Identification of Putative Novel Class-I Lanthipeptides in Firmicutes: A Combinatorial In Silico Analysis Approach Performed on Genome Sequenced Bacteria and a Close Inspection of Z-Geobacillin Lanthipeptide Biosynthesis Gene Cluster of the Thermophilic Geobacillus sp. Strain ZGt-1
Abstract
:1. Introduction
2. Results and Discussion
2.1. Lanthipeptide Identification Workflow
2.2. Identification of Putative Novel Lanthipeptides
2.3. Class-I Lanthipeptide Biosynthetic Gene Clusters in Firmicutes
2.3.1. Identification of Bacillus-associated Lanthipeptide Gene Clusters
2.3.2. Identification of Geobacillus-associated Lanthipeptide Gene Clusters
2.3.3. Identification of Lactococcus-associated Lanthipeptide Gene Clusters
2.3.4. Identification of Paenibacillus-associated Lanthipeptide Gene Clusters
2.3.5. Identification of Staphylococcus-associated Lanthipeptide Gene Clusters
2.3.6. Identification of Streptococcus-associated Lanthipeptide Gene Clusters
3. Methods
3.1. Selection of the Genome Sequences to be Analyzed
3.2. Identification of Class-I Lanthipeptides Using antiSMASH
3.3. Analysis of the Identified Class-I Lanthipeptides
3.3.1. NCBI BLAST Analysis
3.3.2. BAGEL Analysis
3.3.3. InterPro Analysis
3.4. Mapping of Z-Geobacillin Biosynthetic Pathway
3.5. Alignment of Lanthipeptide Sequences of Geobacillus strains
4. Conclusions
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
Abbreviations
aa | amino acid |
ABC transporters | ATP-binding cassette transporters |
antiSMASH | Antibiotics and Secondary Metabolite Analysis Shell |
BAGEL | bacteriocin genome mining tool |
BSA | bacteriocin of Staphylococcus aureus |
Dha | dehydroalanine |
Dhb | dehydrobutyrine |
GeoAI | geobacillin I precursor peptide |
GeoB | geobacillin I dehydratase enzyme |
GeoC | geobacillin I cyclase enzyme |
GeoGEF | self-immunity ABC transporter proteins |
GeoI | geobacillin I self-immunity protein |
GeoK | geobacillin I sensor histidine kinase protein; part of the two-component response regulatory system |
GeoR | geobacillin I response regulatory protein; part of the two-component response regulatory system |
GeoTI | geobacillin I ABC transporter protein |
KAAS | KEGG Automatic Annotation Server |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
Lan | lanthionine |
LanP | lanthipepttide processing protease |
MeLan | (2S,3S,6R)-3-methyllanthionine |
Nt | nucleotide |
PGAP | prokaryotic genome annotation pipeline |
RODEO | Rapid ORF Description and Evaluation Online genome-mining platform |
ZgeoA | Z-geobacillin precursor peptide |
ZgeoB | Z-geobacillin dehydratase enzyme |
ZgeoC | Z-geobacillin cyclase enzyme |
ZgeoGEF | Z-geobacillin self-immunity ABC transporter proteins |
ZgeoI | Z-geobacillin self-immunity protein |
ZgeoK | Z-geobacillin sensor histidine kinase protein; part of the two-component response regulatory system |
ZgeoR | Z-geobacillin response regulatory protein; part of the two-component response regulatory system |
ZgeoT | Z-geobacillin ABC transporter protein |
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Bacterial Species, Strain (Lanthipeptide Reference Number) | RefSeq Genome Accession Number | Annotation of the Lanthipeptide-Coding Gene | |
