The Phylogenomic Characterization of Planotetraspora Species and Their Cellulases for Biotechnological Applications
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genomic Dataset
2.2. Phylogenetic and Phylogenomic Analyses
2.3. Core Gene and Pangenome Analysis
2.4. Genome Annotation
2.5. Carbohydrate-Active Enzymes (CAZyme)
2.6. Sequence Retrieval
2.7. In Silico Physico-Chemical Properties
2.8. Homology Modeling and Model Confirmation
2.9. Molecular Docking Analysis
3. Results and Discussion
3.1. Phylogenetic and Phylogenomic Analyses
3.2. Core Gene and Pangenome Analysis
3.3. Genome Annotation
3.4. Carbohydrate-Active Enzymes (CAZymes) and Cazome
3.5. Sequence Retrieval and Physico-Chemical Properties
3.6. Homology Modeling and Model Confirmation
3.7. Molecular Docking 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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Pk | Pm | Pp | Ps | Pt | Na | |
---|---|---|---|---|---|---|
Genome assembly | ASM1686289v1 | ASM1686327v1 | ASM1686329v1 | ASM1686331v1 | ASM1686333v1 | ASM1420369v1 |
GenBank assembly accession number | GCA_016862895.1 | GCA_016863275.1 | GCA_016863295.1 | GCA_016863315.1 | GCA_016863335.1 | GCA_014203695.1 |
Total length (bp) | 8,768,202 | 9,027,692 | 9,167,700 | 8,664,980 | 8,961,068 | 4,812,129 |
GC content (%) | 69.7 (69.5 a) | 69.3 (69.5 a) | 69.6 (69.5 a) | 69.3 (69.5 a) | 69.2 (69.0 a) | 71.3 (71.5 a) |
Gap Ratio (%) | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.017684% |
No. of CDSs | 8191 | 8439 | 8579 | 8033 | 8304 | 4265 |
No. of rRNA | 3 | 2 | 2 | 1 | 2 | 2 |
No. of tRNA | 75 | 69 | 72 | 72 | 76 | 65 |
No. of CRISPRS | 4 | 15 | 3 | 18 | 64 | 6 |
Coding ratio (%) | 88.2% | 88.1% | 88.0% | 87.6% | 87.7% | 86.5% |
Pk | Pm | Pp | Ps | Pt | |
---|---|---|---|---|---|
AA3 | 2 | 1 | 1 | 1 | 1 |
AA10 + CBM12 | 1 | 0 | 0 | 0 | 0 |
CBM2|GH6 | 0 | 1 | 0 | 0 | 0 |
CBM2|GH18 | 2 | 3 | 3 | 3 | 2 |
CBM3|GH0 | 1 | 1 | 1 | 1 | 1 |
CBM5|GH18 | 0 | 0 | 1 | 0 | 1 |
CBM6 | 5 | 4 | 5 | 3 | 5 |
CBM6|GH3 | 0 | 2 | 2 | 1 | 0 |
CBM6|GH99 | 1 | 1 | 1 | 1 | 0 |
CBM13 | 1 | 1 | 1 | 1 | 0 |
CBM13 + CBM6 | 1 | 0 | 0 | 0 | 0 |
CBM13 + CBM92 | 0 | 0 | 0 | 1 | 0 |
CBM13|GH18 | 1 | 0 | 1 | 1 | 1 |
CBM13|GH30 | 1 | 1 | 1 | 1 | 1 |
CBM13|GH39 | 2 | 2 | 2 | 0 | 0 |
CBM13|GH55 | 1 | 1 | 0 | 1 | 1 |
