Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi
Abstract
:1. Introduction
2. Results
2.1. Characterization of Growth and Overall Oxidative and Cellulolytic Activities during the Cultivation on Solid Agar Media Containing Various Types of Sawdust
2.2. Characterization of Growth and Overall Oxidative activity during Cultivation on Solid Agar Media Containing Different Wood-Derived Polysaccharides and Lignin
2.3. Characterization of Exoproteomes during Semi-Solid Cultivation on Media Containing Various Types of Sawdust
3. Discussion
3.1. General Comparison of P. lycii LE-BIN 2142 and T. hirsuta LE-BIN 072
3.2. Secretion of Enzymes Related to Degradation of Wood Polysaccharides: Cellulose, Hemicelluloses and Pectin
3.3. Secretion of Enzymes Related to Degradation of Lignin
4. Materials and Methods
4.1. Fungal Strains
4.2. Cultivation on Solid Media
4.3. Cultivation on Semi-Solid Media
4.4. Agar Plate Assays of Overall Oxidative and Cellulolytic Activities
4.5. Study of Exoproteomes
4.6. Statistical Data Analysis and Database Search
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Hit Accession | Hit Species 1 | Hit Description | EC | CAZY | SignalP | GP 2 | AL | BR | PN |
---|---|---|---|---|---|---|---|---|---|
Peniophora lycii LE-BIN 2142 | |||||||||
Plant cell wall—Cellulose | |||||||||
KZV77634.1 | PenSpv1 | Lytic polysaccharide monooxygenase | 1.14.99.54 | AA9 | Yes | 1 | 1 | 1 | 1 |
KZV61898.1 | PenSpv1 | GMC oxidoreductase | AA3_2 | No | 0 | 1 | 1 | 1 | |
VDB89641.1 | PenCBMAI | N-terminal domain of expansins | Yes | 0 | 0 | 0 | 1 | ||
Plant cell wall—Hemicellulose | |||||||||
KZV62723.1 | PenSpv1 | endo-α-L-arabinanase | 3.2.1.55|3.2.1.99 | GH43 | Yes | 1 | 1 | 1 | 1 |
KZV64181.1 | PenSpv1 | Esterases and lipases | 3.1.1.- | CE15 | Yes | 0 | 1 | 1 | 0 |
Plant cell wall—Pectine | |||||||||
KZV68058.1 | PenSpv1 | Unsaturated glucuronyl hydrolase | 3.2.1.- | GH88 | Yes | 0 | 1 | 0 | 1 |
Plant cell wall—Starch | |||||||||
KZV59596.1 | PenSpv1 | Glucoamylase | 3.2.1.3 | GH15 + CBM20 | Yes | 0 | 1 | 1 | 1 |
Plant cell wall—Lignin | |||||||||
KZV72897.1 | PenSpv1 | Laccase 53 | 1.10.3.2 | AA1_1 | Yes | 1 | 1 | 1 | 1 |
KZV76831.1 | PenSpv1 | Laccase 7 | 1.10.3.2 | AA1_1 | Yes | 1 | 1 | 0 | 1 |
KZV67752.1 | PenSpv1 | Laccase 8 | 1.10.3.2 | AA1_1 | Yes | 1 | 1 | 0 | 1 |
KZV69698.1 | PenSpv1 | Laccase 15 | 1.10.3.2 | AA1_1 | Yes | 0 | 1 | 0 | 0 |
KZV66389.1 | PenSpv1 | Laccase 18 | 1.10.3.2 | AA1_1 | Yes | 0 | 1 | 0 | 0 |
