We sought to leverage both C. burnetii and host genomic diversity to predict widely useful T-cell epitopes across a range of hosts for this zoonotic pathogen. Epitopes were identified by leveraging an array of MHCII and MHCI alleles for antigen presentation, thereby capturing epitopes incorporated in both MHC systems across multiple host species. The results highlight broadly useful epitopes, including many with minimal prior study, that can be used for future work and vaccine development.
Foundational data aimed to capture broad representation of C. burnetii and focus on proteins that would avoid self-reactive antigens. In particular, we selected at least one sequence from each genomic group (Table 1), including the relatively minimal genome of virulent Nine Mile Phase I (RSA 493) as a reference. This resulted in a refined list of 1,413 conserved proteins for further analysis. This list was further screened for homology within human, mouse, and ruminant host proteins to avoid stimulating potential autoimmune responses. 391 such proteins were identified, suggesting large-scale use of host protein domain structures by C. burnetii. During assembly of the protein query list, it became apparent that a substantial number of annotated genes within the Nine Mile Phase 1 (RSA 493) genome lack discovery work and that many underlying functions are suggested by homology to alternate bacterial proteins. This promotes analyzing the bacterial proteome in its entirety, as the importance of many C. burnetii proteins has yet to be determined.
Relatively few Gram-negative bacteria have been examined for T-cell epitopes on a proteome-wide basis (34), leaving much of the previous epitope studies examining effector proteins or proteins residing at the cellular surface (24, 48–50). This is no exception for studies examining C. burnetii proteins for host cell epitopes, wherein previous work has focused on proteins injected into the host cytoplasm by the type four secretion system (T4SS) or proteins which elicit an antibody response (13, 14, 17). Resolution of C. burnetii infection is known to rely on the production of a Th1 type immune response that results in the production of IFN-γ (15, 32, 33). This immune response is accomplished by coordination of T-helper cells through interaction with MHC class II peptide loaded molecules and a harmonized cytokine environment (22). Therefore proteome-wide analysis for C. burnetii contained epitopes began with identifying MHC class II interacting peptides (See Repository). The MHC class II analysis herein identified numerous epitopes with relatively high allelic interactions (Additional Table 3), many with cross-species presentation (Additional Table 4). Some had presentation by an exceptional range of host alleles (Table 3), and many were clustered in epitope dense proteins of special interest (Table 4). Studies looking at the importance of different immune cellular subsets during C. burnetii infection has led to increased interest in CD8+ T-cell stimulation, which requires MHC class I presentation of peptides (27, 31). As such, similar methodology was implemented to identify epitopes binding an exceptional number of host MHC class I alleles (Table 5 and Additional Table 5) and epitope dense proteins characterized by MHC class I binding (Table 6).
Examination of either the MHC class I or II datasets demonstrates the return of proteins which have not previously been studied for T-cell epitopes. As mentioned before, much of the earlier work identifying T-cell epitopes has focused on certain protein subsets (9, 13, 14, 16, 19). Therefore, return of novel epitope-containing proteins does not preclude epitopes defined within this work; instead, these epitopes may represent more immunogenic peptides that exemplify a range of host species. For example, a group of novel epitope-containing proteins can be seen within the MHC class II and I datasets and are responsible for bacterial cell division, encompassing AAO89704.2 (ftsA), AAO89682.2 (ftsI), and AAO90095.2 (rodA) (51). The MHC class I analysis for bacterial epitopes supports the addition of a ruminant species to the dataset. It is believed that many human outbreaks arise from domestic ruminants, consisting of sheep, goats, and cattle, therefore vaccination efforts in ruminants may help in the prevention of zoonotic spread (3, 6, 7). Furthermore, coxiellosis in animals does not come without consequence, where sheep and goats present most frequently with late-term abortions and cattle have decreased birthing weights and possible mastitis (8). Consequently, Coxiella burnetii infection in these species causes clear economic losses and requires intervention.
