Actinobaculum massiliense Proteome Profiled in Polymicrobial Urethral Catheter Biofilms
Abstract
:1. Introduction
2. Methods
2.1. Ethics Statement
2.2. Clinical Background and Patient Specimens
2.3. Catheter Sample Processing for Microbial Cultures, 16S rRNA Sequencing, and Proteomics
2.4. In Vitro Liquid Culture of Actinotignum massiliense in Rich Growth Media
2.5. Catheter Biofilm Extraction
2.6. Cell Lysis and Preparation of CCP and CB Lysates for Proteomics
2.7. Shotgun Proteomics Using LC-MS/MS
2.8. Computational Methods to Profile and Quantify the Metaproteomes
2.9. 16S rRNA Analysis
2.10. Protein Function and Biological Pathway Analyses
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene Locus 1 | Protein Description 2 | Functional Group or Domain 3 | Put. Role in Inter-Action with Host 4 | Predict. Location 5 | Q (ivv vs ivt) 6 | Q Avg (ivv) 7 |
---|---|---|---|---|---|---|
01095 | Putative subtilisin-like protease | fibronectin type III, S8pro | invasion, inflammation | CW; SP motif | >8 | 0.0617 |
00826 | Rib/alpha/Esp surface antigen repeat-containing protein | Ca2+/cadherin bndg type III repeat and Ig-like fold | adhesion, biofilm formation | CW; SP motif | >8 | 0.0434 |
00810 | Putative subtilisin-like protease | fibronectin type III, S8pro | invasion and inflammation | CW; SP motif | 2–8 | 0.0406 |
01185 | Oligopeptide/nickel binding protein | ABC transporter su., MppA–type | metal/heme/peptide uptake | CW; SP motif | 2–8 | 0.0230 |
01650 | l–arginine:glycine amidinotransferase | creatine synthesis from arginine | part of PKS pathway | CY | >8 | 0.0196 |
00827 | Rib/alpha/Esp surface antigen repeat-containing protein | Ca2+/cadherin bndg type III repeat | adhesion, biofilm formation | CW; SP motif | 2–8 | 0.0092 |
01410 | Bacterial Ig-like domain protein | Ig-like domain | adhesion | not predicted | 2–8 | 0.0047 |
01413 | Listeria-Bacteroides repeat domain | Cadherin E-binding domain | adhesion, invasion | CW; SP motif | 2–8 | 0.0045 |
01648 | Ornithine carbamoyltransferase (ArcB) | arginine metabolism | part of PKS pathway | CY | >8 | 0.0042 |
00680 | Oligopeptide/nickel binding protein | ABC transporter su., MppA-type | metal/heme/peptide uptake | CW; SP motif | <2 | 0.0038 |
01649 | Carbamate kinase (ArcC) | arginine metabolism | part of PKS pathway | CY | >8 | 0.0034 |
01184 | Oligopeptide ABC transporter, ATP-binding domain | ABC transporter su. | metal/heme/peptide uptake | CM | <2 | 0.0031 |
00954 | Papain-like cysteine protease | cysteine protease | extracellular proteolysis | not predicted | 2–8 | 0.0023 |
00866 | LPXTG-domain-containing cell wall anchor protein | pilin subunit D1 domain | adhesion | LPLTG CW anchor | 2–8 | 0.0022 |
01647 | Arginine deiminase (ArcA) | arginine metabolism | part of PKS pathway | CY | >8 | 0.0021 |
01182 | Oligopeptide ABC transporter, permease | ABC transporter su. | metal/heme/peptide uptake | CM | 2–8 | 0.0017 |
00677 | Oligopeptide ABC transporter, ATP-binding domain | ABC transporter su. | metal/heme/peptide uptake | CM | <2 | 0.0017 |
01364 | Putative polyketide synthase | multifunctional enzyme | polyketide biosynthesis | CY | <2 | 0.0015 |
00649 | Fe/B12 periplasmic binding protein | ABC transporter su., FecB-like | metal/cofactor uptake | CW; SP motif | >8 | 0.0015 |
00581 | LPXTG-domain-containing cell wall anchor protein | G5 repeat domains | cell surface modulation | LPHTG CW anchor | >8 | 0.0014 |
