Table 1 Caspase-3 substrates in Lm supernatants assessed by TAILS and 2D SDS-PAGE proteomics.

From: Executioner caspases degrade essential mediators of pathogen-host interactions to inhibit growth of intracellular Listeria monocytogenes

Lm 10403S protein Name	Lm 10403S protein Accession number	Name of the homologous gene in Lm serovar 1/2a (strain ATCC BAA-679 / EGD-e)	Position of the cleavage (in Lm 10403S protein)	Cleavage sequence (in Lm 10403S protein)
Thiol-activated cytolysin (listeriolysin O, LLO)	A0A0H3GD84	lmo0202	A0A0H3GD84 [63-89]	[D].KYIQGLDYNKNNVLVYHGDAVTNVPPR.[K]
Phosphatidylcholine cholinephosphohydrolase (PlcB)	A0A0H3G8P1	lmo0205	A0A0H3G8P1 [205-220]	[D].TIKHNYQATEDMVAKR.[F]
	A0A0H3G8P1		A0A0H3G8P1 [229-236]	[D].WLYENAKR.[A]
Fumarate reductase flavoprotein subunit	A0A0H3GDC3	lmo0355	A0A0H3GDC3 [160-178]	[D].SMDIKLNNLTITGGMSEKR.[T]
	A0A0H3GDC3		A0A0H3GDC3 [458-479]	[D].GKPITGLFAAGEVTGGLHGENR.[I]
	A0A0H3GDC3		A0A0H3GDC3 [160-178]	[D].SMDIKLNNLTITGGMSEKR.[T]
	A0A0H3GDC3		A0A0H3GDC3 [172-178]	[T].GGMSEKR.[T]
Peptidase_M23 domain-containing protein	A0A0H3GFN8	lmo2504	A0A0H3GFN8 [144-151]	[D].DFKELVDR.[V]
Peptidoglycan bound protein	A0A0H3GGA1	lmo2714	A0A0H3GGA1 [107-116]	[D].YTDTKLTNYR.[L]
Peptide/nickel transport system substrate-binding protein	A0A0H3GJB6	lmo2196	A0A0H3GJB6 [485-503]	[D].YDKILNDASVTYAADDQKR.[W]
Transcriptional regulator LytR	A0A0H3GKG2	lmo2518	A0A0H3GKG2 [198-224]	[D].SKDNAGAITLKKGPQHLNAEQALALAR.[T]
60 kDa chaperonin	A0A0H3GLZ0	lmo2068	A0A0H3GLZ0 [190-195]	[E].GMQFDR.[G]
D-glutamyl-L-m-Dpm peptidase P45	A0A0H3GN80	lmo2505	A0A0H3GN80 [222-230]	[D].KAAKEATAR.[A]
Quinol oxidase subunit 2	A0A0H3G8T0	lmo0013	A0A0H3G8T0 [198-205]	[D].EVGTYKGR.[N]
NusG_II domain-containing protein	A0A0H3G991	lmo0408	A0A0H3G991 [69-85]	[T].IKGKGAQYNLMEVDGER.[I]
Cysteine synthase	A0A0H3G9A7	lmo0223	A0A0H3G9A7 [234-253]	[D].TKVYDGILKVSSEDALETAR.[E]
Uncharacterized protein	A0A0H3G9Q4	lmo0592	A0A0H3G9Q4 [99-111]	[D].AGEVKDALNVFER.[T]
Glycerophosphoryl diester phosphodiesterase	A0A0H3G9S8	lmo0616	A0A0H3G9S8 [331-342]	[T].LYEPNTKIIAHR.[G]
Lipoprotein	A0A0H3G9T8	lmo0366	A0A0H3G9T8 [225-233]	[D].WTGFHVIER.[A]
