Diversity and evolution of cytochrome P450 monooxygenases in Oomycetes

Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes

BACKGROUND

Microbial eukaryotes play a crucial role in biochemical cycles and aquatic trophic food webs. Their taxonomic and functional diversity are increasingly well described due to recent advances in sequencing technologies. However, the vast amount of data produced by -omics approaches require data-driven methodologies to make predictions about these microorganisms' role within ecosystems. Using metatranscriptomics data, we employed a sequence similarity network-based approach to explore the metabolic specificities of microbial eukaryotes with different trophic modes in a freshwater ecosystem (Lake Pavin, France).

RESULTS

A total of 2,165,106 proteins were clustered in connected components enabling analysis of a great number of sequences without any references in public databases. This approach coupled with the use of an in-house trophic modes database improved the number of proteins considered by 42%. Our study confirmed the versatility of mixotrophic metabolisms with a large number of shared protein families among mixotrophic and phototrophic microorganisms as well as mixotrophic and heterotrophic microorganisms. Genetic similarities in proteins of saprotrophs and parasites also suggest that fungi-like organisms from Lake Pavin, such as Chytridiomycota and Oomycetes, exhibit a wide range of lifestyles, influenced by their degree of dependence on a host. This plasticity may occur at a fine taxonomic level (e.g., species level) and likely within a single organism in response to environmental parameters. While we observed a relative functional redundancy of primary metabolisms (e.g., amino acid and carbohydrate metabolism) nearly 130,000 protein families appeared to be trophic mode-specific. We found a particular specificity in obligate parasite-related Specific Protein Clusters, underscoring a high degree of specialization in these organisms.

CONCLUSIONS

Although no universal marker for parasitism was identified, candidate genes can be proposed at a fine taxonomic scale. We notably provide several protein families that could serve as keys to understanding host-parasite interactions representing pathogenicity factors (e.g., involved in hijacking host resources, or associated with immune evasion mechanisms). All these protein families could offer valuable insights for developing antiparasitic treatments in health and economic contexts. Video Abstract.

Cytochrome P450 monooxygenase systems: Diversity and plasticity for adaptive stress response

Superfamily of cytochromes P450 (CYPs) is composed of heme-thiolate-containing monooxygenase enzymes, which play crucial roles in the biosynthesis, bioactivation, and detoxification of a variety of organic compounds, both endogenic and exogenic. Majority of CYP monooxygenase systems are multi-component and contain various redox partners, cofactors and auxiliary proteins, which contribute to their diversity in both prokaryotes and eukaryotes. Recent progress in bioinformatics and computational biology approaches make it possible to undertake whole-genome and phylogenetic analyses of CYPomes of a variety of organisms. Considerable variations in sequences within and between CYP families and high similarity in secondary and tertiary structures between all CYPs along with dramatic conformational changes in secondary structure elements of a substrate binding site during catalysis have been reported. This provides structural plasticity and substrate promiscuity, which underlie functional diversity of CYPs. Gene duplication and mutation events underlie CYP evolutionary diversity and emergence of novel selectable functions, which provide the involvement of CYPs in high adaptability to changing environmental conditions and dietary restrictions. In our review, we discuss the recent advancements and challenges in the elucidating the evolutionary origin and mechanisms underlying the CYP monooxygenase system diversity and plasticity. Our review is in the view of hypothesis that diversity of CYP monooxygenase systems is translated into the broad metabolic profiles, and this has been acquired during the long evolutionary time to provide structural plasticity leading to high adaptative capabilities to environmental stress conditions.

Comprehensive Review on Plant Cytochrome P450 Evolution: Copy Number, Diversity, and Motif Analysis From Chlorophyta to Dicotyledoneae

Cytochrome P450 enzymes (CYPs) are widely distributed among various plant groups and constitute approximately 1% of the total number of protein-coding genes. Extensive studies suggest that CYPs are involved in nearly all molecular processes that occur in plants. Over the past two decades, the identification of CYP genes has expanded rapidly, with more than 40,000 CYP genes and 819 CYP families being discovered. Copy number variation is a significant evolutionary characteristic of gene families, yet a systematic characterization of the copy evolution patterns in plant CYP gene families has been lacking, resulting in confusion and challenges in understanding CYP functions. To address these concerns, this review provides comprehensive statistics and analyses of the copy number and diversity of almost all plant CYP gene families, focusing on CYP evolution from Chlorophyta to Dicotyledoneae. Additionally, we examined the subfamily characteristics of certain CYP families with restricted copy changes and identified several CYP subfamilies that play pivotal roles in this event. Furthermore, we analyzed the structural conservation of CYPs across different taxa and compiled a comprehensive database to support plant CYP studies. Our analysis revealed differences in the six core conserved motifs of plant CYP proteins among various clans and plant taxa, while demonstrating similar conservation patterns for the ERR (glutamic acid-arginine-arginine) triad motifs. These findings will significantly facilitate the understanding of plant CYP gene evolution and metabolic diversity and serve as a valuable reference for researchers studying CYP enzymes.