A potential pitfall of bioinformatic analysis of T-cell epitopes is the possibility of false positives (14, 21, 52). This hinderance has been largely combated through the inclusion of more MHC ligand elution data during server training (21, 23, 47). During this research, alleviation of false positives was attempted by assessing a plethora of different MHCI and MHCII alleles and investigating the peptides which had high allelic coverage. It is presumed that false positives arise due to a lack of training data between alleles and that analysis of a myriad of alleles would promote dilution of false positives (21, 47, 52). When considering the 8 murine alleles tested during use of either NetMHCpan 4.1 or NetMHCIIpan 4.0, as compared to either 82–206 human alleles or 105 bovine alleles, it is noticeable that there were an increasing number of peptides falling within the filtered data sets (Additional Tables 2 and 5). This data is suspected to contain a number of false positives, but comparison with high binding peptides of human and cattle alleles is believed to lessen this burden. Moreover, once data had been acquired for both MHC class I and II alleles, it became possible to cross-analyze outputs.
Investigation into overlapping MHC class II and I epitopes defined 31 peptides of interest (Table 7). Com1, a well-studied C. burnetii protein of interest, was represented within this output. Importantly, former analysis of Com1 as a vaccine candidate against C. burnetii has demonstrated a decent amount of promise (13, 18, 19). Specifically, mice exposed to Com1 were afforded better protection during challenge assays and produced IFN-γ during immune system stimulation. Unfortunately, Com1 was categorized as a secreted protein by Inmembrane, where it is a well-studied surface associated protein (16, 18, 36). It is likely that there is a secondary processing step that is not recognized by Inmembrane. This does not disqualify the overall purpose for such notation, as many vaccination efforts have focused on surface proteins, where it is believed that these proteins most readily interact with the immune system during infection (1, 25, 53). While care should be taken regarding protein location, proteins residing at the level of the membrane or that are secreted would suggest improved immune recognition.
Com1 did not remain in the MHC class I and II cross-analysis when assessing for epitope dense proteins (Table 8). Likewise, none of the previously studied proteins present in Additional Table 1 are represented in the 33 epitope dense proteins composed from MHC class I and II data. Of these novel epitope-containing proteins, there were seven that were not returned when assessing MHC class I or II epitope dense proteins alone. These are AAO89890.1 (thiDE), AAO90155.1 (yaeT), AAO90323.2, AAO90990.2, AAO91128.1 (icmO), AAO91393.1, and AAO91455.1 (hemA), which represent epitope rich proteins that have a balanced MHC class I and II coverage. Three of the previously mentioned proteins are designated as secreted or membrane exposed proteins by Inmembrane, AAO90155.1 (yaeT), AAO91128.1 (icmO), and AAO91393.1. Therefore, these proteins are suggested to more readily interact with the immune system upon arrival of the bacterium within host tissues. IcmO and YaeT are significant proteins in regards to host:pathogen interaction as IcmO is part of the multi-subunit T4SS and YaeT is responsible for assembly of beta-barrel surface proteins (54–56).
Table 8
