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Article

An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species

by
Nsikelelo Allison Malinga
1,
Nomfundo Nzuza
1,
Tiara Padayachee
1,
Puleng Rosinah Syed
2,
Rajshekhar Karpoormath
2,
Dominik Gront
3,
David R. Nelson
4,* and
Khajamohiddin Syed
1,*
1
Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa
2
Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
3
Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
4
Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
*
Authors to whom correspondence should be addressed.
Microorganisms 2022, 10(5), 871; https://doi.org/10.3390/microorganisms10050871
Submission received: 4 April 2022 / Revised: 15 April 2022 / Accepted: 19 April 2022 / Published: 21 April 2022
(This article belongs to the Special Issue Going Further with Microbial Secondary Metabolites and Biotechnology)
Browse Figures
Versions Notes

Abstract

:
Cytochrome P450 monooxygenases (CYPs/P450s) are heme thiolate proteins present in species across the biological kingdoms. By virtue of their broad substrate promiscuity and regio- and stereo-selectivity, these enzymes enhance or attribute diversity to secondary metabolites. Actinomycetes species are well-known producers of secondary metabolites, especially Salinispora species. Despite the importance of P450s, a comprehensive comparative analysis of P450s and their role in secondary metabolism in Salinispora species is not reported. We therefore analyzed P450s in 126 strains from three different species Salinispora arenicola, S. pacifica, and S. tropica. The study revealed the presence of 2643 P450s that can be grouped into 45 families and 103 subfamilies. CYP107 and CYP125 families are conserved, and CYP105 and CYP107 families are bloomed (a P450 family with many members) across Salinispora species. Analysis of P450s that are part of secondary metabolite biosynthetic gene clusters (smBGCs) revealed Salinispora species have an unprecedented number of P450s (1236 P450s-47%) part of smBGCs compared to other bacterial species belonging to the genera Streptomyces (23%) and Mycobacterium (11%), phyla Cyanobacteria (8%) and Firmicutes (18%) and the classes Alphaproteobacteria (2%) and Gammaproteobacteria (18%). A peculiar characteristic of up to six P450s in smBGCs was observed in Salinispora species. Future characterization Salinispora species P450s and their smBGCs have the potential for discovering novel secondary metabolites.

1. Introduction

Cytochrome P450 monooxygenases (CYPs/P450s) comprise a superfamily of heme-thiolate proteins. P450s are present in all species of different biological kingdoms, including in viruses considered non-living entities [1,2]. This suggests that these enzymes play an important role in species’ primary and secondary metabolism. These enzymes were initially identified as monooxygenases due to their ability to introduce one oxygen atom into a substrate [3]. Subsequent research revealed that P450s are catalytically diverse enzymes performing some unusual enzymatic reactions [4,5,6,7,8]. The regio- and stereo-specific oxidation of many substrates by P450s caught the attention of researchers for biotechnological exploration of these enzymes [9,10,11,12]. P450s reactions are essential in designing drugs such that drug toxicity of prodrugs is primarily assessed against these enzymes [13]. Also, P450s play a vital role in xenobiotic compounds’ detoxification [14]. Microbial P450s, especially from lower eukaryotes such as fungal CYP51, have been used as an azole drug target [15,16]. The study also suggested that fungal CYP53 can act as a potential alternative drug target [17]. One of the best examples of P450s biotechnological applications includes the synthesis of antibiotics and anticancer drugs [18,19,20,21].
The utilization of P450s in the generation of secondary metabolites or natural products, organic compounds not directly involved in an organism’s normal growth, development, or reproduction, is gaining momentum as reactions catalyzed by these enzymes contribute to the secondary metabolite diversity [22,23]. Secondary metabolites, their structural diversity, bioactivity, and ecological functions, including their application in almost all areas of biology, have been thoroughly reviewed [24,25,26,27,28,29]. For example, secondary metabolites are widely used in human and veterinary medicine, agriculture, and manufacturing [30].
Secondary metabolites in organisms are produced by a set of genes usually located next to each other as a cluster known as secondary metabolite biosynthetic gene cluster (smBGCs) [30,31]. Earlier, researchers used to clone and sequence smBGCs to identify the genes/proteins involved in producing a particular secondary metabolite. The onset of genome sequencing and the advancement of science, especially in bioinformatics, led to the development of software programs that can automatically detect smBGCs [32]. Due to this advancement, many smBGCs were reported in species belonging to different biological kingdoms [30,31,33].
In the bacterial kingdom, species belonging to the phylum Actinobacteria are well-known for producing secondary metabolites [33,34,35,36], especially species of the genus Streptomyces [37]. It is a well-known fact that two-thirds of the clinically valuable antibiotics come from Streptomyces species [37]. Actinomycetes belonging to the genus Salinispora produce biotechnologically valuable secondary metabolites [38,39,40,41,42,43,44,45,46,47]. Salinosporamide A, a secondary metabolite, is one of the best examples, which is now under clinical trials as an anticancer drug [48].
Salinispora is the first genus of Actinobacteria identified for its requirement of seawater for growth [49]. This genus includes three distinct but closely related species Salinispora arenicola, S. pacifica, and S. tropica [36,50,51]. Salinispora species are widely distributed in tropical and subtropical marine environments with distinct geographical patterns [49,52]. The genome sequence of S. tropica revealed a large percentage of its genome (~9.9%) is dedicated to natural products biosynthesis, which was greater than any other natural product producing actinomycetes [47]. The genome sequencing analysis revealed that P450s were also part of smBGCs [47]. CYP107 from S. arenicola CNS-205 is involved in the biosynthesis of secondary metabolites, saliniketal, and rifampicin [53]. Apart from these notable mentions, no information is available on Salinispora species P450s.
Despite knowing that Salinispora species produce different types of human valuable secondary metabolites/natural products and the role of P450s in attributing diversity to these compounds, to date, comparative analysis of P450s and their role in secondary metabolism in Salinispora species is not reported. This study is aimed to address this research gap by performing genome-wide data mining, identification, annotation (assigning family and subfamily), and phylogenetic analysis of P450s in Salinispora species. The study also encompasses identification of P450s part of smBGCs, and comparative analysis of Salinispora P450 features with other bacterial species belonging to the genera, Streptomyces and Mycobacterium, phyla Firmicutes and Bacteroidetes, and the classes Alpha- and Gamma-proteobacteria.