CBM13|GH141 | 1 | 0 | 0 | 0 | 0 |
CBM16|GH18 | 2 | 2 | 2 | 2 | 3 |
CBM32 | 6 | 6 | 7 | 6 | 6 |
CBM32|CBM6 | 1 | 1 | 1 | 1 | 1 |
CBM32|GH2 | 2 | 2 | 2 | 1 | 1 |
CBM32|GH3 | 0 | 0 | 0 | 0 | 1 |
CBM32|GH16 | 1 | 2 | 2 | 2 | 2 |
CBM32|GH20 | 1 | 1 | 1 | 1 | 1 |
CBM32|GH28|GH29 | 1 | 1 | 0 | 0 | 0 |
CBM32|GH29 | 2 | 1 | 2 | 1 | 3 |
CBM32|GH46 | 1 | 1 | 1 | 1 | 0 |
CBM32|GH55 | 1 | 1 | 1 | 1 | 1 |
CBM32|GH85 | 1 | 1 | 1 | 0 | 1 |
CBM32|GH87 | 3 | 3 | 3 | 3 | 3 |
CBM32|GH92 | 1 | 1 | 1 | 1 | 1 |
CBM32|GH95 | 0 | 1 | 0 | 1 | 1 |
CBM32|GH99 | 1 | 1 | 1 | 1 | 0 |
CBM32|GH120|GH95 | 0 | 0 | 1 | 0 | 1 |
CBM32|GH141 | 1 | 1 | 0 | 1 | 1 |
CBM32|GH158|GH16 | 1 | 1 | 1 | 1 | 0 |
CBM35|GH2 | 1 | 1 | 1 | 1 | 0 |
CBM35|GH20 | 1 | 1 | 1 | 0 | 0 |
CBM35|GH27 | 0 | 0 | 1 | 0 | 1 |
CBM35|GH75 | 1 | 1 | 1 | 1 | 1 |
CBM48|GH13 | 4 | 4 | 4 | 4 | 4 |
CBM51|GH27 | 1 | 1 | 1 | 1 | 1 |
CBM51|GH97 | 1 | 1 | 1 | 1 | 1 |
CBM57 | 0 | 1 | 0 | 0 | 1 |
CBM57|GH18 | 1 | 1 | 1 | 1 | 0 |
CBM61|GH53 | 0 | 1 | 1 | 1 | 0 |
CBM67|GH78 | 0 | 0 | 0 | 0 | 1 |
CBM92 | 1 | 1 | 1 | 1 | 1 |
CE0 | 1 | 1 | 1 | 0 | 0 |
CE1 | 1 | 1 | 1 | 1 | 1 |
CE4|GT2 | 1 | 1 | 1 | 1 | 1 |
CE7 | 2 | 2 | 2 | 2 | 2 |
CE9 | 1 | 1 | 1 | 1 | 1 |
CE14 | 3 | 3 | 3 | 3 | 3 |
GH0 | 2 | 2 | 2 | 2 | 1 |
GH1 | 7 | 8 | 7 | 6 | 6 |
GH2 | 4 | 5 | 5 | 3 | 5 |
GH3 | 9 | 9 | 9 | 8 | 6 |
GH4 | 3 | 3 | 3 | 3 | 3 |
GH5 | 2 | 2 | 2 | 2 | 2 |
GH6 | 0 | 0 | 0 | 0 | 1 |
GH9 | 1 | 1 | 1 | 0 | 0 |
GH13 | 8 | 8 | 8 | 8 | 8 |
GH15 | 3 | 2 | 2 | 3 | 3 |
GH18 | 2 | 1 | 2 | 1 | 1 |
GH20 | 5 | 5 | 5 | 4 | 4 |
GH23 | 2 | 2 | 2 | 2 | 2 |
GH27 | 1 | 1 | 1 | 1 | 0 |
GH29 | 0 | 1 | 0 | 0 | 0 |
GH31 | 2 | 3 | 2 | 3 | 0 |
GH33 | 0 | 1 | 1 | 0 | 0 |
GH35 | 1 | 1 | 1 | 1 | 2 |
GH36 | 4 | 3 | 3 | 3 | 3 |
GH38 | 6 | 6 | 6 | 6 | 5 |
GH42 | 0 | 2 | 1 | 2 | 0 |
GH43 | 1 | 1 | 2 | 1 | 1 |
GH46 | 0 | 0 | 0 | 0 | 1 |
GH50 | 0 | 2 | 0 | 0 | 0 |
GH51 | 1 | 2 | 1 | 1 | 0 |
GH55 | 1 | 1 | 1 | 1 | 1 |
GH63 | 1 | 1 | 1 | 0 | 0 |
GH65 | 1 | 1 | 1 | 1 | 1 |
GH78 | 0 | 1 | 0 | 0 | 3 |
GH87 | 1 | 1 | 1 | 1 | 1 |
GH92 | 1 | 1 | 2 | 1 | 2 |
GH93 | 0 | 0 | 0 | 1 | 0 |
GH95 | 2 | 2 | 2 | 1 | 2 |
GH99 | 0 | 0 | 0 | 0 | 1 |
GH106 | 0 | 1 | 0 | 0 | 3 |
GH110 | 2 | 1 | 1 | 1 | 0 |
GH114 | 1 | 1 | 1 | 1 | 0 |
GH121 | 2 | 1 | 2 | 1 | 1 |
GH127 | 2 | 2 | 2 | 1 | 1 |
GH128 | 1 | 1 | 1 | 1 | 1 |
GH130 | 0 | 1 | 0 | 1 | 0 |