Internalin B	A0A0H3G9Y9	lmo0434	A0A0H3G9Y9 [331-343]	[D].GTVIKTKVEAGTR.[I]
Tagatose 1,6-diphosphate aldolase	A0A0H3GA75	lmo0539	A0A0H3GA75 [284-297]	[D].GIEVYGKQGDDALR.[E]
Spermidine/putrescine transport system permease	A0A0H3GAF1	lmo0808	A0A0H3GAF1 [168-173]	[T].LIQASR.[D]
Sulfatase domain-containing protein	A0A0H3GAG2	lmo0644	A0A0H3GAG2 [576-588]	[D].GTNKELSSDVKKR.[F]
Uncharacterized protein	A0A0H3GBD8	lmo0944	A0A0H3GBD8 [19-26]	[D].VANGNGIR.[L]
GW domain-containing protein	A0A0H3GBE7	lmo1215	A0A0H3GBE7 [97-107]	[D].GKWIEINANFR.[K]
Uncharacterized protein	A0A0H3GBP9	lmo1076	A0A0H3GBP9 [35-46]	[D].SSEQEDNTEVAR.[E]
ABC transport system	A0A0H3GBZ4	lmo1388	A0A0H3GBZ4 [80-101]	[D].GYNYLQSASEADYKTNLNTAVR.[S]
	A0A0H3GBZ4		A0A0H3GBZ4 [92-101]	[D].YKTNLNTAVR.[S]
	A0A0H3GBZ4		A0A0H3GBZ4 [277-290]	[D].GKDYNVTLTSEIKR.[V]
Signal peptidase I	A0A0H3GC68	lmo1271	A0A0H3GC68 [130-145]	[D].GGKIPKDTYFVLGDNR.[R]
	A0A0H3GC68		A0A0H3GC68 [130-146]	[D].GGKIPKDTYFVLGDNRR.[A]
DNA gyrase subunit B	A0A0H3GCB7	lmo0006	A0A0H3GCB7 [439-448]	[D].SAGGSAKQGR.[D]
Universal stress protein	A0A0H3GCF8	lmo1580	A0A0H3GCF8 [14-20]	[D].GSKEAER.[A]
Protease IV	A0A0H3GCG3	lmo1585	A0A0H3GCG3 [78-100]	[D].SGSLFSEAGYNHSFFMQQLEQVR.[N]
Uncharacterized protein	A0A0H3GCN8	lmo0130	A0A0H3GCN8 [137-144]	[D].EGLPEYKR.[I]
	A0A0H3GCN8		A0A0H3GCN8 [420-429]	[D].FAMTNNGGIR.[S]
	A0A0H3GCN8		A0A0H3GCN8 [75-94]	[D].NATNSFLQANPGATTDNAIR.[V]
	A0A0H3GCN8		A0A0H3GCN8 [290-308]	[D].LVLAGHNHQYTNGLVGKTR.[I]
Peptide/nickel transport system substrate-binding protein	A0A0H3GCP2	lmo0135	A0A0H3GCP2 [224-234]	[D].GKPKLDKVTFR.[I]
	A0A0H3GCP2		A0A0H3GCP2 [110-135]	[D].GKPLTADDVVFTVNSILDTKQNSPNR.[G]
	A0A0H3GCP2		A0A0H3GCP2 [207-217]	[E].YKTGEYVSLER.[F]
G5 domain-containing protein	A0A0H3GCT9	lmo0186	A0A0H3GCT9 [77-98]	[D].EIAPGKNAEIKDGMEIKYLPAR.[Q]
	A0A0H3GCT9		A0A0H3GCT9 [77-98]	[D].EIAPGKNAEIKDGMEIKYLPAR.[Q]
	A0A0H3GCT9		A0A0H3GCT9 [141-153]	[D].TKLKNGLEVNINR.[A]
	A0A0H3GCT9		A0A0H3GCT9 [89-98]	[D].GMEIKYLPAR.[Q]
Putative septation protein SpoVG	A0A0H3GCV1	lmo0196	A0A0H3GCV1 [27-35]	[D].GEFVIHDIR.[V]
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B	A0A0H3GCW2	lmo1754	A0A0H3GCW2 [279-288]	[D].LFIDDAWKER.[I]
