Depolymerisation of the Klebsiella pneumoniae Capsular Polysaccharide K21 by Klebsiella Phage K5
Abstract
:1. Introduction
2. Results
2.1. General Biological Properties
2.2. General Characterisation of Genome
2.3. Taxonomy and Phylogeny
2.3.1. Related Phages
2.3.2. VIRIDIC Intergenomic Similarity
2.3.3. Phylogenetic Analysis
2.4. In Silico Analysis of K5 RBPs
2.5. Cloning and Expression of Putative Capsule Depolymerases
2.6. Structure of the Capsular Polysaccharide and Its Cleavage by RBP2
3. Discussion
4. Materials and Methods
4.1. Klebsiella Phage K5: Isolation and Growth Conditions
4.2. One-Step Growth and Adsorption Curves
4.3. Host Range
4.4. Phage Genome Sequencing and Annotation
4.5. Genome Analysis and AlphaFold Modelling
4.6. Tail Spike Protein Cloning, Expression and Purification
4.7. Spot Assay
4.8. Isolation of Capsular Polysaccharides
4.9. Isolation of the O-Polysaccharide
4.10. Smith Degradation
4.11. Monosaccharide Analysis
4.12. NMR Spectroscopy
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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N° | Strain | K Type | Lysis |
---|---|---|---|
1 | K.pneumoniae 62867 | K1 | - |
2 | K.pneumoniae 77245 | K2 | - |
3 | K.pneumoniae 69402 | K12 | - |
4 | K.pneumoniae KL12 | K12 | - |
5 | K.pneumoniae KL13 | K13 | - |
6 | K.pneumoniae kot L | K14 | - |
7 | K.pneumoniae 88166 | K15 | - |
8 | K.pneumoniae KphM | K16 | - |
9 | K.pneumoniae 77840 | K16 | - |
10 | K.pneumoniae 74610 | K17 | - |
11 | K.pneumoniae 80384 | K20 | - |
12 | K.pneumoniae Kph1 | K20 | - |
13 | K.pneumoniae K5 (isolation host) | K21 | + |
14 | K.pneumoniae Kph5 | K23 | - |
15 | K.pneumoniae 78315 | K24 | - |
16 | K.pneumoniae 77680 | K25 | - |
17 | K.pneumoniae 77487 | K39 | - |
18 | K.oxytoca 1620 | K55 | - |
19 | K.pneumoniae 81841 | K62 | - |
20 | K.pneumoniae 77864 | K64 | - |
21 | K.pneumoniae Kph13 | K107 | - |
22 | K.pneumoniae 1333 | K108 | - |
23 | K.pneumoniae 1226 | K112 | - |
24 | K.pneumoniae 19.01 | K114 | - |
25 | K.pneumoniae 15 | K161 | - |
26 | K.pneumoniae 3 | Uncharacterised | - |
27 | K.pneumoniae 1 | Uncharacterised | - |
28 | K.pneumoniae 3.1 | Uncharacterised | - |
29 | K.pneumoniae OX2 | Uncharacterised | - |
30 | K.pneumoniae 1481 | Uncharacterised | - |
31 | K.pneumoniae 224 | Uncharacterised | - |
32 | K.pneumoniae OX140 | Uncharacterised | - |
33 | K.pneumoniae 203 | Uncharacterised | - |