2. Materials and Methods

2.1. Species and Database Information

A total of 126 Salinispora species genomes (permanent and finished draft genomes) are available for public use at the Joint Genome Institute Integrated Microbial Genomes and Microbiomes (JGI IMG/M) [54,55] were used in this study (last accessed on 2 February 2022). Information on the species and their genome IDs used in the study is provided in Table S1.

2.2. Genome Data Mining and Identification of P450s

Genome data mining and identification of P450s in Salinispora species were carried out following the protocol described elsewhere [56,57]. Each Salinispora species genome available at JGI IMG/M [54,55] was searched for P450s using the InterPro code “IPR001128”. The hit protein sequences were then searched for the presence of P450 characteristic motifs such as EXXR and CXG [58,59]. Proteins with one of these motifs or short amino acid length are considered P450-fragments. P450 fragments were not considered for the final P450 family and subfamily count.

2.3. Assigning Family and Subfamily to P450s

Above selected P450s were assigned to different families and subfamilies based on the International P450 Nomenclature Committee rule [60,61,62], proteins with a percentage identity greater than 40% were assigned to the same family as named homolog P450s, and those that had greater than 55% identity were assigned to the same subfamily as named homolog P450s. Proteins with a percentage identity of less than 40% were assigned to a new family. Salinispora species P450s, along with P450-fragments, are presented in Table S2.

2.4. Phylogenetic Analysis of P450s

Phylogenetic analysis of P450s was carried out following the procedure described elsewhere [63,64]. The phylogenetic tree of P450s was constructed using protein sequences. Firstly, the MAFFT v6.864 [65] was used to align the Trex web server’s protein sequences [66]. The alignments were then used to interpret the best tree by the Trex web server [66]. Finally, the best-inferred tree was visualized, colored, and generated by a web-based tool, VisuaLife [67].

2.5. Salinispora Species P450s Profile Heat-Maps

P450 profile heat-maps were generated following a method described elsewhere [64,68] to check the presence and absence of or co-presence of or conserved nature of P450 families in Salinispora species. Briefly, a tab-delimited file was imported into Multi-Experiment Viewer (Mev) [69], and hierarchical clustering using a Euclidean distance metric was used to cluster the data. 126 Salinispora species formed the vertical axis, and P450 families formed the horizontal axis. Data were presented as −3 for family absence (green) and 3 for family presence (red).