50S ribosomal protein L25	A0A0H3GCW8	lmo0211	A0A0H3GCW8 [45-53]	[D].SLELIKAVR.[D]
YycH protein	A0A0H3GD67	lmo0289	A0A0H3GD67 [252-274]	[D].GSSVIEMDTDNKVLEYVNPSQER.[T]
DivIC protein	A0A0H3GD99	lmo0217	A0A0H3GD99 [85-104]	[D].SLNEQIKKLHNDDYIAKLAR.[S]
	A0A0H3GD99		A0A0H3GD99 [85-104]	[D].SLNEQIKKLHNDDYIAKLAR.[S]
Probable transcriptional regulatory protein LMRG_00061	A0A0H3GDD6	lmo0369	A0A0H3GDD6 [210-217]	[G].EDLEKFER.[L]
Peptidoglycan-N-acetylglucosamine deacetylase PgdA	A0A0H3GDH9	lmo0415	A0A0H3GDH9 [125-135]	[K].AVQSEYVKEGR.[T]
Probable succinyl-diaminopimelate desuccinylase	A0A0H3GDI0	lmo0265	A0A0H3GDI0 [158-168]	[D].GLIIGEPSGHR.[I]
LytR_cpsA_psr domain-containing protein	A0A0H3GDK2	lmo0443	A0A0H3GDK2 [191-199]	[D].GKTLLQYAR.[F]
10 kDa chaperonin	A0A0H3GDS3	lmo2069	A0A0H3GDS3 [29-46]	[D].SAKEKPQSGKIVAVGSGR.[V]
Manganese-binding lipoprotein mntA	A0A0H3GDS9	lmo1847	A0A0H3GDS9 [282-298]	[D].STAKKGEVGDTYLEMMR.[Y]
4-hydroxy-tetrahydrodipicolinate reductase	A0A0H3GDZ1	lmo1907	A0A0H3GDZ1 [159-175]	[D].APSGTGVKTAEMMAETR.[E]
Histidine kinase	A0A0H3GE39	lmo1947	A0A0H3GE39 [36-41]	[E].KNNITR.[I]
Flagellar hook protein FlgE	A0A0H3GEC2	lmo0697	A0A0H3GEC2 [79-89]	[D].YTAGSPTSTGR.[N]
Phage capsid protein	A0A0H3GEG6	lmo2296	A0A0H3GEG6 [262-272]	[D].ASKGNDQVFTR.[R]
Aminotransferase	A0A0H3GEK9	lmo2370	A0A0H3GEK9 [20-27]	[D].GAEELFGR.[K]
Peptidoglycan bound protein	A0A0H3GES0	lmo0842	A0A0H3GES0 [364-383]	[D].SYNYTKSYSVVNGSNSLDSR.[G]
CBM6 domain-containing protein	A0A0H3GET7	lmo2446	A0A0H3GET7 [1013-1022]	[D].GASDYTMEVR.[Y]
30S ribosomal protein S5	A0A0H3GFB3	lmo2615	A0A0H3GFB3 [7-15]	[D].GNKLDLEER.[V]
Phosphoglycerol transferase	A0A0H3GFC6	lmo0927	A0A0H3GFC6 [446-452]	[D].TYFQTAR.[Y]
	A0A0H3GFC6		A0A0H3GFC6 [617-625]	[D].SVLQGDLLR.[F]
	A0A0H3GFC6		A0A0H3GFC6 [442-452]	[D].SSVDTYFQTAR.[Y]
FeS assembly protein SufD	A0A0H3GFE5	lmo2414	A0A0H3GFE5 [370-380]	[D].VVAGHAASVGR.[V]
Uncharacterized protein	A0A0H3GFH4	lmo2444	A0A0H3GFH4 [179-187]	[D].GGIFDGGVR.[F]
Potassium-transporting ATPase KdpC subunit	A0A0H3GFI3	lmo2680	A0A0H3GFI3 [82-101]	[D].GVATNLNPTSEEQKQLVEKR.[I]
Glyceraldehyde-3-phosphate dehydrogenase	A0A0H3GFI9	lmo2459	A0A0H3GFI9 [189-197]	[D].APHPKGDFR.[R]