34 | K.pneumoniae 186 | Uncharacterised | - |
35 | K.pneumoniae 197 | Uncharacterised | - |
Monosaccharide Residue | C1 | C2 | C3 | C4 | C5 | C6 | |
---|---|---|---|---|---|---|---|
H1 | H2 | H3 | H4 | H5 | H6 (6a, 6b) | ||
CPS | |||||||
→3,4-α-d-GlcpA-(1→3 | A | 101.5 | 73.2 | 80.5 | 71.3 | 74.1 | 175.1 |
5.25 | 3.87 | 4.31 | 3.92 | 4.21 | – | ||
→3-α-d-Manp-(1→2 | B | 103.3 | 70.9 | 79.6 | 74.5 | 74.6 | 62.3 |
5.02 | 4.19 | 3.91 | 3.79 | 3.71 | 3.85; 3.74 | ||
→2-α-d-Manp-(1→3 | C | 95.9 | 80.3 | 71.4 | 68.3 | 76.8 | 62.3 |
5.23 | 4.01 | 3.97 | 3.68 | 3.90 | 3.85; 3.74 | ||
→3-β-d-Galp-(1→3 | D | 104.2 | 71.2 | 77.8 | 65.9 | 76.4 | 62.3 |
4.85 | 3.66 | 3.76 | 4.13 | 3.64 | 3.87 | ||
(4,6)-Pyr-α-d-Galp-(1→4 | E | 100.7 | 69.5 | 69.2 | 72.6 | 63.9 | 66.1 |
5.50 | 3.88 | 3.84 | 4.17 | 3.72 | 3.98, 3.85 | ||
4,6-pyruvate | 5.33 | 1.44 | |||||
176.3 | 101.6 | 26.4 | |||||
MPS | |||||||
→3,4-α-d-GlcpA-(1→3 | A | 101.7 | 73.2 | 80.5 | 75.7 | 74.1 | 175.1 |
5.23 | 3.88 | 4.37 | 3.93 | 4.28 | - | ||
→3-α-d-Manp-(1→2 | B | 103.4 | 71.0 | 79.7 | 67.5 | 74.6 | 62.3 |
5.03 | 4.23 | 3.93 | 3.82 | 3.81 | 3.85; 3.74 | ||
→2-α-d-Manp-(1→3 | C | 95.8 | 80.5 | 71.3 | 68.3 | 74.1 | 62.3 |
5.23 | 4.01 | 3.99 | 3.67 | 3.88 | 3.85; 3.74 | ||
→3-β-d-Galp-(1→3 | D | 104.2 | 71.2 | 77.7 | 65.8 | 76.4 | 62.3 |
4.89 | 3.65 | 3.78 | 4.15 | 3.65 | 3.87 | ||
α-d-Galp-(1→4 | E | 99.7 | 69.8 | 70.6 | 70.2 | 72.0 | 62.3 |
5.58 | 3.80 | 3.80 | 3.98 | 3.90 | 3.87 |
Monosaccharide Residue | C1 | C2 | C3 | C4 | C5 | C6 | |
---|---|---|---|---|---|---|---|
H1 | H2 | H3 | H4 | H5 | H6 (6a, 6b) | ||
OS1 | |||||||
→3-α-d-GlcpA-(1→3 | A | 101.9 | 72.4 | 81.9 | 71.3 | 73.0 | 175.9 |
5.28 | 3.82 | 4.06 | 4.07 | 4.29 | - | ||
→3-α-d-Manp-(1→2 | B | 100.3 | 71.1 | 80.5 | 67.0 | 74.2 | 62.5 |
5.07 | 4.16 | 3.94 | 3.87 | 3.92 | 3.93; 3.90 | ||
→3-β-d-Galp-(1→3 | D | 104.4 | 72.5 | 73.8 | 69.9 | 76.5 | 62.4 |
4.67 | 3.59 | 3.67 | 3.91 | 3.71 | 3.86 | ||
Gro | C | 90.3 | 81.1 | 62.3 | |||
5.13 | 3.67 | 3.75 | |||||
OS2 | |||||||
→3-α-d-GlcpA-(1→3 | A | 101.9 | 72.4 | 81.9 | 71.3 | 73.0 | 175.9 |
5.28 | 3.82 | 4.06 | 4.07 | 4.29 | - | ||
→3-α-d-Manp-(1→2 | B | 100.5 | 71.0 | 80.6 | 67.0 | 74.2 | 62.5 |
5.04 | 4.17 | 3.98 | 3.87 | 3.92 | 3.93; 3.90 | ||
→3-β-d-Galp-(1→3 | D | 104.4 | 72.5 | 73.8 | 69.9 | 76.5 | 62.4 |
4.67 | 3.59 | 3.67 | 3.91 | 3.71 | 3.86 | ||