2.6. Identification of P450s Part of smBGCs

P450s that are part of smBGCs were identified following the method described elsewhere [56,57]. Briefly, for each Salinispora species genome available at JGI IMG/M [54,55], the smBGCs were searched for the presence of P450s using the P450 gene ID. The cluster type is noted if a P450 is found as part of the cluster. Results were recorded on Excel spreadsheets and represented species-wise smBGCs, smBGC type, and P450s part of specific smBGCs. Among 126, only 103 Salinispora species smBGCs information is available at JGI IMG/M [54,55]. Thus the same 103 Salinispora species smBGCs were analyzed for the presence of P450s (Table S1).

2.7. Data Analysis

All calculations were carried out following the procedure reported previously by our laboratory [68]. The average number of P450s was calculated using the formula: Average number of P450s = Number of P450s/Number of species. The P450 diversity percentage was calculated using the formula: P450 diversity percentage = 100 × Total number of P450 families/Total number of P450s × Number of species with P450s. The percentage of P450s that formed part of BGCs was calculated using the formula: Percentage of P450s part of BGCs = 100 × Number of P450s part of BGCs/Total number of P450s present in species.

2.8. Comparative Analysis of P450s and smBGCs Data

For comparative analysis of P450s and smBGCs, information for bacterial species belonging to different groups such as classes, Alpha- and Gamma-proteobacteria [64,68], phyla, Firmicutes [70] and Cyanobacteria [71], and the genera, Streptomyces [56,72], Mycobacterium [72,73], was resourced from published articles.

3. Results and Discussion

3.1. Salinispora Species P450 Profiles

Genome-wide data mining and annotation of P450s in 126 Salinispora species revealed the presence of 2643 P450s in their genomes (Figure 1, Table 1 and Table 2). The P450 count in Salinispora species ranged from 10 to 35 P450s, with an average of 21 P450s (Table 1 and Table 2). Apart from the complete P450 sequences, 129 P450 fragments were also found in some Salinispora species (Table 2). P450 fragments in species are natural [58,70,74], and thus, these were excluded from further analysis. Among Salinispora species, S. arenicola CNY280 has the highest number of P450s (35 P450s), and S. pacifica CNS801 and S. pacifica CNT148 have the lowest number of P450s (10 P450s each) (Table 2). Comparative analysis revealed that Salinispora species have the highest average number of P450s than species belonging to Cyanobacteria, Firmicutes, Alphaproteobacteria, and Gammaproteobacteria (Table 1). However, Salinispora species had the lowest average number of P450s compared to species belonging to Streptomyces and Mycobacterium (Table 1). A point to be noted is that, among bacterial species, species belonging to the phylum Actinobacteria have the highest average number of P450s (Table 1). This indicates selective enrichment of P450s in these species due to their adaptation to ecological niches vis a vis P450s, helping them adapt to diverse ecological niches described elsewhere [58,74,75]. Salinispora species P450s, along with P450-fragments, are presented in Table S2.