Proteins with ≥ 5 epitopes present overall for MHCI and MHCII.
GenBank ID
|
Pos
|
Peptide
|
Gene Name
|
Locus Tag
|
T-cell Epitope
|
Location
|
AAO89610.1
|
72
|
YLKKHLESL
|
|
CBU_0041
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89610.1
|
450
|
SKKTFSFAKTQALPH
|
|
CBU_0041
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO89610.1
|
453
|
FSFAKTQAL
|
|
CBU_0041
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89610.1
|
459
|
QALPHLWEL
|
|
CBU_0041
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89610.1
|
523
|
KVADTHIAF
|
|
CBU_0041
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89757.1
|
95
|
HADNIKIVL
|
|
CBU_0197
|
MHCI
|
PSE-Membrane
|
AAO89757.1
|
146
|
NQIEFNHAL
|
|
CBU_0197
|
MHCI
|
PSE-Membrane
|
AAO89757.1
|
164
|
QPYPVNVYL
|
|
CBU_0197
|
MHCI
|
PSE-Membrane
|
AAO89757.1
|
374
|
HVHTPVHRL
|
|
CBU_0197
|
MHCI
|
PSE-Membrane
|
AAO89757.1
|
636
|
RAILKPTTF
|
|
CBU_0197
|
MHCI
|
PSE-Membrane
|
AAO89757.1
|
748
|
VRAIRTMKTSPIVPQ
|
|
CBU_0197
|
MHCII
|
PSE-Membrane
|
AAO89757.1
|
754
|
KTSPIVPQL
|
|
CBU_0197
|
MHCI
|
PSE-Membrane
|
AAO89774.2
|
37
|
RIYRPLFSL
|
|
CBU_0215
|
MHCI
|
PSE-Cellwall
|
AAO89774.2
|
59
|
AADDSTISL
|
|
CBU_0215
|
MHCI
|
PSE-Cellwall
|
AAO89774.2
|
283
|
LAAIIHTKTNVIDDQ
|
|
CBU_0215
|
MHCII
|
PSE-Cellwall
|
AAO89774.2
|
354
|
HMATVITTL
|
|
CBU_0215
|
MHCI
|
PSE-Cellwall
|
AAO89774.2
|
420
|
YLIEKGHHL
|
|
CBU_0215
|
MHCI
|
PSE-Cellwall
|
AAO89774.2
|
487
|
LQYPEDPSL
|
|
CBU_0215
|
MHCI
|
PSE-Cellwall
|
AAO89774.2
|
508
|
YLDELPNYL
|
|
CBU_0215
|
MHCI
|
PSE-Cellwall
|
AAO89890.1
|
33
|
HAASIITTI
|
thiDE
|
CBU_0334
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89890.1
|
35
|
AASIITTITAQNAEQ
|
thiDE
|
CBU_0334
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO89890.1
|
70
|
TLPPTVIKL
|
thiDE
|
CBU_0334
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89890.1
|
215
|
SAISSAIAL
|
thiDE
|
CBU_0334
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89890.1
|
384
|
HTLYELSRAHAIQPS
|
thiDE
|
CBU_0334
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO89918.2
|
6
|
VQNPTLESL
|
|
CBU_0364
|
MHCI
|
MEMBRANE(non-PSE)
|
AAO89918.2
|
173
|
MAFHLPHAL
|
|
CBU_0364
|
MHCI
|
MEMBRANE(non-PSE)
|
AAO89918.2
|
233
|
AVATPVQKL
|
|
CBU_0364
|
MHCI
|
MEMBRANE(non-PSE)
|
AAO89918.2
|
276
|
KAISPHASL
|
|
CBU_0364
|
MHCI
|
MEMBRANE(non-PSE)
|
AAO89918.2
|
281
|
HASLLKHTL
|
|
CBU_0364
|
MHCI
|
MEMBRANE(non-PSE)
|
AAO89941.1
|
421
|
DSYPIIQSL
|
|
CBU_0388
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89941.1
|
488
|
MAFEILEQL
|
|
CBU_0388
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89941.1
|
1009
|
SIIERVKAL
|
|
CBU_0388
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89941.1
|
1009
|
KSIIERVKALVSVDK
|
|
CBU_0388
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO89941.1
|
1248
|
VAAPLFMTL
|
|
CBU_0388
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89941.1
|
1264
|
RMFAKVFSL
|
|
CBU_0388
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89941.1
|
1270
|
FSLPIEVEL
|
|
CBU_0388
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89977.1
|
9
|
VVDSKPHEL
|
|
CBU_0425
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89977.1
|
13
|
KPHELTLLF
|
|
CBU_0425
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89977.1
|
37
|
SQIENLHKIL
|
|
CBU_0425
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO89977.1
|
84
|
NATDFEYSETQPIET
|
|
CBU_0425
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO89977.1
|
140
|
SQLFRTIDAILVKTS
|
|
CBU_0425