KZV64391.1 | PenSpv1 | FAD-binding domain-containing protein | AA7 | Yes | 1 | 1 | 1 | 1 | |
KZV64574.1 | PenSpv1 | FAD-binding domain-containing protein | AA7 | Yes | 1 | 1 | 1 | 1 | |
KZV63916.1 | PenSpv1 | FAD-binding domain-containing protein | AA7 | Yes | 1 | 1 | 1 | 1 | |
Fungal cell wall | |||||||||
KZV74929.1 | PenSpv1 | β-1,3-glucanase; β-1,3-glucosidase | 3.2.1.39|3.2.1.- | GH128 | Yes | 1 | 1 | 1 | 1 |
KZV74469.1 | PenSpv1 | endo-β-1,3(4)-glucanase | 3.2.1.6 | GH16_1 | Yes | 1 | 1 | 1 | 1 |
KZV69996.1 | PenSpv1 | endo-β-1,3(4)-glucanase | 3.2.1.6 | GH16_1 | Yes | 1 | 1 | 1 | 1 |
KZV69997.1 | PenSpv1 | endo-β-1,3(4)-glucanase | 3.2.1.6 | GH16_1 | Yes | 1 | 1 | 1 | 1 |
KZV61773.1 | PenSpv1 | β-1,3-glucanase | 3.2.1.39 | GH152 | Yes | 1 | 1 | 1 | 1 |
KZV69792.1 | PenSpv1 | β-1,3-glucanase | 3.2.1.39 | GH152 | Yes | 1 | 1 | 1 | 1 |
KZV61339.1 | PenSpv1 | Type II chitinase | 3.2.1.14 | GH18 | Yes | 1 | 1 | 1 | 1 |
KZV67604.1 | PenSpv1 | β-1,3-glucanosyltransglycosylase | 2.4.1.- | GH72 + CBM43 | Yes | 0 | 1 | 1 | 1 |
KZV73237.1 | PenSpv1 | α-1,3-glucanase | 3.2.1.59 | GH71 | Yes | 0 | 0 | 1 | 0 |
Other | |||||||||
KZV69230.1 | PenSpv1 | Peptidase S53 | No | 1 | 1 | 1 | 1 | ||
KZV67034.1 | PenSpv1 | Ricin B lectin | No | 1 | 1 | 1 | 0 | ||
KZV71566.1 | PenSpv1 | Lipase class 3 | Yes | 0 | 1 | 1 | 0 | ||
KZV69610.1 | PenSpv1 | Putative isomerase YbhE | No | 0 | 1 | 1 | 0 | ||
KZV64666.1 | PenSpv1 | Cerato-platanin | Yes | 0 | 1 | 1 | 0 | ||
KZV63020.1 | PenSpv1 | Glycopeptide | Yes | 1 | 0 | 0 | 0 | ||
Hypothetical proteins | |||||||||
KZV63574.1 | PenSpv1 | Hypothetical protein (143 aa) | Yes | 1 | 1 | 1 | 1 | ||
KZV71782.1 | PenSpv1 | Hypothetical protein (445 aa) | Yes | 1 | 1 | 1 | 1 | ||
KZV75687.1 | PenSpv1 | Hypothetical protein (195 aa) | No | 1 | 1 | 1 | 1 | ||
KZV75838.1 | PenSpv1 | Hypothetical protein (390 aa) | Yes | 1 | 1 | 1 | 1 | ||
KZV66557.1 | PenSpv1 | Hypothetical protein (269 aa) | Yes | 1 | 1 | 1 | 1 | ||
KZV74951.1 | PenSpv1 | Hypothetical protein (143 aa) | Yes | 1 | 1 | 0 | 0 | ||
VDC00636.1 | PenCBMAI | Hypothetical protein (446 aa) | Yes | 0 | 0 | 1 | 1 | ||
KZV68227.1 | PenSpv1 | Hypothetical protein (190 aa) | Yes | 0 | 1 | 0 | 0 | ||
KZV75056.1 | PenSpv1 | Hypothetical protein (244 aa) | No | 0 | 1 | 0 | 0 | ||
KZV69008.1 | PenSpv1 | Hypothetical protein (104 aa) | No | 0 | 1 | 0 | 0 | ||
KZV75686.1 | PenSpv1 | Hypothetical protein (187 aa) | Yes | 0 | 0 | 0 | 1 | ||
