa PAO1 (Pa) WT	Joe Bondy-Denomy Lab	NCBI: NC_002516.2
Pa^CBASS (PAO1 attTn7::Pa011 CBASS; CapV, CdnA, Cap2, Cap3, DUF2188)	This study	N/A
Pa^EV (Integration of mini-Tn7 empty vector)	This study	N/A
Pa^CBASS (JBD67 WT) lysogen	This study	N/A
Pa^CBASS (JBD67Δacb2) lysogen	This study	N/A
Pa^EV (JBD67 WT) lysogen	This study	N/A
Pa^EV (JBD67Δacb2) lysogen	This study	N/A
Pa^haCas3 (PAO1 attTn7::I-C CRISPR-Cas3 helicase attenuated (haCas3) system)	This study	N/A
Pa^Cas13a (PAO1 attTn7::VI-A CRISPR-Ca13a system)	Joe Bondy-Denomy Lab²¹	N/A
E. coli DH5α	NEB	Cat #C2987H
E. coli SM10	NEB	Cat #C3019H
E. coli BL21 (DE3)	Weidi Biotechnology	Cat #EC1002
PaMx33	Gabriel Guarneros Peña Lab²⁴	NCBI: KU884561
PaMx35	Gabriel Guarneros Peña Lab²⁴	NCBI: KU884562
PaMx41	Gabriel Guarneros Peña Lab²⁴	NCBI: KU884563
PaMx43	Gabriel Guarneros Peña Lab²⁴	NCBI: KU884564
JBD18	Alan Davidson Lab⁵⁷	NCBI: JX495041.1
JBD67	Alan Davidson Lab⁵⁷	NCBI: NC_042135.1
JBD67Δacb2 #1 (Removal of 23005–23232bp orf34)	This study	N/A
JBD67Δacb21 #2 (Removal of 23047–23235bp orf34)	This study	N/A
JBD67Δacb2 #3 (Removal of 23066–23239bp orf34)	This study	N/A
D3	Alan Davison Lab⁵⁸	NCBI: AF165214.2
PB-1	Alan Davison Lab⁵⁹	NCBI: NC_011810
F8	Alan Davison Lab⁵⁹	NCBI: NC_011703
14-1	Alan Davison Lab⁵⁹	NCBI: NC_007810
Lind109	Alan Davison Lab	N/A
Ab27	Christine Pourcel Lab⁶⁰	NCBI: LN610579
Ab28	Christine Pourcel Lab⁶⁰	NCBI: LN610589
PII10A	Christine Pourcel Lab⁶¹	NCBI: LT594786
PhiKZ	Alan Davison Lab⁶²	NCBI: AF399011
PA3	Alan Davison Lab⁶³	NCBI: HQ630627
Ab03	Christine Pourcel Lab⁶⁰	NCBI: LN610573
Ab04	Christine Pourcel Lab⁶⁰	NCBI: LN610581
Ab06	Christine Pourcel Lab⁶⁰	NCBI: LN610582
Ab11	Christine Pourcel Lab⁶⁰	NCBI: LN610583
Ab17	Christine Pourcel Lab⁶⁰	NCBI: LN610576
M6	Peter Weigele⁶⁴	NCBI: NC_007809
YuA	Rob Lavigne Lab⁶⁵	NCBI: NC_010116
Ab18	Christine Pourcel Lab⁶⁰	NCBI: LN610577
Ab19	Christine Pourcel Lab⁶⁰	NCBI: NC_042115
Ab20	Christine Pourcel Lab⁶⁰	NCBI: LN610585
Ab21	Christine Pourcel Lab⁶⁰	NCBI: NC_042115
PA5oct	Rob Lavigne Lab⁶⁶	NCBI: MK797984
PA-1	Peter Weigele⁶⁴	NCBI: MN504636.1
DMS3	Alan Davison Lab⁵⁷	NCBI: DQ631426.1
JBD25	Alan Davison Lab⁵⁷	NCBI: JX495042.1
JBD30	Alan Davison Lab⁶⁷	NCBI: NC_020198.1
Ab30	Christine Pourcel Lab⁶⁰	NCBI: LN610590
JBD68	Alan Davison Lab⁶⁸	NCBI: KY707339.1
LKD16	Rob Lavigne Lab⁶⁹	NCBI: AM265638
LKD19	Rob Lavigne Lab⁷⁰	NCBI: AM910651
KMV	Rob Lavigne Lab⁷¹	NCBI: AJ505558
Ab05	Christine Pourcel Lab⁶⁰	NCBI: LN610574
Ab12	Christine Pourcel Lab⁶⁰	NCBI: NC_047967
LUZ7	Rob Lavigne Lab⁷²	NCBI: NC_013691.1
Lit1	Rob Lavigne Lab⁷²	NCBI: NC_013692.1
Ab09	Christine Pourcel Lab⁶⁰	NCBI: HG962375
P3P1	Christine Pourcel Lab⁶¹	NCBI: LT594787
Ab22	Christine Pourcel Lab⁶⁰	NCBI: LN610578
Chemicals, peptides, and recombinant proteins
HEPES sodium salt	Sigma-Aldrich	CAS: 7365-45-9 Cat #V900477-500G
Tris base	Sigma-Aldrich	CAS: 77-86-1 Cat #RDD008-2.5KG
Sodium dihydrogen phosphate dihydrate	Sigma-Aldrich	CAS: 13472-35-0 Cat #1063420250
Disodium hydrogen phosphate dodecahydrate	Sigma-Aldrich	CAS: 10039-32-4 Cat #1065790500