Robust Profiling of Cytochrome P450s (P450ome) in Notable Aspergillus spp

Cytochrome P450s (P450ome) constitute an extended superfamily group of heme-thiolate enzymes identified in all biological domains. P450omes play a critical role in the oxidation of steroids and fatty acids, xenobiotic degradation of hydrophobic compounds, biosynthesis of hormones, and primary and secondary metabolism in organisms. Aspergillus species are among the most economically important fungal organisms in human medicine, industry, and agriculture worldwide. Exploring insight on the genome-wide annotations of cytochrome P450s in Aspergillus species is necessary for their biosynthetic applications. In this present study, we report the identification of 306 cytochrome P450s and their robust profiling in eight notable Aspergillus species (A. carbonarius, A. clavatus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. oryzae, and A. terreus). Based on the evolutionary relationship, the Aspergillus P450s families clustered into 15 clades, with clades V, I, and XIII recording higher percentages (17.3%, 15.00%, and 14.71%, respectively) of Cyp families. Cyps were classified into 120 families 64 clans, and their putative functions were also elucidated. P450s were predicted to be located in 13 subcellular components, but the endoplasm reticulum was the dominant location across the eight Aspergillus species. Cyps genes of Aspergillus species were associated with seven secondary metabolism-related gene clusters. Elucidating the genome-wide annotations of P450s enzymes in Aspergillus species will form vital potential biotechnological tools that could be harnessed for industrial, pharmaceutical, and agricultural use.

Novel Synthetic Analogues of 19(S/R)-Hydroxyeicosatetraenoic Acid Exhibit Noncompetitive Inhibitory Effect on the Activity of Cytochrome P450 1A1 and 1B1

BACKGROUND AND OBJECTIVES

Cytochrome P450 (CYP) 1A1 and CYP1B1 enzymes play a significant role in the pathogenesis of cancer and cardiovascular diseases (CVD) such as cardiac hypertrophy and heart failure. Previously, we have demonstrated that R- and S-enantiomers of 19-hydroxyeicosatetraenoic acid (19-HETE), an arachidonic acid endogenous metabolite, enantioselectively inhibit CYP1B1. The current study was conducted to test the possible inhibitory effect of novel synthetic analogues of R- and S-enantiomers of 19-HETE on the activity of CYP1A1, CYP1A2, and CYP1B1.

METHODS

The O-dealkylation rate of 7-ethoxyresorufin (EROD) by recombinant human CYP1A1 and CYP1B1, in addition to the O-dealkylation rate of 7-methoxyresorufin (MROD) by recombinant human CYP1A2, were measured in the absence and presence of varying concentrations (0-40 nM) of the synthetic analogues of 19(R)- and 19(S)-HETE. Also, the possible inhibitory effect of both analogues on the catalytic activity of EROD and MROD, using RL-14 cells and human liver microsomes, was assessed.

RESULTS

The results showed that both synthetic analogues of 19(R)- and 19(S)-HETE exhibited direct inhibitory effects on the activity of CYP1A1 and CYP1B1, while they had no significant effect on CYP1A2 activity. Nonlinear regression analysis and comparisons showed that the mode of inhibition for both analogues is noncompetitive inhibition of CYP1A1 and CYP1B1 enzymes. Also, nonlinear regression analysis and Dixon plots showed that the R- and S-analogues have K_I values of 15.7 ± 4.4 and 6.1 ± 1.5 nM for CYP1A1 and 26.1 ± 2.9 and 9.1 ± 1.8 nM for CYP1B1, respectively. Moreover, both analogues were able to inhibit EROD and MROD activities in a cell-based assay and human liver microsomes.

CONCLUSIONS

Therefore, the synthetic analogues of 19-HETE could be considered as a novel therapeutic approach in the treatment of cancer and CVD.

