Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance
<p>Genomic maps of the chromosome and plasmids of (<b>A</b>) KKP 3001, (<b>B</b>) KKP 3001, and (<b>C</b>) KKP 3002 constructed with Proksee.</p> "> Figure 2
<p>An unrooted tree of homologous RsmA proteins identified and constructed using RAxML and visualized on the iTOL server.</p> "> Figure 3
<p>Classification of proteins encoded by KKP 3000, KKP 3001, and KKP 3002 into (<b>A</b>) KEGG functional categories and (<b>B</b>) KEGG pathways.</p> "> Figure 4
<p><span class="html-italic">Alicyclobacillus</span> strains KKP 3000, KKP 3001, and KKP 3002 code for proteins involved in (<b>A</b>) flagellar assembly and (<b>B</b>) chemotaxis. The maps were produced using KEGG Mapper. The proteins encoded by the strains are indicated in green.</p> "> Figure 5
<p>Arrangement of <span class="html-italic">vdc</span> operons in novel strains, compared to <span class="html-italic">A. fastidiosus</span> DSM17978, <span class="html-italic">A. acidoterrestris</span> DSM3922, and <span class="html-italic">A.dauci</span> DSM28700.</p> "> Figure 6
<p>Comparison of Vdc proteins. Phylograms were prepared using UniProt software <a href="https://www.uniprot.org/" target="_blank">https://www.uniprot.org/</a> (accessed on 24 April 2024).</p> "> Figure 7
<p>(<b>A</b>) ANI of KKP 3000, KKP 3001, and KKP 3002 with members of the <span class="html-italic">A. fastidiosus</span> species (i.e., DSM 17978 and NBRC103109). (<b>B</b>) The phylogenomic tree containing the three novel strains and members of the <span class="html-italic">Alicyclobacillus</span> genus. <span class="html-italic">Phenylobacterium aquaticum</span> KACC 18306 was used as an outgroup. The tree was calculated on the TYGS server and visualized using iTOL.</p> "> Figure 8
<p>BRIG diagram showing homologous chromosome segments of the three novel strains (KKP 3000, KKP 3001, KKP 3002) to the <span class="html-italic">A. fastidiosus</span> type strain DSM 17978.</p> ">
Abstract
:1. Introduction
2. Results and Discussion
2.1. Assessment of Antibiotic Resistance
2.2. Genome Characteristics
2.3. Functional Annotation
2.4. Vdc Operons
2.5. ANI, and Phylogenomic Analysis
3. Materials and Methods
3.1. Bacterial Strains and Growth Conditions
3.2. Genomic DNA Isolation and Sequencing
3.3. Antibiotic Resistance
3.4. Genome Annotation and Analysis
3.5. Phylogenomic Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Minimum Inhibition Concentrations Tested [μg/mL] | |||||||||
---|---|---|---|---|---|---|---|---|---|
Bacteria | AM | GM | KM | SM | EM | CM | TC | CL | VA |
KKP 3000 | 0.094 | 0.047 | 0.19 | 0.5 | >256 | 0.5 | 0.016 | 0.5 | 0.19 |
KKP 3001 | 0.064 | 0.064 | 0.38 | 0.5 | >256 | 0.5 | 0.016 | 0.75 | 0.19 |
KKP 3002 | 0.047 | 0.047 | 0.5 | 0.5 | >256 | 0.75 | 0.016 | 0.75 | 0.25 |
A. fastidiosus DSM 17978 | 0.016 | 0.064 | 0.5 | 0.5 | >256 | 0.047 | 0.016 | 0.38 | 0.19 |
Genome Characteristics | Alicyclobacillus KKP 3000 | Alicyclobacillus KKP 3001 | Alicyclobacillus KKP 3002 |
---|---|---|---|
Length | 4,859,599 bp | 4,972,367 bp | 4,977,437 bp |
GC content | 52.95% | 53% | 52.92% |