Trametes hirsuta LE-BIN 072 | |||||||||
Plant cell wall—Cellulose | |||||||||
FUN_000808 | TraHir | Cellulase | 3.2.1.4 | GH5_5 + CBM1 | Yes | 0 | 0 | 0 | 1 |
FUN_005645 | TraHir | Cellobiohydrolase I | 3.2.1.176 | GH6 + CBM1 | Yes | 0 | 0 | 0 | 1 |
FUN_000756 | TraHir | Cellobiohydrolase II | 3.2.1.91 | GH7 + CBM1 | Yes | 0 | 0 | 0 | 1 |
FUN_010354 | TraHir | Cellobiose dehydrogenase | 1.1.99.18 | AA8 + AA3_1 | Yes | 0 | 1 | 1 | 1 |
FUN_000419 | TraHir | Lytic polysaccharide monooxygenase | 1.14.99.54 | AA9 | Yes | 1 | 0 | 0 | 0 |
Plant cell wall—Hemicellulose | |||||||||
FUN_001307 | TraHir | β-mannosidase | 3.2.1.25 | GH2 | Yes | 0 | 1 | 0 | 1 |
Plant cell wall—Pectine | |||||||||
FUN_002751 | TraHir | Polygalacturonase | 3.2.1.15 | GH28 | Yes | 1 | 1 | 1 | 1 |
FUN_008017 | TraHir | Tannase; feruloyl esterase | 3.1.1.20|3.1.1.73 | CE1 | Yes | 1 | 0 | 0 | 0 |
Plant cell wall—Starch | |||||||||
FUN_006083 | TraHir | Glucoamylase | 3.2.1.3 | GH15 + CBM20 | Yes | 1 | 1 | 1 | 1 |
FUN_010348 | TraHir | Maltogenic Amylase | 3.2.1.1|3.2.1.98|3.2.1.116 | GH13_32 + CBM20 | Yes | 0 | 0 | 1 | 1 |
Plant cell wall—Lignin | |||||||||
FUN_001030 | TraHir | Laccase A | 1.10.3.2 | AA1_1 | Yes | 1 | 1 | 1 | 1 |
FUN_010573 | TraHir | Laccase C | 1.10.3.2 | AA1_1 | Yes | 0 | 0 | 1 | 0 |
FUN_007604 | TraHir | VP2 (POD17) | 1.11.1.16 | AA2 | Yes | 1 | 1 | 1 | 1 |
FUN_002850 | TraHir | MnP5 (POD05) | 1.11.1.13 | AA2 | Yes | 1 | 1 | 0 | 1 |
FUN_007002 | TraHir | LiP9 (POD18) | 1.11.1.14 | AA2 | Yes | 1 | 0 | 0 | 1 |
FUN_007983 | TraHir | MnP6 (POD06) | 1.11.1.13 | AA2 | Yes | 1 | 0 | 0 | 0 |
FUN_010480 | TraHir | Glyoxal oxidase GLOX | 1.2.3.15 | AA5_1 | Yes | 1 | 1 | 1 | 1 |
FUN_001506 | TraHir | Glyoxal oxidase GLOX | 1.2.3.15 | AA5_1 | Yes | 1 | 1 | 1 | 1 |
Fungal cell wall | |||||||||
FUN_000340 | TraHir | β-1,3-glucanosyltransglycosylase | 2.4.1.- | GH72 + CBM43 | No | 0 | 1 | 1 | 1 |
FUN_002148 | TraHir | endo-β-1,3(4)-glucanase | GH16_1 | Yes | 1 | 1 | 0 | 1 | |
FUN_010090 | TraHir | β-1,3-glucanase | 3.2.1.39 | GH152 | Yes | 0 | 1 | 0 | 0 |
Proteases | |||||||||
FUN_008047 | TraHir | Peptidase S53 | Yes | 1 | 1 | 1 | 1 | ||
FUN_006633 | TraHir | Peptidase S53 | Yes | 1 | 1 | 1 | 1 | ||
FUN_009590 | TraHir | Peptidase S10 | No | 1 | 1 | 1 | 1 | ||
FUN_006927 | TraHir | Peptidase S8 | Yes | 1 | 1 | 0 | 1 | ||
FUN_001546 | TraHir | Metallopeptidase M36 | Yes | 0 | 1 | 0 | 1 | ||