In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria

The impact of lifestyle on shaping the genome content of an organism is a well-known phenomenon and cytochrome P450 enzymes (CYPs/P450s), heme-thiolate proteins that are ubiquitously present in organisms, are no exception. Recent studies focusing on a few bacterial species such as Streptomyces, Mycobacterium, Cyanobacteria and Firmicutes revealed that the impact of lifestyle affected the P450 repertoire in these species. However, this phenomenon needs to be understood in other bacterial species. We therefore performed genome data mining, annotation, phylogenetic analysis of P450s and their role in secondary metabolism in the bacterial class Gammaproteobacteria. Genome-wide data mining for P450s in 1261 Gammaproteobacterial species belonging to 161 genera revealed that only 169 species belonging to 41 genera have P450s. A total of 277 P450s found in 169 species grouped into 84 P450 families and 105 P450 subfamilies, where 38 new P450 families were found. Only 18% of P450s were found to be involved in secondary metabolism in Gammaproteobacterial species, as observed in Firmicutes as well. The pathogenic or commensal lifestyle of Gammaproteobacterial species influences them to such an extent that they have the lowest number of P450s compared to other bacterial species, indicating the impact of lifestyle on shaping the P450 repertoire. This study is the first report on comprehensive analysis of P450s in Gammaproteobacteria.

An overview of the factors playing a role in cytochrome P450 monooxygenase and ferredoxin interactions

Cytochrome P450 monooxygenases (CYPs/P450s) are heme-thiolate proteins that are ubiquitously present in organisms, including non-living entities such as viruses. With the exception of self-sufficient P450s, all other P450 enzymes need electrons to perform their enzymatic activity and these electrons are supplied by P450 redox proteins. Different types of P450 redox proteins can be found in organisms and are classified into different classes. Bacterial P450s (class I) receive electrons from ferredoxins which are iron-sulfur cluster proteins. The presence of more than one copy and different types of ferredoxins within a bacterial species poses fundamental questions about the selectivity of P450s and ferredoxins in relation to each other. Apart from transferring electrons, ferredoxins have also been found to modulate P450 functions. Achieving an understanding of the interaction between ferredoxins and P450s is required to harness their biotechnological potential for designing a universal electron transfer protein. A brief overview of factors playing a role in ferredoxin and P450 interactions is presented in this review article.

Impact of lifestyle on cytochrome P450 monooxygenase repertoire is clearly evident in the bacterial phylum Firmicutes

Cytochrome P450 monooxygenases (CYPs/P450s), heme thiolate proteins, are well known for their role in organisms' primary and secondary metabolism. Research on eukaryotes such as animals, plants, oomycetes and fungi has shown that P450s profiles in these organisms are affected by their lifestyle. However, the impact of lifestyle on P450 profiling in bacteria is scarcely reported. This study is such an example where the impact of lifestyle seems to profoundly affect the P450 profiles in the bacterial species belonging to the phylum Firmicutes. Genome-wide analysis of P450s in 972 Firmicutes species belonging to 158 genera revealed that only 229 species belonging to 37 genera have P450s; 38% of Bacilli species, followed by 14% of Clostridia and 2.7% of other Firmicutes species, have P450s. The pathogenic or commensal lifestyle influences P450 content to such an extent that species belonging to the genera Streptococcus, Listeria, Staphylococcus, Lactobacillus, Lactococcus and Leuconostoc do not have P450s, with the exception of a handful of Staphylococcus species that have a single P450. Only 18% of P450s are found to be involved in secondary metabolism and 89 P450s that function in the synthesis of specific secondary metabolites are predicted. This study is the first report on comprehensive analysis of P450s in Firmicutes.

Comparative Analysis, Structural Insights, and Substrate/Drug Interaction of CYP128A1 in Mycobacterium tuberculosis

Cytochrome P450 monooxygenases (CYPs/P450s) are well known for their role in organisms' primary and secondary metabolism. Among 20 P450s of the tuberculosis-causing Mycobacterium tuberculosis H37Rv, CYP128A1 is particularly important owing to its involvement in synthesizing electron transport molecules such as menaquinone-9 (MK9). This study employs different in silico approaches to understand CYP128 P450 family's distribution and structural aspects. Genome data-mining of 4250 mycobacterial species has revealed the presence of 2674 CYP128 P450s in 2646 mycobacterial species belonging to six different categories. Contrast features were observed in the CYP128 gene distribution, subfamily patterns, and characteristics of the secondary metabolite biosynthetic gene cluster (BGCs) between M. tuberculosis complex (MTBC) and other mycobacterial category species. In all MTBC species (except one) CYP128 P450s belong to subfamily A, whereas subfamily B is predominant in another four mycobacterial category species. Of CYP128 P450s, 78% was a part of BGCs with CYP124A1, or together with CYP124A1 and CYP121A1. The CYP128 family ranked fifth in the conservation ranking. Unique amino acid patterns are present at the EXXR and CXG motifs. Molecular dynamic simulation studies indicate that the CYP128A1 bind to MK9 with the highest affinity compared to the azole drugs analyzed. This study provides comprehensive comparative analysis and structural insights of CYP128A1 in M. tuberculosis.