01361 | Biotin-[acetyl-CoA-carboxylase] ligase | part of PKS pathway | part of PKS pathway | CY | <2 | 0.0012 |
00678 | Oligopeptide ABC transporter, ATP-binding domain | ABC transporter su. | metal/heme/peptide uptake | CM | <2 | 0.0010 |
01183 | Oligopeptide ABC transporter, permease | ABC transporter su. | metal/heme/peptide uptake | CM | <2 | 0.0005 |
01418 | Oligopeptide/nickel binding protein | ABC transporter su., MppA-type | metal/heme/peptide uptake | CW; SP motif | >8 | 0.0004 |
00679 | Oligopeptide ABC transporter, permease | ABC transporter su. | metal/heme/peptide uptake | CM | <2 | 0.0004 |
01362 | ATP grasp family protein | part of PKS pathway | part of PKS pathway | CY | <2 | 0.0003 |
Accession 1 | Description 2 | Average CB 3 |
---|---|---|
P02768 | 6 Serum albumin = ALB [ALBU_HUMAN] | 0.0793 |
P02788 | 4,7 Lactotransferrin = LTF [TRFL_HUMAN] | 0.0365 |
P13645 | 5 Keratin, type I cytoskeletal 10 = KRT10 [K1C10_HUMAN] | 0.0333 |
P05164 | 4 Myeloperoxidase = MPO [PERM_HUMAN] | 0.0314 |
P06702 | 4 Protein S100-A9 = S100A9 [S10A9_HUMAN] | 0.0306 |
P04264 | 5 Keratin, type II cytoskeletal 1 = KRT [K2C1_HUMAN] | 0.0293 |
P01834 | 6,8 Immunoglobulin kappa constant chain = IGKC [IGKC_HUMAN] | 0.0200 |
P0DOX5 | 6,8 Immunoglobulin gamma-1 heavy chain [IGG1_HUMAN] | 0.0191 |
P02538 | 5 Keratin, type II cytoskeletal 6A = KRT6A [K2C6A_HUMAN] | 0.0187 |
P04259 | 5 Keratin, type II cytoskeletal 6B = KRT6B [K2C6B_HUMAN] | 0.0173 |
P35908 | 5 Keratin, type II cytoskeletal 2 epidermal = KRT2 [K22E_HUMAN] | 0.0167 |
P59665 | 4,7 Neutrophil defensin = DEFA1 [DEF1_HUMAN] | 0.0165 |
P02787 | 6 Serotransferrin = TF [TRFE_HUMAN] | 0.0151 |
P0DOX7 | 6,8 Immunoglobulin kappa light chain [IGK_HUMAN] | 0.0151 |
P01024 | 8 Complement C3 =C3 [CO3_HUMAN] | 0.0146 |
P13646 | 5 Keratin, type I cytoskeletal 13 = KRT13 [K1C13_HUMAN] | 0.0143 |
P13647 | 5 Keratin, type II cytoskeletal 5 OS = KRT5 [K2C5_HUMAN] | 0.0137 |
P02533 | 5 Keratin, type I cytoskeletal 14 = KRT14 [K1C14_HUMAN] | 0.0121 |
P08779 | 5 Keratin, type I cytoskeletal 16 = KRT16 [K1C16_HUMAN] | 0.0116 |
P01876 | 6,8 Immunoglobulin heavy constant alpha 1 = IGHA1 [IGHA1_HUMAN] | 0.0114 |
P02675 | 8 Fibrinogen beta chain = FGB [FIBB_HUMAN] | 0.0112 |
P02679 | 8 Fibrinogen gamma chain = FGG [FIBG_HUMAN] | 0.0109 |
P01861 | 6,8 Immunoglobulin heavy constant gamma 4 = IGHG4 [IGHG4_HUMAN] | 0.0107 |
P05109 | 4 Protein S100-A8 = S100A8 [S10A8_HUMAN] | 0.0101 |
P08311 | 4 Cathepsin G = CTSG [CATG_HUMAN] | 0.0101 |
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Share and Cite
Yu, Y.; Tsitrin, T.; Singh, H.; Doerfert, S.N.; Sizova, M.V.; Epstein, S.S.; Pieper, R. Actinobaculum massiliense Proteome Profiled in Polymicrobial Urethral Catheter Biofilms. Proteomes 2018, 6, 52. https://doi.org/10.3390/proteomes6040052
Yu Y, Tsitrin T, Singh H, Doerfert SN, Sizova MV, Epstein SS, Pieper R. Actinobaculum massiliense Proteome Profiled in Polymicrobial Urethral Catheter Biofilms. Proteomes. 2018; 6(4):52. https://doi.org/10.3390/proteomes6040052
Chicago/Turabian StyleYu, Yanbao, Tamara Tsitrin, Harinder Singh, Sebastian N. Doerfert, Maria V. Sizova, Slava S. Epstein, and Rembert Pieper. 2018. "Actinobaculum massiliense Proteome Profiled in Polymicrobial Urethral Catheter Biofilms" Proteomes 6, no. 4: 52. https://doi.org/10.3390/proteomes6040052