FUN_006898 | TraHir | Aspartyl (acid) protease | Yes | 0 | 0 | 1 | 1 | ||
FUN_009658 | TraHir | Protease family A1 | Yes | 0 | 0 | 1 | 1 | ||
FUN_002544 | TraHir | Protease family A1 | Yes | 0 | 0 | 0 | 1 | ||
Other | |||||||||
FUN_002582 | TraHir | Lipase/esterase | No | 0 | 1 | 1 | 1 | ||
FUN_002005 | TraHir | Fungal phospholipase B | Yes | 0 | 1 | 1 | 1 | ||
FUN_010217 | TraHir | MBL-fold metallo-hydrolase | Yes | 0 | 1 | 1 | 1 | ||
FUN_010277 | TraHir | Putative isomerase YbhE | No | 1 | 1 | 0 | 1 | ||
FUN_006612 | TraHir | α,α-trehalase | 3.2.1.28 | GH37 | Yes | 1 | 0 | 1 | 1 |
FUN_010625 | TraHir | Lytic murein transglycosylase D | Yes | 0 | 0 | 1 | 1 | ||
FUN_003015 | TraHir | Metal-dependent hydrolase | Yes | 0 | 0 | 1 | 1 | ||
FUN_007614 | TraHir | Ferritin-like superfamily | No | 0 | 0 | 1 | 1 | ||
FUN_000583 | TraHir | Polysaccharide lyase | 4.2.2.- | PL8_4 | Yes | 1 | 0 | 0 | 0 |
FUN_000786 | TraHir | Alginate lyase | PL35 | No | 1 | 0 | 0 | 0 | |
FUN_000797 | TraHir | Alginate lyase | PL35 | No | 1 | 0 | 0 | 0 | |
FUN_002699 | TraHir | Amidase | Yes | 0 | 0 | 0 | 1 | ||
Hypothetical proteins | |||||||||
FUN_004762 | TraHir | Hypothetical protein (165 aa) | Yes | 1 | 1 | 1 | 1 | ||
FUN_009768 | TraHir | Hypothetical protein (385 aa) | Yes | 0 | 1 | 1 | 1 | ||
FUN_000138 | TraHir | Hypothetical protein (641 aa) | No | 0 | 0 | 1 | 1 | ||
FUN_007129 | TraHir | Hypothetical protein (139 aa) | Yes | 0 | 0 | 1 | 1 | ||
FUN_006467 | TraHir | Hypothetical protein (173 aa) | Yes | 0 | 0 | 0 | 1 | ||
FUN_006175 | TraHir | Hypothetical protein (145 aa) | Yes | 0 | 1 | 0 | 0 | ||
FUN_000212 | TraHir | Hypothetical protein (166 aa) | Yes | 1 | 0 | 0 | 0 |
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Shabaev, A.V.; Moiseenko, K.V.; Glazunova, O.A.; Savinova, O.S.; Fedorova, T.V. Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi. Int. J. Mol. Sci. 2022, 23, 10322. https://doi.org/10.3390/ijms231810322
Shabaev AV, Moiseenko KV, Glazunova OA, Savinova OS, Fedorova TV. Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi. International Journal of Molecular Sciences. 2022; 23(18):10322. https://doi.org/10.3390/ijms231810322
Chicago/Turabian StyleShabaev, Alexander V., Konstantin V. Moiseenko, Olga A. Glazunova, Olga S. Savinova, and Tatyana V. Fedorova. 2022. "Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi" International Journal of Molecular Sciences 23, no. 18: 10322. https://doi.org/10.3390/ijms231810322