CDSs | 4872 | 4924 | 4928 |
rRNAs | 3 | 45 | 45 |
tRNAs | 40 | 131 | 131 |
No. of CRISPR Arrays | 1 | 1 | 1 |
IS elements | 52 | 14 | 14 |
Phages | |||
Intact | 0 | 0 | 0 |
Incomplete | 5 | 7 | 5 |
Questionable | 0 | 1 | 1 |
Antibiotic resistance genes | |||
Perfect hits | 0 | 0 | 0 |
Strict hits | 5 | 5 | 5 |
Loose hits | 302 | 297 | 297 |
Virulence genes | 0 | 0 | 0 |
Plasmids | 0 | 2 | 2 |
Clusters of Orthologous Groups | Alicyclobacillus KKP 3000 | Alicyclobacillus KKP 3001 | Alicyclobacillus KKP 3002 |
---|---|---|---|
C-Energy production and conversion | 212 (4.96%) | 214 (5.5%) | 214 (5.5%) |
D-Cell cycle control and mitosis | 59 (1.38%) | 58 (1.49%) | 58 (1.49%) |
E-Amino Acid metabolism and transport | 482 (11.29%) | 434 (11.15%) | 434 (11,15%) |
F-Nucleotide metabolism and transport | 99 (2.32%) | 99 (2.54%) | 99 (2.54%) |
G-Carbohydrate metabolism and transport | 425 (9.95%) | 320 (8.22%) | 320 (8.22%) |
H-Coenzyme metabolism | 183 (4.29%) | 163 (4.19%) | 163 (4.19%) |
I-Lipid metabolism | 158 (3.7%) | 156 (4.01%) | 156 (4.01%) |
J-Translation | 201 (4.7%) | 187 (4.80%) | 187 (4.8%) |
K-Transcription | 374 (8.76%) | 352 (9.04%) | 352 (9.04%) |
L-Replication and repair | 218 (5.11%) | 265 (6.81%) | 268 (6.88%) |
M-Cell wall/membrane/envelope biogenesis | 217 (5.08%) | 193 (4.96%) | 193 (4.96%) |
N-Cell motility | 47 (1.1%) | 47 (1.21%) | 47 (1.21%) |
O-Post-translational modification, protein turnover, chaperone functions | 90 (2.11%) | 80 (2.06%) | 80 (2.05%) |
P-Inorganic ion transport and metabolism | 278 (6.51%) | 201 (5.16%) | 200 (5.14%) |
Q-Secondary Structure | 118 (2.76%) | 67 (1.72%) | 67 (1.72%) |
T-Signal Transduction | 151 (3.54%) | 111 (2.85%) | 111 (2.85%) |
U-Intracellular trafficking and secretion | 49 (1.15%) | 31 (0.80%) | 31 (0.8%) |
V-Defence mechanisms | 56 (1.31%) | 58 (1.49%) | 58 (1.49%) |
S-Function Unknown | 696 (16.3%) | 697 (17.91%) | 696 (17.9%) |
No annotation | 157 (3.68%) | 159 (4.09%) | 159 (4.09%) |
Total (%) | 4270 (100%) | 3892 (100%) | 3893 (100%) |
Alicyclobacillus KKP 3000 | Alicyclobacillus KKP 3001 | Alicyclobacillus KKP 3002 | Predicted Protein | Gene |
---|---|---|---|---|
Sporulation and Germination | ||||
KFAPOJEI_02576 | PLKKBLCC_02372 | PKEAFELD_02372 | stage III sporulation protein AG | spoIIIAG |
KFAPOJEI_02575 | PLKKBLCC_02373 | PKEAFELD_02373 | Stage III sporulation protein AF | spoIIIAF |
KFAPOJEI_02574 | PLKKBLCC_02374 | PKEAFELD_02374 | stage III sporulation protein AE | spoIIIAE |
KFAPOJEI_02573 | PLKKBLCC_02375 | PKEAFELD_02375 | Stage III sporulation protein AD | spoIIIAD |
KFAPOJEI_02572 | PLKKBLCC_02376 | PKEAFELD_02376 | stage III sporulation protein AC | spoIIIAC |
KFAPOJEI_02571 | PLKKBLCC_02377 | PKEAFELD_02377 | Stage III sporulation protein AB | spoIIIAB |
KFAPOJEI_02570 | PLKKBLCC_02378 | PKEAFELD_02378 | stage III sporulation protein AA | spoIIIAA |
KFAPOJEI_03030 | PLKKBLCC_01460 | PKEAFELD_01459 | Sporulation sigma-E factor-processing peptidase | spoIIGA |
KFAPOJEI_02435 | PLKKBLCC_04809 | PKEAFELD_04813 | Stage II sporulation protein R | spoIIR |
KFAPOJEI_01887 | PLKKBLCC_04452 | PKEAFELD_04456 | Spore cortex biosynthesis protein YabQ | yabQ |