HTH lacI-type domain-containing protein	A0A0H3GFM6	lmo1030	A0A0H3GFM6 [1-8]	[-].MKLEDIAR.[L]
SSD domain-containing protein	A0A0H3GFS0	lmo1226	A0A0H3GFS0 [135-141]	[D].ASVKSIR.[N]
	A0A0H3GFS0		A0A0H3GFS0 [127-141]	[A].SLTVDDTDASVKSIR.[N]
Peptide/nickel transport system substrate-binding protein	A0A0H3GFV1	lmo2569	A0A0H3GFV1 [98-107]	[D].GGKTLIFKIR.[E]
Signal peptidase I	A0A0H3GFV8	lmo1269	A0A0H3GFV8 [50-63]	[D].GEHLFINKVSDPKR.[F]
	A0A0H3GFV8		A0A0H3GFV8 [50-63]	[D].GEHLFINKVSDPKR.[F]
30S ribosomal protein S19	A0A0H3GG04	lmo2628	A0A0H3GG04 [68-78]	[V].GHKLGEFAPTR.[T]
Elongation factor Tu	A0A0H3GG29	lmo2653	A0A0H3GG29 [198-205]	[D].SYIPTPER.[D]
	A0A0H3GG29		A0A0H3GG29 [111-117]	[D].GPMPQTR.[E]
	A0A0H3GGA1		A0A0H3GGA1 [110-116]	[D].TKLTNYR.[L]
	A0A0H3GGA1		A0A0H3GGA1 [110-116]	[D].TKLTNYR.[L]
	A0A0H3GGA1		A0A0H3GGA1 [100-116]	[D].FTATLTDYTDTKLTNYR.[L]
Transcription elongation factor GreA	A0A0H3GGF0	lmo1496	A0A0H3GGF0 [53-64]	[D].SAKDEQAFVEGR.[I]
N-acetylmuramoyl-L-alanine amidase	A0A0H3GGH0	lmo1521	A0A0H3GGH0 [179-184]	[D].DSTNIR.[N]
	A0A0H3GGH0		A0A0H3GGH0 [235-242]	[D].KGQTSSPR.[S]
	A0A0H3GGH0		A0A0H3GGH0 [351-370]	[D].KSLAESINTTLGKDLPTTNR.[G]
Transketolase	A0A0H3GGH6	lmo1305	A0A0H3GGH6 [7-14]	[D].SLAVNTIR.[T]
Glutamyl-tRNA(Gln) amidotransferase subunit A	A0A0H3GH17	lmo1755	A0A0H3GH17 [236-245]	[D].STSINQPVER.[F]
Multifunctional fusion protein	A0A0H3GH33	lmo1527	A0A0H3GH33 [65-72]	[D].TVTSLDKR.[V]
Cell shape-determining protein MreC	A0A0H3GH53	lmo1547	A0A0H3GH53 [65-82]	[D].GVVDLKNTYTENQHLKER.[L]
Actin-assembly inducing protein ActA	A0A0H3GH64	lmo0204	A0A0H3GH64 [412-424]	[D].DENSETTEEEIDR.[L]
	A0A0H3GH64		A0A0H3GH64 [36-60]	[D].SSLNTDEWEEEKTEEQPSEVNTGPR.[Y]
	A0A0H3GH64		A0A0H3GH64 [167-174]	[D].KPTKANKR.[K]
	A0A0H3GH64		A0A0H3GH64 [412-424]	[D].DENSETTEEEIDR.[L]
	A0A0H3GH64		A0A0H3GH64 [125-132]	[D].RPTLQVER.[R]
30S ribosomal protein S2	A0A0H3GHH8	lmo1658	A0A0H3GHH8 [15-21]	[V].HFGHQTR.[R]
Carboxyl-terminal processing protease	A0A0H3GI96	lmo1851	A0A0H3GI96 [171-187]	[D].GKSVKGDTATEATQKIR.[G]
	A0A0H3GI96		A0A0H3GI96 [440-452]	[D].GLYDTDTEYAVQR.[F]
Flagellin	A0A0H3GID7	lmo0690	A0A0H3GID7 [42-51]	[D].DAAGLAVVTR.[M]