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO89977.1
|
197
|
TVYDTTITL
|
|
CBU_0425
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90011.1
|
58
|
HTPYLNTIPAETEAQ
|
pdhA
|
CBU_0461
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90011.1
|
171
|
SSYPHPFLM
|
pdhA
|
CBU_0461
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90011.1
|
362
|
DPQKVYAAYTEAMKD
|
pdhA
|
CBU_0461
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90011.1
|
508
|
IRDRIVPIVADEART
|
pdhA
|
CBU_0461
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90011.1
|
636
|
HQDSHNLLM
|
pdhA
|
CBU_0461
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90011.1
|
843
|
AKMVVYTALKALADQ
|
pdhA
|
CBU_0461
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90093.1
|
90
|
IAYDQAIQL
|
|
CBU_0547
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90093.1
|
124
|
KAYQKAIAL
|
|
CBU_0547
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90093.1
|
382
|
LQYQVPQKL
|
|
CBU_0547
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90093.1
|
521
|
SKKYIIALIKRNNFK
|
|
CBU_0547
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90093.1
|
549
|
KAIEGYLVL
|
|
CBU_0547
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90130.1
|
99
|
FAFKKFYVL
|
|
CBU_0586
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90130.1
|
574
|
VQAYYIAQVEKTARR
|
|
CBU_0586
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90130.1
|
725
|
RSIFVATGAKPNIAY
|
|
CBU_0586
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90130.1
|
738
|
YVYEHKGTF
|
|
CBU_0586
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90130.1
|
799
|
HPVFHGSVVKAIASA
|
|
CBU_0586
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90130.1
|
967
|
MAAAHLRSL
|
|
CBU_0586
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90130.1
|
984
|
GHRVFYVALIEKAEE
|
|
CBU_0586
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90155.1
|
257
|
DKKHVYITIHLVEGP
|
yaeT
|
CBU_0611
|
MHCII
|
PSE-Membrane
|
AAO90155.1
|
320
|
GDRGYAFARVNVIPT
|
yaeT
|
CBU_0611
|
MHCII
|
PSE-Membrane
|
AAO90155.1
|
469
|
SQYQQNYSF
|
yaeT
|
CBU_0611
|
MHCI
|
PSE-Membrane
|
AAO90155.1
|
550
|
IAAPSVLAF
|
yaeT
|
CBU_0611
|
MHCI
|
PSE-Membrane
|
AAO90155.1
|
794
|
FQFSFGVSL
|
yaeT
|
CBU_0611
|
MHCI
|
PSE-Membrane
|
AAO90229.1
|
497
|
PVDIKYDTNNLAQSA
|
|
CBU_0685
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90229.1
|
738
|
VVSPVPPVL
|
|
CBU_0685
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90229.1
|
784
|
YAKPILHPM
|
|
CBU_0685
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90229.1
|
855
|
SAYPATDRLYF
|
|
CBU_0685
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90229.1
|
940
|
TAAEVQWRL
|
|
CBU_0685
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90293.1
|
97
|
YGVNVYEVANQIRDK
|
|
CBU_0753
|
MHCII
|
PSE-Membrane
|
AAO90293.1
|
265
|
SADQSIVTL
|
|
CBU_0753
|
MHCI
|
PSE-Membrane
|
AAO90293.1
|
453
|
QAANIFRSF
|
|
CBU_0753
|
MHCI
|
PSE-Membrane
|
AAO90293.1
|
602
|
KAFDSVFAM
|
|
CBU_0753
|
MHCI
|
PSE-Membrane
|
AAO90293.1
|
785
|
VVLPHYNHL
|
|
CBU_0753
|
MHCI
|
PSE-Membrane
|
AAO90293.1
|
999
|
YAYKFKLFL
|
|
CBU_0753
|
MHCI
|
PSE-Membrane
|
AAO90323.2
|
57
|
AANDFAIKL
|
|
CBU_0789
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90323.2
|
278
|
QLEIQRQKAEAANKA
|
|
CBU_0789
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90323.2
|
481
|
TIFEHFSRL
|
|
CBU_0789
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90323.2
|
694
|
EQFIFRAKAEKEAKS
|
|
CBU_0789
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90323.2
|
816