Bis-Tris propane	Sigma-Aldrich	CAS: 64431-96-5 Cat #B6755-25G
Sodium bromide	Sigma-Aldrich	CAS: 7647-15-6 Cat #310506-100G
PEG 3350	Biorigin	CAS: 25322-68-3 Cat #BN33640
Ethylene glycol	Sigma-Aldrich	CAS: 107-21-1 Cat #102466
Glycerol	Sigma-Aldrich	CAS: 56-81-5 Cat#V900122-500ML
Imidazole	Sigma-Aldrich	CAS: 288-32-4 Cat #V900153-500G
Resorufin butyrate	CHEMEGEN	CAS: 15585-42-9 Cat #CY17497
Phenol:chloroform:isoamyl alcohol 25:24:1	Sigma-Aldrich	CAS: 108-95-2; 6766-3; 123-51-3 Cat #P3803
Chloroform	Sigma-Aldrich	CAS: 67-66-3 Cat #C2432
Lysozyme	Sigma-Aldric	CAS: 12650-88-3 Cat #L6876
2X Phanta Max Master Mix	Vazyme	Cat #P515-03
2X Rapid Taq Master Mix	Vazyme	Cat #P222-AA
Gibson Assembly HiFi DNA Master Mix	NEB	Cat #E2621
KOD-Plus-Neo	TOYOBO	Cat #KOD-401
DpnI	NEB	Cat #R0176s
SacI	NEB	Cat #R3156S
PstI	NEB	Cat #R3140S
HindIII	NEB	Cat #R3104S
BamHI	NEB	Cat #R3136S
Proteinase K	NEB	Cat #P8107S
RNaseA	Omega Bio-TEK	Cat #AC118
High Affinity Ni-NTA Resin	GenScript	Cat #L00250-100
Pa011 CdnA recombinant protein	This study	N/A
Pa011 CapV recombinant protein	This study	N/A
Pa011 Cap2 (E1/E2) recombinant protein	This study	N/A
Pa011 Cap2^C105A/C479A recombinant protein	This study	N/A
P1011 CdnA-Cap2^C105A/C479A recombinant protein	This study	N/A
PaMx33 Acb2 WT recombinant protein	This study	N/A
PaMx33 Acb2^Y11A recombinant protein	This study	N/A
PaMx33 Acb2^K26A recombinant protein	This study	N/A
Critical commercial assays
DNA Clean & Concentrator Kit	Zymo Research	Cat #D4034
Gel DNA Recovery Kit	Zymo Research	Cat #D4008
Plasmid Miniprep Kit	Zymo Research	Cat #ZD4037
Qubit 1X dsDNA High Sensitivity Assay Kit	ThermoFisher	Cat #Q33231
Illumina DNA Prep Kit	Illumina	Cat #20015825
Illumina Miseq v3 Reagents	Illumia	Cat #15043894
Plasmid Miniprep Kit	Vazyme	Cat #DC201-01
Gel DNA Extraction Mini Kit	Vazyme	Cat #DC301-01
LFS Crystallization Screen Kit	Molecular Dimensions	Cat #MD1-121
3’,3’ cyclic GAMP ELISA Kit	Arbor Assays	Cat #K073-H1
Deposited data
Structure of Acb2	This study	PDB: 8H2X
Structure of Acb2 bound with 3’,3’-cGAMP	This study	PDB: 8H2J
Structure of Acb2 bound with c-di-AMP	This study	PDB: 8H39
Oligonucleotides
PaMx41 orf11 crRNA guide #4: gatacgaccagtctgacgcttgac	This study	N/A
PaMx41 orf11 crRNA guide #5: tctgacgcttgacggtaagattga	This study	N/A
JBD67 orf34 crRNA guide #3: tctgacgcttgacggtaagattga	This study	N/A
JBD67 orf34 crRNA guide #4: ctggctgcagagccgttgcgctgggctgcgatcg	This study	N/A
3’,3’-cGAMP	Sigma-Aldrich	CAS: 849214-04-6 Cat #SML1232-5UMO
2’,3’-cGAMP	Sigma-Aldrich	CAS:1441190-66-4 Cat #SML1229-5UMO
c-di-GMP	Sigma-Aldrich	CAS: 61093-23-0 Cat #SML1228-1UMO
c-di-AMP	Sigma-Aldrich	CAS: 54447-84-6 Cat #SML1231-1UMO
3’,3’-c-UMP-GMP	Biolog Life Science Institute	CAS: 232933-52-7 Cat #C371
3’,3’-c-di-UMP	Biolog Life Science Institute	CAS: 73120-97-5 Cat #C256
3’,3’-c-UMP-AMP	Biolog Life Science Institute	CAS: 83799-66-0 Cat #C357
Recombinant DNA
pHERD30T (p30T)	³⁹	N/A
p30T-Pa011 CBASS	This study	N/A
p30T-PaMx41-short orf24-v1 (37 a.a. with stop codon)	This study	N/A
p30T-PaMx41-short orf24-v2 (94 a.a. with stop codon)	This study	N/A