UPF0302 protein LMRG_01068	A0A0H3GIF4	lmo1921	A0A0H3GIF4 [163-171]	[D].EAAFHKLVR.[I]
Uncharacterized protein	A0A0H3GJ46	lmo2522	A0A0H3GJ46 [211-216]	[D].LNDNSR.[V]
	A0A0H3GJB6		A0A0H3GJB6 [127-132]	[D].YVYSWR.[R]
	A0A0H3GJB6		A0A0H3GJB6 [263-277]	[D].SGTGLNLYNTDKVDR.[T]
Pyruvate dehydrogenase E1 component subunit alpha	A0A0H3GJB7	lmo1052	A0A0H3GJB7 [238-252]	[D].GMDPLAVYAVTKFAR.[E]
50S ribosomal protein L18	A0A0H3GJD7	lmo2616	A0A0H3GJD7 [79-90]	[D].AASKVGELVAKR.[A]
FAD:protein FMN transferase	A0A0H3GJF7	lmo2636	A0A0H3GJF7 [56-72]	[L].KIYDKGKEDVLDKGFDR.[I]
	A0A0H3GJF7		A0A0H3GJF7 [256-262]	[V].TSGIYER.[Y]
30S ribosomal protein S12	A0A0H3GJH5	lmo2656	A0A0H3GJH5 [85-96]	[G].HNLQEHSVVLIR.[G]
Polar amino acid transport system ATP-binding protein	A0A0H3GJI6	lmo2251	A0A0H3GJI6 [190-200]	[M].VVVTHEMGFAR.[E]
Dihydroxyacetone kinase L subunit	A0A0H3GJL3	lmo2696	A0A0H3GJL3 [102-119]	[D].AVGLTKVIEAGLEGIEKR.[G]
dITP/XTP pyrophosphatase	A0A0H3GJR4	lmo1239	A0A0H3GJR4 [80-88]	[D].GAPGVYSAR.[Y]
Multiple sugar transport system substrate-binding protein	A0A0H3GJY9	lmo2839	A0A0H3GJY9 [119-134]	[D].SVGEDKYYEGATNLVR.[S]
Uncharacterized protein	A0A0H3GK85	lmo1438	A0A0H3GK85 [62-71]	[D].NVTVSKNVPR.[G]
	A0A0H3GK85		A0A0H3GK85 [36-41]	[F].SVLILR.[L]
	A0A0H3GKG2		A0A0H3GKG2 [201-224]	[D].NAGAITLKKGPQHLNAEQALALAR.[T]
N-acetylmuramoyl-L-alanine amidase	A0A0H3GKJ7	lmo2558	A0A0H3GKJ7 [41-51]	[D].GQATYIPKGVR.[D]
	A0A0H3GKJ7		A0A0H3GKJ7 [40-51]	[V].DGQATYIPKGVR.[D]
	A0A0H3GKJ7		A0A0H3GKJ7 [31-51]	[A].ASIDPVQKVDGQATYIPKGVR.[D]
50S ribosomal protein L14	A0A0H3GKP3	lmo2622	A0A0H3GKP3 [10-17]	[K].VADNSGAR.[E]
Peptidoglycan bound protein	A0A0H3GKR6	lmo1666	A0A0H3GKR6 [36-45]	[D].DISPEISDNR.[F]
Polar amino acid transport system substrate-binding protein	A0A0H3GKX3	lmo1738	A0A0H3GKX3 [227-232]	[D].FAVGMR.[K]
	A0A0H3GKX3		A0A0H3GKX3 [182-191]	[D].TAFIDLNNKR.[I]
	A0A0H3GLZ0		A0A0H3GLZ0 [25-35]	[N].AVKVTLGPKGR.[N]
	A0A0H3GLZ0		A0A0H3GLZ0 [488-498]	[D].AGIVDPTKVTR.[S]
Polar amino acid transport system substrate-binding protein	A0A0H3GMT4	lmo2349	A0A0H3GMT4 [132-146]	[D].SNNSINSTKDLAGKR.[V]
	A0A0H3GMT4		A0A0H3GMT4 [132-146]	[D].SNNSINSTKDLAGKR.[V]
Enolase	A0A0H3GN27	lmo2455	A0A0H3GN27 [295-304]	[D].WDGFKLLTER.[I]