More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus, Cyanobacteria, and Mycobacterium

Unraveling the role of cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins present in living and non-living entities, in secondary metabolite synthesis is gaining momentum. In this direction, in this study, we analyzed the genomes of 203 Streptomyces species for P450s and unraveled their association with secondary metabolism. Our analyses revealed the presence of 5460 P450s, grouped into 253 families and 698 subfamilies. The CYP107 family was found to be conserved and highly populated in Streptomyces and Bacillus species, indicating its key role in the synthesis of secondary metabolites. Streptomyces species had a higher number of P450s than Bacillus and cyanobacterial species. The average number of secondary metabolite biosynthetic gene clusters (BGCs) and the number of P450s located in BGCs were higher in Streptomyces species than in Bacillus, mycobacterial, and cyanobacterial species, corroborating the superior capacity of Streptomyces species for generating diverse secondary metabolites. Functional analysis via data mining confirmed that many Streptomyces P450s are involved in the biosynthesis of secondary metabolites. This study was the first of its kind to conduct a comparative analysis of P450s in such a large number (203) of Streptomyces species, revealing the P450s’ association with secondary metabolite synthesis in Streptomyces species. Future studies should include the selection of Streptomyces species with a higher number of P450s and BGCs and explore the biotechnological value of secondary metabolites they produce.

Fungal P450 monooxygenases - the diversity in catalysis and their promising roles in biocontrol activity

The fungal P_450s catalyze vital monooxygenation reactions in primary and secondary metabolism, which may lead to the production of diverse secondary metabolites. Many of these, such as from the family of trichothecenes, involve in biocontrol activities. The diversified nature of fungal P₄₅₀ monooxygenases makes their host organisms adoptable to various ecological niches. The available genome data analysis provided an insight into the activity and mechanisms of the fungal P_450s. However, still more structural and functional studies are needed to elucidate the details of its catalytic mechanism, and the advance studies are also required to decipher further about their dynamic role in various aspects of trichothecene oxygenations. This mini review will provide updated information on different fungal P₄₅₀ monooxygenases, their genetic diversity, and their role in catalyzing various biochemical reactions leading to the production of plant growth promoting secondary metabolites.

Comparative Sequence Analysis of TRI1 of Fusarium

Trichothecene mycotoxins are a class of secondary metabolites produced by multiple genera of fungi, including certain plant pathogenic Fusarium species. Functional variation in the TRI1 gene produces a novel Type A trichothecene called NX-2 in strains of F. graminearum. Using a bioinformatics approach, a systematic analysis of 52 translated TRI1 sequences of Fusarium species, including five F. graminearum NX-2 producers and four F. graminearum non-NX-2 producers, was conducted to explain the functional difference of TRI1p of FGNX-2. An assessment of several signature motifs of fungal P450s revealed amino acid substitutions in addition to the post-translational N-X-S/T sequons motif, which is indicative of N-linked glycosylation of this TRI1-encoded protein characteristic of NX-2 producers. There was evidence of selection bias, where TRI1 gene sequences were found to be under positive selection and, therefore, under functional constraints. The cumulative amino acid changes in the TRI1p sequences were reflected in the phylogenetic analyses which revealed species-specific clustering with a distinct separation of FGNX-2 from FG-non-NX-2 producers with high bootstrap support. Together, our findings provide insight into the amino acid sequence features responsible for the functional diversification of this TRI1p.

Distribution and Diversity of Cytochrome P450 Monooxygenases in the Fungal Class Tremellomycetes

Tremellomycetes, a fungal class in the subphylum Agaricomycotina, contain well-known opportunistic and emerging human pathogens. The azole drug fluconazole, used in the treatment of diseases caused by some species of Tremellomycetes, inhibits cytochrome P450 monooxygenase CYP51, an enzyme that converts lanosterol into an essential component of the fungal cell membrane ergosterol. Studies indicate that mutations and over-expression of CYP51 in species of Tremellomycetes are one of the reasons for fluconazole resistance. Moreover, the novel drug, VT-1129, that is in the pipeline is reported to exert its effect by binding and inhibiting CYP51. Despite the importance of CYPs, the CYP repertoire in species of Tremellomycetes has not been reported to date. This study intends to address this research gap. Comprehensive genome-wide CYP analysis revealed the presence of 203 CYPs (excluding 16 pseudo-CYPs) in 23 species of Tremellomycetes that can be grouped into 38 CYP families and 72 CYP subfamilies. Twenty-three CYP families are new and three CYP families (CYP5139, CYP51 and CYP61) were conserved across 23 species of Tremellomycetes. Pathogenic cryptococcal species have 50% fewer CYP genes than non-pathogenic species. The results of this study will serve as reference for future annotation and characterization of CYPs in species of Tremellomycetes.