|
KAIEAFLKM
|
|
CBU_0789
|
MHCI
|
CYTOPLASM(non-PSE)
|
ACI15273.1
|
10
|
YSSEIPQNL
|
|
CBU_1067a
|
MHCI
|
PSE-Membrane
|
ACI15273.1
|
63
|
IAAPLPIQL
|
|
CBU_1067a
|
MHCI
|
PSE-Membrane
|
ACI15273.1
|
105
|
RQFQPLATL
|
|
CBU_1067a
|
MHCI
|
PSE-Membrane
|
ACI15273.1
|
193
|
AQFTDPITF
|
|
CBU_1067a
|
MHCI
|
PSE-Membrane
|
ACI15273.1
|
280
|
YLKEIVTVL
|
|
CBU_1067a
|
MHCI
|
PSE-Membrane
|
ACI15273.1
|
535
|
FMRDGVLSL
|
|
CBU_1067a
|
MHCI
|
PSE-Membrane
|
AAO90660.1
|
70
|
SADTPILHF
|
mfd
|
CBU_1148
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90660.1
|
212
|
VEKIESVRLLPAREY
|
mfd
|
CBU_1148
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90660.1
|
531
|
KIYVPVSSL
|
mfd
|
CBU_1148
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90660.1
|
665
|
VAVLVPTTL
|
mfd
|
CBU_1148
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90660.1
|
768
|
TATPIPRTL
|
mfd
|
CBU_1148
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90735.2
|
42
|
FIRLYYAHVALEDIK
|
|
CBU_1226
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90735.2
|
81
|
EVKIRVFNPQLDRDG
|
|
CBU_1226
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90735.2
|
160
|
STLEAPISM
|
|
CBU_1226
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90735.2
|
339
|
FIGLYTSDVYRSDPR
|
|
CBU_1226
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90735.2
|
921
|
AADKGTATF
|
|
CBU_1226
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90735.2
|
1015
|
AAFDHRHIF
|
|
CBU_1226
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90735.2
|
1484
|
GTAPLFHAL
|
|
CBU_1226
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90737.1
|
149
|
TLYDPATEL
|
qseC
|
CBU_1228
|
MHCI
|
PSE-Membrane
|
AAO90737.1
|
254
|
EKRFTADAAHELRTP
|
qseC
|
CBU_1228
|
MHCII
|
PSE-Membrane
|
AAO90737.1
|
256
|
FTADAAHEL
|
qseC
|
CBU_1228
|
MHCI
|
PSE-Membrane
|
AAO90737.1
|
418
|
RVFERFFRM
|
qseC
|
CBU_1228
|
MHCI
|
PSE-Membrane
|
AAO90737.1
|
467
|
VTFPLIHNF
|
qseC
|
CBU_1228
|
MHCI
|
PSE-Membrane
|
AAO90739.1
|
8
|
QALDPQQSF
|
|
CBU_1230
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90739.1
|
312
|
RMKDLLSQL
|
|
CBU_1230
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90739.1
|
411
|
FQDTSIIQF
|
|
CBU_1230
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90739.1
|
568
|
QLIEITPAL
|
|
CBU_1230
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90739.1
|
581
|
DIPFHAVEIEKLAHR
|
|
CBU_1230
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90739.1
|
745
|
AKNPIQIMTIHKAKG
|
|
CBU_1230
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90739.1
|
806
|
KADPVYNYL
|
|
CBU_1230
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90739.1
|
827
|
ITRLLYVAATRAKES
|
|
CBU_1230
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90739.1
|
1038
|
RWIIDYKSATPNDEP
|
|
CBU_1230
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90751.1
|
22
|
FAFINPAEL
|
|
CBU_1242
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90751.1
|
55
|
VTIPTGLSF
|
|
CBU_1242
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90751.1
|
129
|
RVNDISPEF
|
|
CBU_1242
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90751.1
|
137
|
FAFSFSPKF
|
|
CBU_1242
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90751.1
|
381
|
NSFAGVTSL
|
|
CBU_1242
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90751.1
|
381
|
DNSFAGVTSLGVNRP
|
|
CBU_1242
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90780.1
|
90
|
RQYERLIEVF
|
|
CBU_1273
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90780.1
|
100
|
KAHDIGYVF