p30T-PaMx41-long orf24 (acb2)	This study	N/A
p30T-HDR-Acb2-AcrVIA1	This study	N/A
p30T-crRNA-4-PaMx41-orf11	This study	N/A
p30T-crRNA-5-PaMx41-orf11	This study	N/A
p30T-crRNA-3-JBD67-orf34	This study	N/A
p30T-crRNA-4-JBD67-orf34	This study	N/A
pUC18-mini-Tn7T-LAC (pTn7)	⁴⁰	N/A
pTn7-Pa011 CBASS	This study	N/A
pTNS3	⁴¹	N/A
pMQ30	⁴²	N/A
pMQ30-HDR-Pa011-CapV-S48A	This study	N/A
pMQ30-HDR-Pa011-CdnA-D87A-D89A	This study	N/A
pMQ30-HDR-Pa011-E1-E2-C450A-C453A	This study	N/A
pMQ30-HDR-Pa011-JAB-E38A	This study	N/A
p30T-PaMx41-orf11-HDR-1-WT	This study	N/A
p30T-PaMx41-orf11-HDR-2-WT	This study	N/A
p30T-PaMx41-orf11-I121S	This study	N/A
p30T-PaMx41-orf11-I121T	This study	N/A
p30T-PaMx41-orf11-S330P	This study	N/A
p30T-PaMx41-Acb2-Y11A	This study	N/A
p30T-PaMx41-Acb2-K26A	This study	N/A
pET28a- His₆-SUMO-Acb2	This study	N/A
pET28a- His₆-SUMO-Acb2-Y11A	This study	N/A
pET28a- His₆-SUMO-Acb2-K26A	This study	N/A
pET28a-His₆-CapV	This study	N/A
pET28a-His₆-CdnA	This study	N/A
pET28a-His₆-Cap2 E1/E2	This study	N/A
pET28a- His₆-Cap2 E1/E2-C105A/C479A	This study	N/A
pRSFDuet- His₆-CdnA-Cap2 E1/E2-C105A/C479A	This study	N/A
Software and algorithms
National Center for Biotechnology Information (NCBI) database	³⁶	https://blast.ncbi.nlmnih.gov/
Integrated Microbial Genomes (IMG) database	³⁷	https://img.jgi.doe.gov/
DefenseFinder	^34,38	https://defensefinder.mdmparislab.com/
Multiple Sequence Comparison by Log-Expectation (MUSCLE)	⁷³	https://www.ebi.ac.uk/Tools/msa/muscle/
NCBI Multiple Sequence Alignment Viewer (MSA)	MSA Software	https://www.ncbi.nlm.nih.gov/tools/msaviewer/
NCBI Constraint-based Multiple Alignment Tool (COBALT)	⁵⁰	https://www.ncbi.nlm.nih.gov/tools/cobalt/re_cobalt.cgi
Interactive Tree of Life (iTOL)	⁵²	https://itol.embl.de/
MMSeqs2	⁷⁴	https://github.com/soedinglab/mmseqs2
Cutadapt	⁴⁵	https://cutadapt.readthedocs.io/en/stable/#
Bowtie2	⁴⁶	https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Integrative Genomics Viewer (IGV)	⁴⁷	https://software.broadinstitute.org/software/igv/
SeqDiff	SeqDiff GitHub Program	https://github.com/hansenlo/SeqDiff
HHpred	⁷⁵	https://toolkit.tuebingen.mpg.de/tools/hhpred
AlphaFold2	⁵³	https://alphafold.ebi.ac.uk/
DALI	²³	http://ekhidna2.biocenter.helsinki.fi/dali/
HKL2000	⁵⁴	http://www.hkl-raycom/
PHENIX	⁵⁶	http://www.phenixonline.org
COOT	⁵⁵	http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot
PyMOL	The PyMOL Molecular Graphics System, Version 2.5.2., Schrodinger, LLC	https://pymol.org/2/
OriginPro 8	OriginPro Software	N/A
GraphPad Prism 9	GraphPad Software	https://www.graphpad.com/
Other
Amicon Ultra-0.5 centrifugal filter unit	Merck	Cat #UFC500396
Lysing Matrix B beads	MP	Cat #6911100
Amicon concentrators (3 K)	Millipore	Cat #UFC800308
Amicon concentrators (10 K)	Millipore	Cat #UFC901096
Amicon concentrators (30 K)	Millipore	Cat #UFC903024
HisTrap FF (5 mL)	GE Healthcare	Cat #17-5255-01
HiTrap Heparin HP (5 mL)	GE Healthcare	Cat #17-0407-03
HiTrap Q Sepharose FF (5 mL)	GE Healthcare	Cat #17-5156-01
Superdex 200 increase 10/300 GL	GE Healthcare	Cat #17517501