Cytochrome P450 Monooxygenase CYP139 Family Involved in the Synthesis of Secondary Metabolites in 824 Mycobacterial Species

Tuberculosis (TB) is one of the top infectious diseases causing numerous human deaths in the world. Despite enormous efforts, the physiology of the causative agent, Mycobacterium tuberculosis, is poorly understood. To contribute to better understanding the physiological capacity of these microbes, we have carried out extensive in silico analyses of the 1111 mycobacterial species genomes focusing on revealing the role of the orphan cytochrome P450 monooxygenase (CYP) CYP139 family. We have found that CYP139 members are present in 894 species belonging to three mycobacterial groups: M. tuberculosis complex (850-species), Mycobacterium avium complex (34-species), and non-tuberculosis mycobacteria (10-species), with all CYP139 members belonging to the subfamily “A”. CYP139 members have unique amino acid patterns at the CXG motif. Amino acid conservation analysis placed this family in the 8th among CYP families belonging to different biological domains and kingdoms. Biosynthetic gene cluster analyses have revealed that 92% of CYP139As might be associated with producing different secondary metabolites. Such enhanced secondary metabolic potentials with the involvement of CYP139A members might have provided mycobacterial species with advantageous traits in diverse niches competing with other microbial or viral agents, and might help these microbes infect hosts by interfering with the hosts’ metabolism and immune system.

Similarities, variations, and evolution of cytochrome P450s in Streptomyces versus Mycobacterium

Cytochrome P450 monooxygenases (P450s) found in all domains of life are known for their catalytic versatility and stereo- and regio-specific activity. While the impact of lifestyle on P450 evolution was reported in many eukaryotes, this remains to be addressed in bacteria. In this report, Streptomyces and Mycobacterium, belonging to the phylum Actinobacteria, were studied owing to their contrasting lifestyles and impacts on human. Analyses of all P450s and those predicted to be associated with secondary metabolism have revealed that different lifestyles have affected the evolution of P450s in these bacterial genera. We have found that while species in both genera have essentially the same number of P450s in the genome, Streptomyces P450s are much more diverse than those of Mycobacterium. Moreover, despite both belonging to Actinobacteria, only 21 P450 families were common, and 123 and 56 families were found to be unique to Streptomyces and Mycobacterium, respectively. The presence of a large and diverse number of P450s in Streptomyces secondary metabolism contributes to antibiotic diversity, helping to secure the niche. Conversely, based on the currently available functional data, types of secondary metabolic pathways and associated P450s, mycobacterial P450s seem to play a role in utilization or synthesis of lipids.

Diversity and evolution of cytochromes P450 in stramenopiles

MAIN CONCLUSION

Comparative genomic analysis of cytochromes P450 revealed high diversification and dynamic changes in stramenopiles, associated with transcriptional responsiveness to various environmental stimuli. Comparative genomic and molecular evolution approaches were used to characterize cytochromes P450 (P450) diversity in stramenopiles. Phylogenetic analysis pointed to a high diversity of P450 in stramenopiles and identified three major clans. The CYP51 and CYP97 clans were present in brown algae, diatoms and Nannochloropsis gaditana, whereas the CYP5014 clan mainly includes oomycetes. Gene gain and loss patterns revealed that six CYP families-CYP51, CYP97, CYP5160, CYP5021, CYP5022, and CYP5165-predated the split of brown algae and diatoms. After they diverged, diatoms gained more CYP families, especially in the cold-adapted species Fragilariopsis cylindrus, in which eight new CYP families were found. Selection analysis revealed that the expanded CYP51 family in the brown alga Cladosiphon okamuranus exhibited a more relaxed selection constraint compared with those of other brown algae and diatoms. Our RNA-seq data further evidenced that most of P450s in Saccharina japonica are highly expressed in large sporophytes, which could potentially promote the large kelp formation in this developmental stage. A survey of Ectocarpus siliculosus and diatom transcriptomes showed that many P450s are responsive to stress, nutrient limitation or light quality, suggesting pivotal roles in detoxification or metabolic processes under adverse environmental conditions. The information provided in this study will be helpful in designing functional experiments and interpreting P450 roles in this particular lineage.