GH141 | 0 | 0 | 0 | 0 | 1 |
GH146 | 0 | 1 | 2 | 1 | 1 |
GH151 | 0 | 1 | 0 | 0 | 0 |
GH154 | 1 | 1 | 1 | 1 | 1 |
GH171 | 2 | 2 | 2 | 1 | 1 |
GT0|GT2 | 0 | 0 | 0 | 1 | 0 |
GT1 | 4 | 4 | 5 | 5 | 5 |
GT2 | 18 | 17 | 20 | 17 | 15 |
GT4 | 26 | 30 | 30 | 30 | 22 |
GT8 | 0 | 0 | 0 | 0 | 1 |
GT9 | 1 | 1 | 1 | 1 | 1 |
GT20 | 2 | 2 | 2 | 2 | 2 |
GT28 | 2 | 2 | 2 | 2 | 3 |
GT35 | 1 | 1 | 1 | 1 | 1 |
GT39 | 3 | 3 | 3 | 3 | 2 |
GT51 | 5 | 5 | 5 | 5 | 5 |
GT81 | 1 | 1 | 1 | 1 | 1 |
GT83 | 1 | 1 | 1 | 1 | 1 |
GT87 | 1 | 1 | 1 | 1 | 1 |
PL1 | 1 | 1 | 1 | 1 | 1 |
CAZYme gene | 214 | 228 | 227 | 204 | 195 |
% CAZome | 2.61 | 2.70 | 2.64 | 2.53 | 2.34 |
Origin | Property | Value |
---|---|---|
P. phitsanulokensis | Number of amino acids (AA) | 461 |
Molecular weight (Da) | 52,821.00 | |
Theoretical pI | 5.11 | |
Total number of negatively charged residues (Asp + Glu) | 73 | |
Total number of positively charged residues (Arg + Lys) | 51 | |
Extinction coefficient (EC) | 92,040 | |
Instability index (II) | 37.30 (Stable) | |
Aliphatic index (AI) | 70.91 | |
Grand average of hydropathicity (GRAVY) | −0.503 | |
P. silvatica | Number of amino acids (AA) | 461 |
Molecular weight (Da) | 52,941.10 | |
Theoretical pI | 4.96 | |
Total number of negatively charged residues (Asp + Glu) | 75 | |
Total number of positively charged residues (Arg + Lys) | 52 | |
Extinction coefficient (EC) | 93,530 | |
Instability index (II) | 37.10 (Stable) | |
Aliphatic index (AI) | 70.69 | |
Grand average of hydropathicity (GRAVY) | −0.531 | |
P. mira | Number of amino acids (AA) | 461 |
Molecular weight (Da) | 52,937.14 | |
Theoretical pI | 5.00 | |
Total number of negatively charged residues (Asp + Glu) | 75 | |
Total number of positively charged residues (Arg + Lys) | 53 | |
Extinction coefficient (EC) | 93,530 | |
Instability index (II) | 37.99 (Stable) | |
Aliphatic index (AI) | 71.97 | |
Grand average of hydropathicity (GRAVY) | −0.525 | |
P. thailandica | Number of amino acids (AA) | 461 |
Molecular weight (Da) | 52,891.07 | |
Theoretical pI | 5.14 | |
Total number of negatively charged residues (Asp + Glu) | 72 | |
Total number of positively charged residues (Arg + Lys) | 52 | |
Extinction coefficient (EC) | 93,530 | |
Instability index (II) | 34.91 (Stable) | |
Aliphatic index (AI) | 68.98 | |
