Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea
Abstract
:1. Introduction
2. Results and Discussion
2.1. Archaea Has the Lowest P450 Diversity
2.2. Some P450 Families and Subfamilies Are Expanded in Archaea
2.3. Plasmid-Mediated Lateral Transfer of P450s from Bacteria to Archaea
2.4. Archaeal P450s Are Bacterial in Origin, Not Vice Versa
2.5. Lateral Transfer of Putative Redox Partners Is Independent of P450s
2.6. CYP109, CYP147 and CYP197 Gave Rise to Archaeal P450s
2.7. Most of the Archaeal P450s Are Orphans with No Known Function
3. Materials and Methods
3.1. Species and Their Genome Database Information
3.2. Genome Data Mining and Annotation of P450s
3.3. Analysis of P450s in Archaeal Plasmids
3.4. Phylogenetic Analysis of P450s
3.5. BLAST Analysis of Archaeal P450 Families for Affinity to CYP109 or CYP197
3.6. Comparative Analysis of P450s
3.7. Genome Data Mining and Annotation of Ferredoxins
3.8. Comparative Analysis of Ferredoxins
3.9. Genome Data Mining of Ferredoxin Reductases
3.10. Retrieving Protein Identification Numbers from NCBI
3.11. Operon Predictions
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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Species Category | Species Subcategory | Species Subcategory P450 Count | Species Category P450 Count | P450 Families |
---|---|---|---|---|
Animals | 37,149 | 1948 * | ||
Mammals | 4558 | 18 | ||
Other vertebrates | 3268 | 19 | ||
Insects | 22,173 | 1031 | ||
Non-insect invertebrates | 7150 | 880 | ||
Plants | 42,102 | 819 | ||
Fungi | 28,260 | 3204 | ||
Protozoa | 5807 | 1374 | ||
Bacteria | 17,236 | 1910 | ||
Archaea | 1204 | 34 | ||
Viruses | 37 | 13 | ||
Total | 131,795 | 9302 |
Species Names | Accession Number | Operon |
---|---|---|
Plasmid DNA | ||
Halorussus sp. RC-68 | NZ_CP035120.1 | Epimerase/dehydratase→Thiamine pyrophosphate-binding protein→CYP109G24 |
Halorussus sp. YCN54 | NZ_CP099994.1 | Cupin domain-containing→ProteinNAD(P)-dependent oxidoreductase→CYP109G32 |
Halorussus sp. XZYJT49 | NZ_CP096661.1 | CYP174A39→PIN domain-containing protein→AbrB/MazE/SpoVT family DNA-binding domain-containing protein |
Haloprofundus salinisoli strain SQT7-1 | NZ_CP083664.1 | Enoyl-CoA hydratase-related protein→CYP109G25 |
Haloprofundus sp. MHR1 | NZ_MN918443.1 | CYP109G22→Enoyl-CoA hydratase-related protein |
Haloprofundus halobius strain SEDH52 | NZ_CP083667.1 | MFS transporter→CYP109G26 |
Saliphagus sp. WLHS1 | NZ_CP100356.1 | CYP1002B4→Putative protein |
Natrinema sp. DC36 | NZ_CP084474.1 | CYP1014C9→Putative protein |
Halorubrum lacusprofundi strain HLS1 | NZ_KX906370.1 | CYP109G27→SDR family oxidoreductase→Putative protein |
Halocatena sp. AD-1 | NZ_CP096021.1 | ABC transporter permease subunit→CYP1014B9 |
NZ_CP096022.1 | Hydroxypyruvate isomerase→dehydrogenase→CYP109AU2 | |
Halobellus limi CGMCC 1.10331 | NZ_CP031313.1 | Amidohydrolase family protein→CYP1002B4 |
Chromosomal DNA | ||
Halorussus halophilus strain ZS-3 | NZ_CP044523.1 | SAM-dependent methyltransferases→CYP1002C17 |
Halorussus sp. YCN54 | NZ_CP099993.1 | CYP1002C24→SAM-dependent methyltransferases |
Halorussus sp. XZYJ18 | NZ_CP100400.1 | SAM-dependent methyltransferases→CYP1002C25 |
Halorussus sp. XZYJT49 | NZ_CP096659.1 | Dehydrogenase→Flavoprotein→CYP174C3 |
Haladaptatus sp. PSR5 | NZ_CP085335.1 | CYP174D1→Putative protein |
Halomicroarcula sp. DT1 | NZ_CP100404.1 | Archaeal kinase→Mevalonate kinase→CYP174A38 |
Halomicroarcula sp. YSSS71 | NZ_CP100407.1 | Archaeal kinase→Mevalonate kinase→CYP174A38 |
Halomicrobium salinisoli strain TH30 | NZ_CP084466.1 | Putative protein→Putative protein→CYP174A35→Mevalonate kinase→Archaeal kinase |
Halomicrobium salinisoli strain LT50 | NZ_CP084463.1 | Archaeal kinase→Mevalonate kinase→CYP174A36→Putative protein→Putative protein |
Halosiccatus urmianus strain IBRC-M: 10911 | NZ_CP084090.1 | Archaeal kinase→Mevalonate kinase→CYP174A37→Putative protein→Tellurite resistance protein and related permeases→Ribosomal protein S2→Enolase→DNA-directed RNA polymerase, subunit K/omega→DNA-directed RNA polymerase, subunit N (RpoN/RPB10)→Ribosomal protein S9→Ribosomal protein L13→Ribosomal protein L18E→Putative protein |
Halalkalicoccus jeotgali B3 | NC_014297.1 | Ketopantoate reductase→Zn finger protein HypA/HybF→CYP109G2 |
Halocatena sp. AD-1 | NZ_CP096019.1 | CYP109F16→Putative protein |
Halobellus limi CGMCC 1.10331 | NZ_CP031311.1 | CYP1014A7→Phosphoribosylaminoimidazole (AIR) synthetase |
Halococcus dombrowskii H4 | NZ_CP095005.1 | ATP-dependent 26S proteasome regulatory subunit→CYP109G4 |
Halosegnis sp. ZY10 | NZ_CP101161.1 | CYP2738A7→Putative protein |
Natribaculum breve TRM20010 | NZ_CP095390.1 | Phytoene/squalene synthetase→CYP197C46 |
Natronobiforma sp. CGA73 | NZ_CP101458.1 | Predicted metal-dependent membrane protease→Holliday junction resolvase-archaeal type→Putative protein→CYP174B67 |
Natronomonas sp. ZY43 | NZ_CP101154.1 | CYP1603A5→Fibrillarin-like rRNA methylase→Protein implicated in ribosomal biogenesis, Nop56p |
Putative protein→Putative protein→CYP1002C26 | ||
CYP1014G24→Aspartate/tyrosine/aromatic aminotransferase |
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Ngcobo, P.E.; Nkosi, B.V.Z.; Chen, W.; Nelson, D.R.; Syed, K. Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea. Int. J. Mol. Sci. 2023, 24, 4161. https://doi.org/10.3390/ijms24044161
Ngcobo PE, Nkosi BVZ, Chen W, Nelson DR, Syed K. Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea. International Journal of Molecular Sciences. 2023; 24(4):4161. https://doi.org/10.3390/ijms24044161
Chicago/Turabian StyleNgcobo, Phelelani Erick, Bridget Valeria Zinhle Nkosi, Wanping Chen, David R. Nelson, and Khajamohiddin Syed. 2023. "Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea" International Journal of Molecular Sciences 24, no. 4: 4161. https://doi.org/10.3390/ijms24044161