Saprophytic to Pathogenic Mycobacteria: Loss of Cytochrome P450s Vis a Vis Their Prominent Involvement in Natural Metabolite Biosynthesis
Abstract
:1. Introduction
2. Results and Discussion
2.1. Saprophytic to Pathogen Life Style Led to the Loss of P450s in Mycobacterial Species
2.2. P450 Family and Subfamily Blooming/Expansion in Mycobacterial Species
2.3. Different Mycobacterial Categories Have Distinct P450 Profiles
2.4. CYP121, CYP124, and CYP128 P450s Are Part of the Same Biosynthetic Gene Cluster
2.5. More P450s Are Involved in Natural Metabolite Biosynthesis in Pathogenic Mycobacterial Species
3. Materials and Methods
3.1. Species and Their Genome Database Information
3.2. Grouping of Mycobacterial Species
3.3. Genome Data Mining and Annotation of P450s
3.4. Identification of P450s Part of BGCs
3.5. P450 Key Features Analysis
3.6. Comparative Analysis of P450s and BGCs Data
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Category | Salinispora species | Streptomyces species | Mycobacterial species | Cyanobacterial species | Bacteroidetes species | Firmicutes species | Alphaproteobacterial species | Betaproteobacterial species | Gammaproteobacterial species | Deltaproteobacterial species | Epsilonproteobacterial species |
---|---|---|---|---|---|---|---|---|---|---|---|
Species analyzed | 126 | 203 | 2666 | 114 | 334 | 972 | 599 | 513 | 1261 | 107 | 216 |
Species with P450s | 126 | 203 | 2666 | 114 | 77 | 229 | 229 | 290 | 169 | 23 | 53 |
Percentage of species with P450s | 100 | 100 | 100 | 100 | 23 | 24 | 38 | 57 | 13 | 21 | 25 |
No. of P450s | 2643 | 5460 | 62,815 | 341 | 98 | 712 | 873 | 603 | 277 | 333 | 53 |
No. of families | 45 | 253 | 182 | 36 | 21 | 14 | 143 | 79 | 81 | 74 | 2 |
No. of subfamilies | 103 | 698 | 345 | 79 | 28 | 53 | 214 | 119 | 102 | 171 | 2 |
Dominant P450 family | CYP105 | CYP107 | CYP135 | CYP110 | CYP1103 | CYP107 | CYP202 | CYP116 | CYP133 & CYP107 | CYP107 | CYP172 |
Average No. of P450s | 21 | 27 | 24 | 3 | 1 | 3 | 4 | 2 | 2 | 14 | 1 |
No. of P450s part of BGCs | 1236 | 1231 | 9399 | 27 | 8 | 126 | 21 | 107 | 49 | 69 | 0 |
No. of P450 families part of BGCs | 35 | 135 | 68 | 6 | 5 | 10 | 16 | 18 | 22 | 37 | 0 |
Percentage of P450s part of BGCs | 47 | 23 | 15 | 8 | 8 | 18 | 2 | 18 | 18 | 21 | 0 |
Reference(s) | [28] | [36,37] | This work | [27] | [32] | [34] | [33] | [30] | [29] | [30] | [30] |
Category | MTBC | MCAC | NTM | MAC | SAP | MCL |
---|---|---|---|---|---|---|
Total No. of species analysed | 2128 | 255 | 163 | 106 | 10 | 4 |
Total No. of P450s | 42,917 | 6519 | 7760 | 5093 | 505 | 21 |
P450 fragments/pseudo | 2 | 10 | 69 | 3 | 6 | 0 |
Average No. of P450s | 20 | 26 | 48 | 48 | 51 | 5 |
Min No. of P450s | 5 | 22 | 9 | 28 | 35 | 3 |
Maximum No. of P450s | 74 | 52 | 89 | 69 | 95 | 7 |
No. of P450 families | 66 | 37 | 145 | 59 | 66 | 9 |
No of P450 subfamilies | 95 | 48 | 261 | 88 | 101 | 9 |