---|---|---|---|
Original Genome Record | RefSeq Genome Record | ||
Bacillus thuringiensis serovar finitimus YBT-020 | NC_017200 | ‘Hypothetical protein’ | Unannotated |
Geobacillus sp. ZGt-1 | LDPD01000000 1 | Lanthipeptide | Unavailable in RefSeq |
Paenibacillus polymyxa M1 (I) | NC_017542 | Unannotated | ‘Hypothetical protein’ |
Paenibacillus polymyxa M1 (II) | NC_017542 | Unannotated | ‘Hypothetical protein’ |
Paenibacillus polymyxa SC2 (I) 2 | NC_014622 | Partly inaccurately annotated | ‘Hypothetical protein’ |
Paenibacillus polymyxa SC2 (II) | NC_014622 | Incorrectly annotated as coding for subtilin | ‘Hypothetical protein’ |
Staphylococcus aureus NCTC 8325 (II) | NC_007795 | Unannotated | Unannotated |
Streptococcus intermedius B196 3 | NC_022246 | Unannotated | ‘Hypothetical protein’ |
Bacterial Strain | RefSeq Genome Accession Number | Total Number of Harbored Class-I Lanthipeptides | Lanthipeptide Reference Number 1 | Identity to Experimentally Verified Lanthipeptide 2 | Reference 3 |
---|---|---|---|---|---|
Bacillus clausii KSM-K16 | NC_006582 | 1 | - 4 | 56% clausin | [30], and this study |
Bacillus megaterium QM B1551 | NC_014023 | 2 | I and II | 56% gallidermin | [30,31], and this study |
Bacillus subtilis BSn5 | NC_014976 | 1 | - 4 | 100% subtilomycin | [32,33], and this study |
Bacillus subtilis spizizenii W23 | NC_014479 | 1 | - 4 | 100% subtilin | This study |
Bacillus thuringiensis serovar finitimus YBT-020 | NC_017200 | 1 | - 4 | No hits | This study |
Bacillus thuringiensis serovar IS5056 | NC_020394 | 5 | I and II III IV V | 100% thuricin 4A-4 86% thuricin 4A-4 84% thuricin 4A-4 82% thuricin 4A-4 | [31], and this study |
Bacillus thuringiensis YBT 1518 | NC_022873 | 2 | I II | 53% gallidermin 51% gallidermin | This study |
Geobacillus kaustophilus HTA426 | NC_006510 | 2 | I II | 91% geobacillin I 79% geobacillin I | [15,34], and this study |
Geobacillus sp. ZGt-1 | LDPD01000000 | 1 | - 4 | 91% geobacillin I | This study |
Geobacillus thermoleovorans CCB_US3_UF5 | NC_016593 | 1 | - 4 | 79% geobacillin I | This study |
Lactococcus lactis CV56 | NC_017486 | 1 | - 4 | 100% nisin A | [15,35], and this study |
Lactococcus lactis IO-1 | NC_020450 | 1 | - 4 | 100% nisin Z | This study |
Paenibacillus polymyxa CR1 | NC_023037 | 1 | - 4 | 94% paenilan | [36,37], and this study |
Paenibacillus polymyxa M1 | NC_017542 | 2 | I II | 64% paenilan 96% paenilan | [36], and this study |
Paenibacillus polymyxa SC2 | NC_014622 | 2 | I II | 64% paenilan 96% paenilan | [30,36,38], and this study |
Staphylococcus aureus 11819-97 | NC_017351 | 2 | I II | 100% BsaA2 83% BsaA2 | This study |
Staphylococcus aureus Bmb 9393 | NC_021670 | 2 | I II | 100% BsaA2 83% BsaA2 | This study |
Staphylococcus aureus COL | NC_002951 | 2 | I II | 100% BsaA2 79% BsaA2 | [8], and this study |
Staphylococcus aureus ED133 | NC_017337 | 2 | I II | 100% BacCH91 85% BsaA2 | [30], and this study |
Staphylococcus aureus LGA251 | NC_017349 | 2 | I II | 81% BsaA2 85% BsaA2 | This study |