|
|
CBU_1273
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90780.1
|
159
|
VAKYIAVSTQEAALD
|
|
CBU_1273
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90780.1
|
287
|
NFKYHWAVADYLQRA
|
|
CBU_1273
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90780.1
|
399
|
VPDYVTLKNQLVAKK
|
|
CBU_1273
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90853.1
|
65
|
SAAGVNIKL
|
glmM
|
CBU_1350
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90853.1
|
133
|
DKPMKTVVADRLGKA
|
glmM
|
CBU_1350
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90853.1
|
162
|
STFPSNLTL
|
glmM
|
CBU_1350
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90853.1
|
187
|
VAPSIFHEL
|
glmM
|
CBU_1350
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90853.1
|
364
|
VMVKHPQVL
|
glmM
|
CBU_1350
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90878.1
|
140
|
KLSERLTTL
|
relA
|
CBU_1375
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90878.1
|
193
|
YLNPNEYSL
|
relA
|
CBU_1375
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90878.1
|
280
|
TALSIVHAL
|
relA
|
CBU_1375
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90878.1
|
306
|
DNGYRSIHTAVIGPE
|
relA
|
CBU_1375
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90878.1
|
428
|
KMVPLTRTL
|
relA
|
CBU_1375
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90965.2
|
108
|
RLFPGHVWL
|
|
CBU_1468
|
MHCI
|
PSE-Membrane
|
AAO90965.2
|
168
|
NIDIYYHTAEGQLIP
|
|
CBU_1468
|
MHCII
|
PSE-Membrane
|
AAO90965.2
|
235
|
SQWESSYFL
|
|
CBU_1468
|
MHCI
|
PSE-Membrane
|
AAO90965.2
|
366
|
YQPKRIQTLF
|
|
CBU_1468
|
MHCI
|
PSE-Membrane
|
AAO90965.2
|
567
|
QLRIVASHANISGNP
|
|
CBU_1468
|
MHCII
|
PSE-Membrane
|
AAO90965.2
|
608
|
ANGFKFLKAAPLSVA
|
|
CBU_1468
|
MHCII
|
PSE-Membrane
|
AAO90965.2
|
700
|
PIAFHIATLNPSSQS
|
|
CBU_1468
|
MHCII
|
PSE-Membrane
|
AAO90965.2
|
951
|
KQWKITHAL
|
|
CBU_1468
|
MHCI
|
PSE-Membrane
|
AAO90965.2
|
951
|
LKQWKITHALEGGKG
|
|
CBU_1468
|
MHCII
|
PSE-Membrane
|
AAO90990.2
|
255
|
KPYEPILNL
|
|
CBU_1493
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90990.2
|
369
|
MASPHVASL
|
|
CBU_1493
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO90990.2
|
426
|
YPPRIVANTVAFNAK
|
|
CBU_1493
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90990.2
|
486
|
KEILYGIETHPNPSP
|
|
CBU_1493
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO90990.2
|
494
|
HPNPSPTIF
|
|
CBU_1493
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91128.1
|
103
|
RQAQGIYYF
|
icmO
|
CBU_1632
|
MHCI
|
PSE-Membrane
|
AAO91128.1
|
174
|
KVFSIVRSM
|
icmO
|
CBU_1632
|
MHCI
|
PSE-Membrane
|
AAO91128.1
|
447
|
YAVEGFAVVPAQARS
|
icmO
|
CBU_1632
|
MHCII
|
PSE-Membrane
|
AAO91128.1
|
571
|
VRGKFFYADPKRTKH
|
icmO
|
CBU_1632
|
MHCII
|
PSE-Membrane
|
AAO91128.1
|
734
|
QAMNIAVEL
|
icmO
|
CBU_1632
|
MHCI
|
PSE-Membrane
|
AAO91182.1
|
46
|
AQADRIYEM
|
|
CBU_1686
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91182.1
|
50
|
RIYEMLQQL
|
|
CBU_1686
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91182.1
|
201
|
KQIPLITRY
|
|
CBU_1686
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91182.1
|
224
|
SILDVFLQL
|
|
CBU_1686
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91182.1
|
265
|
RLIDNRFSF
|
|
CBU_1686
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91182.1
|
512
|
SQQEKTIQL
|
|
CBU_1686
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91182.1
|
618
|
SVNEHANQF
|
|
CBU_1686
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91357.1
|
259
|
GEIVITALPHQVSGN
|