	A0A0H3GN80		A0A0H3GN80 [206-220]	[D].QASAENAKAGLVSER.[D]
	A0A0H3GN80		A0A0H3GN80 [206-220]	[D].QASAENAKAGLVSER.[D]
DD-transpeptidase	A0A0H3GDX6	lmo1892	A0A0H3GDX6 [163-170]	[D].YTNKTLAR.[K]
	A0A0H3GDX6		A0A0H3GDX6 [60-73]	[D].YAKDAPKLTDSKLR.[D]
	A0A0H3GDX6		A0A0H3GDX6 [317-326]	[D].GLTIHTALDR.[D]

Lm 10403S protein Name	Lm 10403S protein Accession number	Name of the homologous gene in Lm serovar 1/2a (strain ATCC BAA-679 / EGD-e)
Internalin D	A0A0H3G8X7	lmo0263
Flagellar hook capping protein	A0A0H3GA06	lmo0696
Peptidoglycan bound protein	A0A0H3GAK6	lmo0880
DUF5105 domain-containing protein	A0A0H3GAX9	lmo0791
Multiple sugar transport system substrate-binding protein	A0A0H3GCT3	lmo0181
Uncharacterized protein (PepSY domain-containing protein)	A0A0H3GCV0	lmo0047
1-phosphatidylinositol phosphodiesterase	A0A0H3GCV8	lmo0201
Invasion-associated protein p60	A0A0H3GDY4	lmo0582
Thioredoxin-like_fold domain-containing protein	A0A0H3GFB7	lmo1059
Phosphocarrier protein HPr	A0A0H3GFK1	lmo1002
Antigen A	A0A0H3GGY8	lmo0118
Beta-lactamase domain-containing protein	A0A0H3GI09	lmo0540
N-acetylmuramoyl-L-alanine amidase	A0A0H3GJB3	lmo2591
DNA-directed RNA polymerase subunit alpha	A0A0H3GJC8	lmo2606
Competence protein ComEA	A0A0H3GKB9	lmo1484
Uncharacterized protein	A0A0H3GMD3	lmo2203
Putative septation protein SpoVG	A0A0H3GD80	lmo0197
Peptide/nickel transport system substrate-binding protein	A0A0H3GH20	lmo0152
Penicillin binding protein 2B	A0A0H3GLV8	lmo2039
FeS assembly ATPase SufC	A0A0H3GMZ0	lmo2415

Cell-free Lm 10403S supernatants were treated with purified caspase-3 before analysis by TAILS degradomics (upper part) and by comparative 2D SDS-PAGE (lower part). The 9 overlapping proteins in the two approaches are indicated at the top of the protein list. In the TAILS proteomics list the identified cleavage site are shown on the right. Only proteins are listed that were found in three independent replicates of the proteomics assays.

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Table 1 Caspase-3 substrates in Lm supernatants assessed by TAILS and 2D SDS-PAGE proteomics.

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