KFAPOJEI_01888 | PLKKBLCC_04453 | PKEAFELD_04457 | Spore coat protein | yabP |
KFAPOJEI_02376 | PLKKBLCC_04750 | PKEAFELD_04754 | Spore Coat Protein X and V domain | cotX |
KFAPOJEI_02378 | PLKKBLCC_04752 | PKEAFELD_04756 | Spore Coat Protein X and V domain | cotX |
KFAPOJEI_02939 | PLKKBLCC_01782 | PKEAFELD_01782 | Outer spore coat protein E | cotE |
KFAPOJEI_03520 | PLKKBLCC_03012 | PKEAFELD_03013 | Spore coat associated protein JA | cotJA |
KFAPOJEI_03586 | PLKKBLCC_01820 | PKEAFELD_01821 | Bacillus/Clostridium GerA spore germination protein | spoVAF |
KFAPOJEI_02916 | PLKKBLCC_01759 | PKEAFELD_01759 | Dipicolinate synthase subunit B | spoVFB |
KFAPOJEI_00796 | PLKKBLCC_02257 | PKEAFELD_02257 | Stage IV sporulation protein A | spoIVA |
KFAPOJEI_00087 | PLKKBLCC_03559 | PKEAFELD_03564 | Spore germination protein | gerBA |
KFAPOJEI_03728 | PLKKBLCC_04348 | PKEAFELD_04352 | Spore gernimation protein | gerD |
KFAPOJEI_01384 | PLKKBLCC_02819 | - | Germination protease | gpr |
KFAPOJEI_00085 | PLKKBLCC_03561 | PKEAFELD_03566 | PFAM spore germination B3 GerAC family protein | yfkR |
KFAPOJEI_02645 | PLKKBLCC_02303 | PKEAFELD_02303 | Sporulation protein YtfJ | ytfJ |
KFAPOJEI_02649 | PLKKBLCC_02299 | PKEAFELD_02299 | Sporulation lipoprotein YhcN/YlaJ | yhcN |
KFAPOJEI_00243 | PLKKBLCC_03402 | PKEAFELD_03408 | Small, acid-soluble spore protein D | sspD |
KFAPOJEI_01029 | PLKKBLCC_03882 | PKEAFELD_03887 | Small, acid-soluble spore protein Tlp | tlp |
KFAPOJEI_02647 | PLKKBLCC_02301 | PKEAFELD_02301 | Spore maturation protein B | spmB |
Flagella formation and Chemotaxis | ||||
KFAPOJEI_02858 | PKEAFELD_01701 | PLKKBLCC_01701 | Flagellar basal body rod protein FlgB | flgB |
KFAPOJEI_02859 | PKEAFELD_01702 | PLKKBLCC_01702 | Flagellar basal-body rod protein FlgC | flgC |
KFAPOJEI_02860 | PKEAFELD_01703 | PLKKBLCC_01703 | Flagellar hook-basal body complex protein FliE | fliE |
KFAPOJEI_02861 | PKEAFELD_01704 | PLKKBLCC_01704 | Flagellar M-ring protein | fliF |
KFAPOJEI_02862 | PKEAFELD_01705 | PLKKBLCC_01705 | Flagellar motor switch protein FliG | fliG |
KFAPOJEI_02863 | PKEAFELD_01706 | PLKKBLCC_01706 | Flagellar assembly protein FliH | fliH |
KFAPOJEI_02864 | PKEAFELD_01707 | PLKKBLCC_01707 | Flagellum-specific ATP synthase | fliI |
KFAPOJEI_02866 | PKEAFELD_01709 | PLKKBLCC_01709 | Flagellar protein FlbB | flbB |
KFAPOJEI_02868 | PKEAFELD_01711 | PLKKBLCC_01711 | Minor extracellular protease Vpr | flgD |
KFAPOJEI_02870 | PKEAFELD_01713 | PLKKBLCC_01713 | Flagellar basal-body rod protein FlgG | flgG |
KFAPOJEI_02871 | PKEAFELD_01714 | PLKKBLCC_01714 | Flagellar protein FlbD | flbD |
KFAPOJEI_02872 | PKEAFELD_01715 | PLKKBLCC_01715 | Flagellar protein FliL | fliL |
KFAPOJEI_02873 | PKEAFELD_01716 | PLKKBLCC_01716 | Flagellar motor switch protein FliM | fliM |
KFAPOJEI_02874 | PKEAFELD_01717 | PLKKBLCC_01717 | Flagellar motor switch protein FliN | fliY |
KFAPOJEI_02875 | PKEAFELD_01718 | PLKKBLCC_01718 | Chemotaxis protein CheY | cheY |
KFAPOJEI_02876 | PKEAFELD_01719 | PLKKBLCC_01719 | Flagellar biosynthesis protein FliO | fliO |