parC
|
CBU_1866
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO91357.1
|
376
|
FVIERLHLL
|
parC
|
CBU_1866
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91357.1
|
439
|
EKKIRDEQAILTKER
|
parC
|
CBU_1866
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO91357.1
|
516
|
KGWIRAAKGHEVEGE
|
parC
|
CBU_1866
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO91357.1
|
678
|
GNKIIQIAPARVANR
|
parC
|
CBU_1866
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO91357.1
|
739
|
PRGFRKVDNVAVDEN
|
parC
|
CBU_1866
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO91378.1
|
79
|
PKPLIHAVLATEDAR
|
ponA
|
CBU_1887
|
MHCII
|
PSE-Membrane
|
AAO91378.1
|
103
|
ISIIRAAKAVILTGK
|
ponA
|
CBU_1887
|
MHCII
|
PSE-Membrane
|
AAO91378.1
|
253
|
TAKYHAATTQVKAPY
|
ponA
|
CBU_1887
|
MHCII
|
PSE-Membrane
|
AAO91378.1
|
539
|
YAIEYLTRF
|
ponA
|
CBU_1887
|
MHCI
|
PSE-Membrane
|
AAO91378.1
|
552
|
NVLPHSLSL
|
ponA
|
CBU_1887
|
MHCI
|
PSE-Membrane
|
AAO91393.1
|
104
|
TADDFTVYF
|
|
CBU_1902
|
MHCI
|
SECRETED
|
AAO91393.1
|
116
|
SADQLPVAF
|
|
CBU_1902
|
MHCI
|
SECRETED
|
AAO91393.1
|
286
|
YALDVLSTL
|
|
CBU_1902
|
MHCI
|
SECRETED
|
AAO91393.1
|
365
|
EEELKRVKAQVIAQN
|
|
CBU_1902
|
MHCII
|
SECRETED
|
AAO91393.1
|
410
|
VKNIEAVTAQQIQQV
|
|
CBU_1902
|
MHCII
|
SECRETED
|
AAO91419.2
|
10
|
QVISLTHQF
|
|
CBU_1928
|
MHCI
|
PSE-Membrane
|
AAO91419.2
|
297
|
SAYGKTLNM
|
|
CBU_1928
|
MHCI
|
PSE-Membrane
|
AAO91419.2
|
504
|
IQFKGPSAM
|
|
CBU_1928
|
MHCI
|
PSE-Membrane
|
AAO91419.2
|
594
|
TEKLIIVAETKEDKK
|
|
CBU_1928
|
MHCII
|
PSE-Membrane
|
AAO91419.2
|
667
|
SAFWQTIKL
|
|
CBU_1928
|
MHCI
|
PSE-Membrane
|
AAO91455.1
|
145
|
TKRIRSETAIGANPV
|
hemA
|
CBU_1966
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO91455.1
|
157
|
NPVSIAYAVVQLAKR
|
hemA
|
CBU_1966
|
MHCII
|
CYTOPLASM(non-PSE)
|
AAO91455.1
|
227
|
RLSDIPTYL
|
hemA
|
CBU_1966
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91455.1
|
383
|
ILHQPTTKL
|
hemA
|
CBU_1966
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91455.1
|
394
|
AAYEDQVQL
|
hemA
|
CBU_1966
|
MHCI
|
CYTOPLASM(non-PSE)
|
AAO91467.1
|
163
|
VADKGTLTL
|
ostA
|
CBU_1978
|
MHCI
|
SECRETED
|
AAO91467.1
|
170
|
TLYPKTAIL
|
ostA
|
CBU_1978
|
MHCI
|
SECRETED
|
AAO91467.1
|
615
|
FSFEQLFAL
|
ostA
|
CBU_1978
|
MHCI
|
SECRETED
|
AAO91467.1
|
730
|
KADIRYLFVHGNEDS
|
ostA
|
CBU_1978
|
MHCII
|
SECRETED
|
AAO91467.1
|
832
|
TAYGFELQL
|
ostA
|
CBU_1978
|
MHCI
|
SECRETED
|
The epitope type is defined in the T-cell epitope column. Protein information is outlined in the following columns: GenBank ID, gene name, and locus tag, where this information is defined through Nine Mile phase I (RSA 493) assembly on NCBI. Pos dictates the peptides starting position within the protein of interest and location was defined through the use of Inmembrane. |
Cross-analysis between MHC class I and II data allows for future vaccination efforts to cover both classes of T-cell epitopes. Furthermore, the investigation herein also aids in epitope decision with regards to alternate vaccine types. For instance, identified epitope dense proteins provide a source of epitopes which can partake in a vectored vaccine (20, 34). On the other hand, when looking at proteins that contain overlapping MHCI and MHCII epitopes, there is the possibility of using the epitopes in a heterologous recombinant subunit vaccine. As a result, the provided data allows for vaccination efforts against Coxiella burnetii to move forward without restrictions on the approach to be used.