Aglycone | C | 103.9 | 77.6 | 62.8 | 63.0 | 77.9 | 67.6 |
5.13 | 3.90 | 3.76 | 3.72; 3.61 | 4.29 | 4.02; 3.81 | ||
OS3 | |||||||
→3,4-α-d-GlcpA-(1→3 | A | 102.1 | 72.8 | 74.4 | 79.7 | 72.4 | 174.8 |
5.32 | 3.67 | 4.03 | 3.84 | 4.42 | |||
→3-α-d-Manp-(1→2 | B | 95.9 | 71.3 | 80.6 | 67.8 | 74.9 | 62.5 |
5.28 | 4.22 | 3.93 | 3.79 | 3.83 | 3.89; 3.72 | ||
→2-α-d-Manp-(1→3 | C | 96.0 | 80.7 | 71.4 | 68.5 | 74.3 | 62.5 |
5.23 | 4.01 | 4.01 | 3.70 | 3.86 | 3.88; 3.77 | ||
→3-β-d-Galp-(1→3 | Dβ | 103.8 | 71.9 | 78.0 | 66.0 | 76.5 | 62.4 |
5.02 | 3.56 | 3.74 | 4.14 | 3.66 | 3.76 | ||
→3-α-d-Galp-(1→3 | Dα | 93.8 | 68.3 | 74.5 | 66.6 | 71.9 | 61.0 |
5.28 | 3.89 | 3.95 | 4.20 | 4.05 | 3.72 | ||
(4,6)-Pyr-α-d-Galp-(1→4 | E | 101.9 | 69.5 | 69.0 | 73.3 | 64.3 | 66.8 |
5.45 | 3.94 | 3.91 | 4.24 | 3.73 | 4.04; 3.93 | ||
4,6-pyruvate | 176.7 | 95.6 | 26.4 | ||||
5.29 | 1.55 |
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Lukianova, A.A.; Shneider, M.M.; Evseev, P.V.; Egorov, M.V.; Kasimova, A.A.; Shpirt, A.M.; Shashkov, A.S.; Knirel, Y.A.; Kostryukova, E.S.; Miroshnikov, K.A. Depolymerisation of the Klebsiella pneumoniae Capsular Polysaccharide K21 by Klebsiella Phage K5. Int. J. Mol. Sci. 2023, 24, 17288. https://doi.org/10.3390/ijms242417288
Lukianova AA, Shneider MM, Evseev PV, Egorov MV, Kasimova AA, Shpirt AM, Shashkov AS, Knirel YA, Kostryukova ES, Miroshnikov KA. Depolymerisation of the Klebsiella pneumoniae Capsular Polysaccharide K21 by Klebsiella Phage K5. International Journal of Molecular Sciences. 2023; 24(24):17288. https://doi.org/10.3390/ijms242417288
Chicago/Turabian StyleLukianova, Anna A., Mikhail M. Shneider, Peter V. Evseev, Mikhail V. Egorov, Anastasiya A. Kasimova, Anna M. Shpirt, Alexander S. Shashkov, Yuriy A. Knirel, Elena S. Kostryukova, and Konstantin A. Miroshnikov. 2023. "Depolymerisation of the Klebsiella pneumoniae Capsular Polysaccharide K21 by Klebsiella Phage K5" International Journal of Molecular Sciences 24, no. 24: 17288. https://doi.org/10.3390/ijms242417288
APA StyleLukianova, A. A., Shneider, M. M., Evseev, P. V., Egorov, M. V., Kasimova, A. A., Shpirt, A. M., Shashkov, A. S., Knirel, Y. A., Kostryukova, E. S., & Miroshnikov, K. A. (2023). Depolymerisation of the Klebsiella pneumoniae Capsular Polysaccharide K21 by Klebsiella Phage K5. International Journal of Molecular Sciences, 24(24), 17288. https://doi.org/10.3390/ijms242417288