Dominant P450 family | CYP135 | CYP125 | CYP125 | CYP150 | CYP189 | CYP136 & CYP184 |
No of the P450s part of BGCs | 8153 | 438 | 450 | 328 | 30 | 0 |
No. of P450 families part of BGCs | 19 | 13 | 56 | 11 | 15 | 0 |
Percentage of P450s part of BGCs | 19.0 | 6.7 | 5.8 | 6.4 | 5.9 | 0 |
Percentage of P450 families part of BGCs | 28.8 | 35.1 | 38.6 | 18.6 | 22.7 | 0 |
P450 Family | Count | Subfamily | Count | Nature of the Subfamily |
---|---|---|---|---|
CYP123 | 3019 | A | 2908 | Bloomed |
CYP125 | 4085 | A | 3978 | Bloomed |
CYP136 | 3017 | A | 2687 | Bloomed |
CYP105 | 674 | Q | 377 | Expanded |
CYP108 | 714 | B | 703 | Expanded |
CYP121 | 2029 | A | 2029 | Expanded |
CYP124 | 2484 | A | 2425 | Expanded |
CYP126 | 2434 | A | 2429 | Expanded |
CYP128 | 2243 | A | 2143 | Expanded |
CYP130 | 2640 | A | 2640 | Expanded |
CYP132 | 2160 | A | 2160 | Expanded |
CYP135 | 4702 | A | 2149 | Expanded |
B | 2543 | Expanded | ||
CYP137 | 2167 | A | 2167 | Expanded |
CYP138 | 2810 | A | 2733 | Expanded |
CYP139 | 2286 | A | 2286 | Expanded |
CYP140 | 2810 | A | 2401 | Expanded |
CYP141 | 2105 | A | 2105 | Expanded |
CYP142 | 2540 | A | 2507 | Expanded |
CYP143 | 2470 | A | 2387 | Expanded |
CYP144 | 2700 | A | 2421 | Expanded |
CYP150 | 1056 | A | 932 | Expanded |
CYP164 | 514 | A | 505 | Expanded |
CYP189 | 1002 | A | 987 | Expanded |
CYP51 | 2680 | B | 2680 | Expanded |
Category | MTBC | MCAC | NTM | MAC | SAP | MCL |
---|---|---|---|---|---|---|
MTBC | 11 | 22 (CYP125) | 49 (CYP189) | 36 (CYP150) | 34 (CYP189) | 8 (CYP136 & CYP164) |
MCAC | 22 (CYP125) | 6 | 28 (CYP125) | 20 (CYP105) | 19 (CYP125) | 5 (CYP136 & CYP164) |
NTM | 49 (CYP189) | 28 (CYP125) | 71 | 34 (CYP189) | 29 (CYP189) | 7 (CYP164) |
MAC | 36 (CYP150) | 20 (CYP105) | 34 (CYP189) | 15 | 25 (CYP189) | 9 (CYP136 & CYP164) |
SAP | 34 (CYP189) | 19 (CYP125) | 29 (CYP189) | 27 (CYP189) | 23 | 5 (CYP136) |
MCL | 8 (CYP136 & CYP164) | 5 (CYP136 & CYP164) | 7 (CYP164) | 9 (CYP136 & CYP164) | 5 (CYP136) | 0 |
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Zondo, N.M.; Padayachee, T.; Nelson, D.R.; Syed, K. Saprophytic to Pathogenic Mycobacteria: Loss of Cytochrome P450s Vis a Vis Their Prominent Involvement in Natural Metabolite Biosynthesis. Int. J. Mol. Sci. 2023, 24, 149. https://doi.org/10.3390/ijms24010149
Zondo NM, Padayachee T, Nelson DR, Syed K. Saprophytic to Pathogenic Mycobacteria: Loss of Cytochrome P450s Vis a Vis Their Prominent Involvement in Natural Metabolite Biosynthesis. International Journal of Molecular Sciences. 2023; 24(1):149. https://doi.org/10.3390/ijms24010149
Chicago/Turabian StyleZondo, Ntokozo Minenhle, Tiara Padayachee, David R. Nelson, and Khajamohiddin Syed. 2023. "Saprophytic to Pathogenic Mycobacteria: Loss of Cytochrome P450s Vis a Vis Their Prominent Involvement in Natural Metabolite Biosynthesis" International Journal of Molecular Sciences 24, no. 1: 149. https://doi.org/10.3390/ijms24010149