Comparative Analyses of Cytochrome P450s and Those Associated with Secondary Metabolism in Bacillus Species

Cytochrome P450 monooxygenases (CYPs/P450s) are among the most catalytically-diverse enzymes, capable of performing enzymatic reactions with chemo-, regio-, and stereo-selectivity. Our understanding of P450s' role in secondary metabolite biosynthesis is becoming broader. Among bacteria, Bacillus species are known to produce secondary metabolites, and recent studies have revealed the presence of secondary metabolite biosynthetic gene clusters (BGCs) in these species. However, a comprehensive comparative analysis of P450s and P450s involved in the synthesis of secondary metabolites in Bacillus species has not been reported. This study intends to address these two research gaps. In silico analysis of P450s in 128 Bacillus species revealed the presence of 507 P450s that can be grouped into 13 P450 families and 28 subfamilies. No P450 family was found to be conserved in Bacillus species. Bacillus species were found to have lower numbers of P450s, P450 families and subfamilies, and a lower P450 diversity percentage compared to mycobacterial species. This study revealed that a large number of P450s (112 P450s) are part of different secondary metabolite BGCs, and also identified an association between a specific P450 family and secondary metabolite BGCs in Bacillus species. This study opened new vistas for further characterization of secondary metabolite BGCs, especially P450s in Bacillus species.

Blooming of Unusual Cytochrome P450s by Tandem Duplication in the Pathogenic Fungus Conidiobolus coronatus

While the Zygomycete fungus Conidiobolus coronatus primarily infects insects, it can be pathogenic to mammals as well, including humans. High variability in the treatment of this fungal infection with currently available drugs, including azole drugs is a very common phenomenon. Azoles bind to the cytochrome P450 monooxygenases (P450s/CYP) including CYP51, a sterol 14-α-demethylase, inhibiting the synthesis of cell membrane ergosterol and thus leading to the elimination of infecting fungi. Despite P450’s role as a drug target, to date, no information on C. coronatus P450s has been reported. Genome-wide data mining has revealed the presence of 142 P450s grouped into 12 families and 21 subfamilies in C. coronatus. Except for CYP51, the remaining 11 P450 families are new (CYP5854-CYP5864). Despite having a large number of P450s among entomopathogenic fungi, C. coronatus has the lowest number of P450 families, which suggests blooming P450s. Further analysis has revealed that 79% of the same family P450s is tandemly positioned, suggesting that P450 tandem duplication led to the blooming of P450s. The results of this study; i.e., unravelling the C. coronatus P450 content, will certainly help in designing experiments to understand P450s’ role in C. coronatus physiology, including a highly variable response to azole drugs with respect to P450s.

Comparative analyses and structural insights of the novel cytochrome P450 fusion protein family CYP5619 in Oomycetes

Phylogenetic and structural analysis of P450 proteins fused to peroxidase/dioxygenase has not been reported yet. We present phylogenetic and in silico structural analysis of the novel P450 fusion family CYP5619 from the deadliest fish pathogenic oomycete, Saprolegnia diclina. Data-mining and annotation of CYP5619 members revealed their unique presence in oomycetes. CYP5619 members have the highest number of conserved amino acids among eukaryotic P450s. The highest number of conserved amino acids (78%) occurred in the peroxidase/dioxygenase domain compared to the P450 domain (22%). In silico structural analysis using a high-quality CYP5619A1 model revealed that CYP5619A1 has characteristic P450 structural motifs including EXXR and CXG. However, the heme-binding domain (CXG) in CYP5619 members was found to be highly degenerated. The in silico substrate binding pattern revealed that CYP5619A1 have a high affinity to medium chain fatty acids. Interestingly, the controlling agent of S. diclina malachite green was predicted to have the highest binding affinity, along with linoleic acid. However, unlike fatty acids, none of the active site amino acids formed hydrogen bonds with malachite green. The study’s results will pave the way for assessing CYP5619A1’s role in S. diclina physiology, including the nature of malachite green binding.