KFAPOJEI_02877 | PKEAFELD_01720 | PLKKBLCC_01720 | Flagellar biosynthetic protein FliP | fliP |
KFAPOJEI_02878 | PKEAFELD_01721 | PLKKBLCC_01721 | Flagellar biosynthetic protein FliQ | fliQ |
KFAPOJEI_02879 | PKEAFELD_01722 | PLKKBLCC_01722 | Flagellar biosynthetic protein FliR | fliR |
KFAPOJEI_02880 | PKEAFELD_01723 | PLKKBLCC_01723 | Flagellar biosynthetic protein FlhB | flhB |
KFAPOJEI_02881 | PKEAFELD_01724 | PLKKBLCC_01724 | Flagellar biosynthesis protein FlhA | flhA |
KFAPOJEI_01101 | PKEAFELD_03959 | PLKKBLCC_03954 | Pilus assembly protein PilZ | pilZ |
KFAPOJEI_04448 | PKEAFELD_04051 | PLKKBLCC_04046 | Transcriptional regulator of flagella formation YvyF | yvyF |
KFAPOJEI_04452 | PKEAFELD_04047 | PLKKBLCC_04042 | Flagellar hook-associated protein 1 | flgK |
KFAPOJEI_04453 | PKEAFELD_04046 | PLKKBLCC_04041 | Flagellar hook-associated protein 3 | flgL |
KFAPOJEI_04454 | PKEAFELD_04045 | PLKKBLCC_04040 | Flagellin | fliC |
KFAPOJEI_04455 | PKEAFELD_04044 | PLKKBLCC_04039 | Flagellar hook-associated protein 2 | fliD |
KFAPOJEI_04457 | PKEAFELD_04042 | PLKKBLCC_04037 | Flagellar secretion chaperone FliS | fliS |
KFAPOJEI_01101 | PKEAFELD_03959 | PLKKBLCC_02269 | Pilus assembly protein PilZ | pilZ |
KFAPOJEI_03756 | PKEAFELD_00013 | PLKKBLCC_00013 | Motility protein A | motA |
KFAPOJEI_03757 | PKEAFELD_00014 | PLKKBLCC_00014 | Motility protein B | motB |
PKEAFELD_02776 | PKEAFELD_02776 | PLKKBLCC_02776 | Putative sensory transducer protein YfmS | yfmS |
PKEAFELD_00239 | PKEAFELD_00239 | PLKKBLCC_00239 | Inhibitor of MCP methylation, homolog of CheC | cheX |
PKEAFELD_01727 | PKEAFELD_01727 | PLKKBLCC_01727 | CheB methylesterase | cheB |
PKEAFELD_01728 | PKEAFELD_01728 | PLKKBLCC_01728 | Signal transducing histidine kinase, homodimeric domain | cheA |
PKEAFELD_01729 | PKEAFELD_01729 | PLKKBLCC_01729 | Two component signalling adaptor domain | cheW |
PKEAFELD_01730 | PKEAFELD_01730 | PLKKBLCC_01730 | CheY-P phosphatase CheC | cheC |
PKEAFELD_01731 | PKEAFELD_01731 | PLKKBLCC_01731 | Chemoreceptor glutamine deamidase CheD | cheD |
PKEAFELD_02249 | PKEAFELD_02249 | PLKKBLCC_02249 | Methyltransferase, chemotaxis proteins | cheR |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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Bucka-Kolendo, J.; Kiousi, D.E.; Dekowska, A.; Mikołajczuk-Szczyrba, A.; Karadedos, D.M.; Michael, P.; Galanis, A.; Sokołowska, B. Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance. Int. J. Mol. Sci. 2024, 25, 8144. https://doi.org/10.3390/ijms25158144
Bucka-Kolendo J, Kiousi DE, Dekowska A, Mikołajczuk-Szczyrba A, Karadedos DM, Michael P, Galanis A, Sokołowska B. Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance. International Journal of Molecular Sciences. 2024; 25(15):8144. https://doi.org/10.3390/ijms25158144
Chicago/Turabian StyleBucka-Kolendo, Joanna, Despoina Eugenia Kiousi, Agnieszka Dekowska, Anna Mikołajczuk-Szczyrba, Dimitrios Marinos Karadedos, Panagiotis Michael, Alex Galanis, and Barbara Sokołowska. 2024. "Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance" International Journal of Molecular Sciences 25, no. 15: 8144. https://doi.org/10.3390/ijms25158144