Staphylococcus aureus M1 | NC_021059 | 2 | I II | 100% BsaA2 83% BsaA2 | This study |
Staphylococcus aureus MSSA476 | NC_002953 | 2 | I II | 100% BsaA2 83% BsaA2 | [8], and this study |
Staphylococcus aureus MW2 | NC_003923 | 2 | I II | 100% BsaA2 83% BsaA2 | [8], and this study |
Staphylococcus aureus NCTC 8325 | NC_007795 | 2 | I II | 100% BsaA2 83% BsaA2 | [8], and this study |
Staphylococcus aureus Newman | NC_009641 | 2 | I II | 100% BsaA2 83% BsaA2 | [8], and this study |
Staphylococcus aureus T0131 | NC_017347 | 2 | I II | 100% BsaA2 83% BsaA2 | This study |
Staphylococcus aureus TW20 | NC_017331 | 2 | I II | 100% BsaA2 83% BsaA2 | This study |
Staphylococcus aureus USA300 FPR3757 | NC_007793 | 2 | I II | 100% BsaA2 83% BsaA2 | [8], and this study |
Staphylococcus aureus USA300_TCH1516 | NC_010079 | 2 | I II | 100% BsaA2 83% BsaA2 | [8], and this study |
Staphylococcus aureus VC40 | NC_016912 | 2 | I II | 100% BsaA2 83% BsaA2 | This study |
Staphylococcus aureus Z172 | NC_022604 | 2 | I II | 100% BsaA2 83% BsaA2 | This study |
Streptococcus intermedius B196 | NC_022246 | 1 | - 4 | No hits | This study |
Streptococcus intermedius C270 | NC_022237 | 1 | - 4 | 81% nisin F | This study |
Streptococcus pasteurianus ATCC 43144 | NC_015600 | 1 | - 4 | 91% nisin U | [39], and this study |
Streptococcus pyogenes MGAS6180 | NC_007296 | 1 | - 4 | 100% streptin | [15], and this study |
Streptococcus pyogenes MGAS9429 | NC_008021 | 1 | - 4 | 100% streptin | This study |
Streptococcus pyogenes MGAS10270 | NC_008022 | 1 | - 4 | 100% streptin | [15], and this study |
Streptococcus pyogenes MGAS10750 | NC_008024 | 1 | - 4 | 98% streptin | [15], and this study |
Streptococcus suis JS14 | NC_017618 | 1 | - 4 | 100% suicin 90-1330 | This study |
Streptococcus suis SC070731 | NC_020526 | 1 | - 4 | 100% suicin 90-1330 | This study |
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Alkhalili, R.N.; Canbäck, B. Identification of Putative Novel Class-I Lanthipeptides in Firmicutes: A Combinatorial In Silico Analysis Approach Performed on Genome Sequenced Bacteria and a Close Inspection of Z-Geobacillin Lanthipeptide Biosynthesis Gene Cluster of the Thermophilic Geobacillus sp. Strain ZGt-1. Int. J. Mol. Sci. 2018, 19, 2650. https://doi.org/10.3390/ijms19092650
Alkhalili RN, Canbäck B. Identification of Putative Novel Class-I Lanthipeptides in Firmicutes: A Combinatorial In Silico Analysis Approach Performed on Genome Sequenced Bacteria and a Close Inspection of Z-Geobacillin Lanthipeptide Biosynthesis Gene Cluster of the Thermophilic Geobacillus sp. Strain ZGt-1. International Journal of Molecular Sciences. 2018; 19(9):2650. https://doi.org/10.3390/ijms19092650
Chicago/Turabian StyleAlkhalili, Rawana N., and Björn Canbäck. 2018. "Identification of Putative Novel Class-I Lanthipeptides in Firmicutes: A Combinatorial In Silico Analysis Approach Performed on Genome Sequenced Bacteria and a Close Inspection of Z-Geobacillin Lanthipeptide Biosynthesis Gene Cluster of the Thermophilic Geobacillus sp. Strain ZGt-1" International Journal of Molecular Sciences 19, no. 9: 2650. https://doi.org/10.3390/ijms19092650