Grand average of hydropathicity (GRAVY) | −0.505 | |
P. kaengkrachanensis | Number of amino acids (AA) | 461 |
Molecular weight (Da) | 52,852.09 | |
Theoretical pI | 5.04 | |
Total number of negatively charged residues (Asp + Glu) | 73 | |
Total number of positively charged residues (Arg + Lys) | 51 | |
Extinction coefficient (EC) | 93,530 | |
Instability index (II) | 36.50 (Stable) | |
Aliphatic index (AI) | 71.95 | |
Grand average of hydropathicity (GRAVY) | −0.478 |
Ligand | Pubchem CID | Molecular Formula | Molecular Weight (g/mol) |
---|---|---|---|
Cellobiose | 10712 | C12H22O11 | 342.30 |
Cellotetraose | 439626 | C24H42O21 | 666.60 |
Laminaribiose | 439637 | C12H22O11 | 342.30 |
Carboxymethylcellulose | 24748 | C8H16O8 | 240.21 |
Glucose | 5793 | C6H12O6 | 180.16 |
Xylose | 135191 | C5H10O5 | 150.13 |
Ligand | Ligand Pubchem CID | Vina Score (kJ/mol) | Cavity Size |
---|---|---|---|
Cellobiose | 10712 | −7.8 | 619 |
Cellotetraose | 439626 | −8.3 | 619 |
Laminaribiose | 439637 | −7.5 | 619 |
Carboxymethyl cellulose | 24748 | −5.3 | 1304 |
Glucose | 5793 | −6.2 | 1304 |
Xylose | 135191 | −5.6 | 1304 |
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Bouras, N.; Bakli, M.; Dif, G.; Smaoui, S.; Șmuleac, L.; Paşcalău, R.; Menendez, E.; Nouioui, I. The Phylogenomic Characterization of Planotetraspora Species and Their Cellulases for Biotechnological Applications. Genes 2024, 15, 1202. https://doi.org/10.3390/genes15091202
Bouras N, Bakli M, Dif G, Smaoui S, Șmuleac L, Paşcalău R, Menendez E, Nouioui I. The Phylogenomic Characterization of Planotetraspora Species and Their Cellulases for Biotechnological Applications. Genes. 2024; 15(9):1202. https://doi.org/10.3390/genes15091202
Chicago/Turabian StyleBouras, Noureddine, Mahfoud Bakli, Guendouz Dif, Slim Smaoui, Laura Șmuleac, Raul Paşcalău, Esther Menendez, and Imen Nouioui. 2024. "The Phylogenomic Characterization of Planotetraspora Species and Their Cellulases for Biotechnological Applications" Genes 15, no. 9: 1202. https://doi.org/10.3390/genes15091202
APA StyleBouras, N., Bakli, M., Dif, G., Smaoui, S., Șmuleac, L., Paşcalău, R., Menendez, E., & Nouioui, I. (2024). The Phylogenomic Characterization of Planotetraspora Species and Their Cellulases for Biotechnological Applications. Genes, 15(9), 1202. https://doi.org/10.3390/genes15091202