Molecular elucidation of a new allelic variation at the Sg-5 gene associated with the absence of group A saponins in wild soybean

In soybean, triterpenoid saponin is one of the major secondary metabolites and is further classified into group A and DDMP saponins. Although they have known health benefits for humans and animals, acetylation of group A saponins causes bitterness and gives an astringent taste to soy products. Therefore, several studies are being conducted to eliminate acetylated group A saponins. Previous studies have isolated and characterized the Sg-5 (Glyma.15g243300) gene, which encodes the cytochrome P450 72A69 enzyme and is responsible for soyasapogenol A biosynthesis. In this study, we elucidated the molecular identity of a novel mutant of Glycine soja, 'CWS5095'. Phenotypic analysis using TLC and LC-PDA/MS/MS showed that the mutant 'CWS5095' did not produce any group A saponins. Segregation analysis showed that the absence of group A saponins is controlled by a single recessive allele. The locus was mapped on chromosome 15 (4.3 Mb) between Affx-89193969 and Affx-89134397 where the previously identified Glyma.15g243300 gene is positioned. Sequence analysis of the coding region for the Glyma.15g243300 gene revealed the presence of four SNPs in 'CWS5095' compared to the control lines. One of these four SNPs (G1127A) leads to the amino acid change Arg376Lys in the EXXR motif, which is invariably conserved among the CYP450 superfamily proteins. Co-segregation analysis showed that the missense mutation (Arg376Lys) was tightly linked with the absence of group A saponins in 'CWS5095'. Even though Arg and Lys have similar chemical features, the 3D modelled protein structure indicates that the replacement of Arg with Lys may cause a loss-of-function of the Sg-5 protein by inhibiting the stable binding of a heme cofactor to the CYP72A69 apoenzyme.

Metabolic Diversity and Novelties in the Oomycetes

The eukaryotic microbes called oomycetes include many important saprophytes and pathogens, with the latter exhibiting necrotrophy, biotrophy, or obligate biotrophy. Understanding oomycete metabolism is fundamental to understanding these lifestyles. Genome mining and biochemical studies have shown that oomycetes, which belong to the kingdom Stramenopila, secrete suites of carbohydrate- and protein-degrading enzymes adapted to their environmental niches and produce unusual lipids and energy storage compounds. Despite having limited secondary metabolism, many oomycetes make chemicals for communicating within their species or with their hosts. Horizontal and endosymbiotic gene transfer events have diversified oomycete metabolism, resulting in biochemical pathways that often depart from standard textbook descriptions by amalgamating enzymes from multiple sources. Gene fusions and duplications have further shaped the composition and expression of the enzymes. Current research is helping us learn how oomycetes interact with host and environment, understand eukaryotic diversity and evolution, and identify targets for drugs and crop protection chemicals.

Cytochrome P450 diversity in the tree of life

Sequencing in all areas of the tree of life has produced >300,000 cytochrome P450 (CYP) sequences that have been mined and collected. Nomenclature has been assigned to >41,000 CYP sequences and the majority of the remainder has been sorted by BLAST searches into clans, families and subfamilies in preparation for naming. The P450 sequence space is being systematically explored and filled in. Well-studied groups like vertebrates are covered in greater depth while new insights are being added into uncharted territories like horseshoe crab (Limulus polyphemus), tardigrades (Hypsibius dujardini), velvet worm (Euperipatoides_rowelli), and basal land plants like hornworts, liverworts and mosses. CYPs from the fungi, one of the most diverse groups, are being explored and organized as nearly 800 fungal species are now sequenced. The CYP clan structure in fungi is emerging with 805 CYP families sorting into 32 CYP clans. >3000 bacterial sequences are named, mostly from terrestrial or freshwater sources. Of 18,379 bacterial sequences downloaded from the CYPED database, all are >43% identical to named CYPs. Therefore, they fit in the 602 named P450 prokaryotic families. Diversity in this group is becoming saturated, however 25% of 3305 seawater bacterial P450s did not match known P450 families, indicating marine bacterial CYPs are not as well sampled as land/freshwater based bacterial CYPs. Future sequencing plans of the Genome 10K project, i5k and GIGA (Global Invertebrate Genomics Alliance) are expected to produce more than one million cytochrome P450 sequences by 2020. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.

Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages

While most commonly associated with prokaryotes, horizontal gene transfer (HGT) can also have a significant influence on the evolution of microscopic eukaryotes. Systematic analysis of HGT in the genomes of the oomycetes, filamentous eukaryotic microorganisms in the Stramenopiles-Alveolates-Rhizaria (SAR) supergroup, has to date focused mainly on intradomain transfer events between oomycetes and fungi. Using systematic whole-genome analysis followed by phylogenetic reconstruction, we have investigated the extent of interdomain HGT between bacteria and plant-pathogenic oomycetes. We report five putative instances of HGT from bacteria into the oomycetes. Two transfers were found in Phytophthora species, including one unique to the cucurbit pathogen Phytophthora capsici. Two were found in Pythium species only, and the final transfer event was present in Phytopythium and Pythium species, the first reported bacterium-inherited genes in these genera. Our putative transfers included one protein that appears to be a member of the Pythium secretome, metabolic proteins, and enzymes that could potentially break down xenobiotics within the cell. Our findings complement both previous reports of bacterial genes in oomycete and SAR genomes and the growing body of evidence suggesting that interdomain transfer from prokaryotes into eukaryotes occurs more frequently than previously thought. IMPORTANCE Horizontal gene transfer (HGT) is the nonvertical inheritance of genetic material by transfer between different species. HGT is an important evolutionary mechanism for prokaryotes and in some cases is responsible for the spread of antibiotic resistance from resistant to benign species. Genome analysis has shown that examples of HGT are not as frequent in eukaryotes, but when they do occur they may have important evolutionary consequences. For example, the acquisition of fungal genes by an ancestral Phytophthora (plant destroyer) species is responsible for the large repertoire of enzymes in the plant-degrading arsenal of modern-day Phytophthora species. In this analysis, we set out to systematically search oomycete genomes for evidence of interdomain HGT (transfer of bacterial genes into oomycete species). Our results show that interdomain HGT is rare in oomycetes but has occurred. We located five well-supported examples, including one that could potentially break down xenobiotics within the cell.

Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s

Since the initial identification of cytochrome P450 monooxygenases (CYPs/P450s), great progress has been made in understanding their structure-function relationship, diversity and application in producing compounds beneficial to humans. However, the molecular evolution of P450s in terms of their dynamics both at protein and DNA levels and functional conservation across kingdoms still needs investigation. In this study, we analyzed 17 598 P450s belonging to 113 P450 families (bacteria -42; fungi -19; plant -28; animal -22; plant and animal -1 and common P450 family -1) and found highly conserved and rapidly evolving P450 families. Results suggested that bacterial P450s, particularly P450s belonging to mycobacteria, are highly conserved both at protein and DNA levels. Mycobacteria possess the highest P450 diversity percentage compared to other microbes and have a high coverage of P450s (≥1%) in their genomes, as found in fungi and plants. Phylogenetic and functional analyses revealed the functional conservation of P450s despite belonging to different biological kingdoms, suggesting the adherence of P450s to their innate function such as their involvement in either generation or oxidation of steroids and structurally related molecules, fatty acids and terpenoids. This study's results offer new understanding of the dynamic structural nature of P450s.

Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens

Fungi are an exceptional source of diverse and novel cytochrome P450 monooxygenases (P450s), heme-thiolate proteins, with catalytic versatility. Agaricomycotina saprophytes have yielded most of the available information on basidiomycete P450s. This resulted in observing similar P450 family types in basidiomycetes with few differences in P450 families among Agaricomycotina saprophytes. The present study demonstrated the presence of unique P450 family patterns in basidiomycete biotrophic plant pathogens that could possibly have originated from the adaptation of these species to different ecological niches (host influence). Systematic analysis of P450s in basidiomycete biotrophic plant pathogens belonging to three different orders, Agaricomycotina (Armillaria mellea), Pucciniomycotina (Melampsora laricis-populina, M. lini, Mixia osmundae and Puccinia graminis) and Ustilaginomycotina (Ustilago maydis, Sporisorium reilianum and Tilletiaria anomala), revealed the presence of numerous putative P450s ranging from 267 (A. mellea) to 14 (M. osmundae). Analysis of P450 families revealed the presence of 41 new P450 families and 27 new P450 subfamilies in these biotrophic plant pathogens. Order-level comparison of P450 families between biotrophic plant pathogens revealed the presence of unique P450 family patterns in these organisms, possibly reflecting the characteristics of their order. Further comparison of P450 families with basidiomycete non-pathogens confirmed that biotrophic plant pathogens harbour the unique P450 families in their genomes. The CYP63, CYP5037, CYP5136, CYP5137 and CYP5341 P450 families were expanded in A. mellea when compared to other Agaricomycotina saprophytes and the CYP5221 and CYP5233 P450 families in P. graminis and M. laricis-populina. The present study revealed that expansion of these P450 families is due to paralogous evolution of member P450s. The presence of unique P450 families in these organisms serves as evidence of how a host/ecological niche can influence shaping the P450 content of an organism. The present study initiates our understanding of P450 family patterns in basidiomycete biotrophic plant pathogens.