3.2. CYP105 and CYP107 Families Are Bloomed in Salinispora Species

Based on the International P450 Nomenclature Committee Rules [60,61,62], all 2643 P450s can be grouped into 45 families and 103 subfamilies (Table 1 and Table 3). Phylogenetic analysis revealed that large P450 families CYP105 and CYP107 were scattered across the evolutionary tree (Figure 1). Previously, this phenomenon was observed for these P450 families [56,72]. Authors suggested that phylogenetic-based annotation of P450s could detect similarity cues beyond a simple percentage identity cutoff [56,72]. Except for CYP105 and CYP107, the rest of the P450s are grouped as per their families (Figure 1). A point to be noted is that most of the P450s are orthologs considering the Salinispora species analyzed in this study are different strains of three species. Comparative analysis revealed that Salinispora species have the lowest number of P450 families and subfamilies compared to other actinomycetes such as Streptomyces and Mycobacterium (Table 1).
Among Salinispora species, S. arenicola CNY280 had the highest number of P450 families (18) and P450 subfamilies (32) in its genome (Table 1). This is quite an interesting observation where a species with the highest number of P450s also had the highest number of P450 families and subfamilies. This phenomenon was not found in other actinomycetes such as Streptomyces [56] and Mycobacterium [72,73]. For example, in Streptomyces species, Streptomyces albulus ZPM had the highest number of P450s, but Streptomyces rimosus rimosus ATCC 10970, and Streptomyces clavuligerus had the highest number of P450 families and subfamilies, respectively [56]. Among mycobacterial species, Mycobacterium rhodesiae NBB3 had the highest P450s and P450 families, but M. marinum had the highest P450 subfamilies [72,73].
Analysis of P450 families and subfamilies suggested that P450s in Salinispora species bloomed (presence of more copies of the same P450 family in a species by duplication of an ancestral gene) (Table 3). Among P450 families, the CYP105 was dominant with 600 members, followed by CYP107 with 551 members, CYP211 with 225 members, CYP125 with 164 members, CYP154 with 155 members, CYP1005 with 127 members, and CYP208 with 126 members (Table 3). These P450 families contributed more than 70% to the total P450s (Table 3). This indicates that P450 families such as CYP105, CYP107, CYP211, CYP125, and CYP154 are bloomed, whereas CYP1005 and CYP208 families are expanded in these species. Comparing the dominant P450 families revealed that CYP105 is prevalent only in Salinispora species (Table 1), where this family was second most dominant in Streptomyces species (Table 1). Interestingly, the second most dominant P450 family of Salinispora species, CYP107, was dominant in species belonging to bacterial groups Streptomyces, Firmicutes and Gammaproteobacteria (Table 1). The blooming was also observed at the subfamily level, indicating these P450s are preferred by Salinispora species for a particular reason. For example, subfamily AB was dominant with 124 members in CYP105; Subfamily AY was dominant with 116 members in CYP107, subfamily A was dominant with 128 members in CYP125, Subfamily M was dominant with 150 members, subfamily A was dominant with 126 members in CYP208, and Subfamily B dominant with 124 members in CYP211 (Table 3). Due to the blooming of specific P450s at the family level, Salinispora species had the lowest P450 diversity percentage, the same as Firmicutes species (Table 1). The blooming or expansion of P450s is a common phenomenon in organisms and is observed in other bacterial species (Table 2). It has been hypothesized that species enrich specific P450s in their genomes that are beneficial to them, particularly to adapt to ecological niches [56,72].

3.3. CYP107 and CYP125 Are Conserved in Salinispora Species

P450 family conservation analysis revealed that CYP107 and CYP125 families are conserved in 126 Salinispora species (Figure 2). Except for a few species, CYP208 (4 species), CYP105 (one species), CYP211 (one species), and CYP1005 (2 species), the rest of the Salinispora species have these families (Figure 2). In addition to this, P450 families such as CYP154, CYP244, CYP245, CYP166, CYP248, and CYP1056 are co-present in many species (Figure 2). This suggests a prominent role of these P450 families in these species, possibly in secondary metabolism as observed in other bacterial species [58,72,74]. Conservation or co-presence of specific P450s in other bacterial species was also reported. The CYP107 family is conserved in all 203 Streptomyces species, and P450 families such as CYP156, CYP105, CYP154, and CYP157 are also present in the majority of the Streptomyces species [56]. Ten P450 families, CYP51, CYP123, CYP125, CYP130, CYP135, CYP136, CYP138, CYP140, CYP144, and CYP1128, were conserved in mycobacterial species [73]. Analysis of conservation of P450 families in 229 Firmicutes species and 114 cyanobacterial species revealed no conservation of the P450 family [70,71]. Still, some of the P450 families were co-present in most of the species. The P450 families CYP152, CYP107, CYP012, and CYP109, were found to be a co-presence in most Firmicutes species [70], and the P450 families CYP110 and CYP120 were found to be a co-presence in most cyanobacterial species [71].
If a P450 family is conserved or few P450 families are co-presence, these families play an important role in a species’s primary- or secondary-metabolism. Previous studies showed that this type of P450s prominently plays a role in secondary metabolism, helping species adapt to diverse ecological niches [58,59,72,74,75]. The importance of P450 families that are conserved and co-presence in Salinispora species is discussed in detail in the next section.

3.4. Unprecedented Number of P450s Involved in smBGCs

Analysis of the P450s part of smBGCs revealed that many P450s (47%) are part of these clusters, indicating their involvement in producing different secondary metabolites in Salinispora species (Table 4 and Table S1). The percentage of P450s part of smBGCs in Salinispora species was found to be unprecedented compared to other bacterial species, including other actinomycetes Streptomyces species and mycobacterial species that had 30% and 27% of P450s as part of smBGCs (Table 1). This suggests that Salinispora species dedicated half of their P450s to the production of secondary metabolites.
Among 2643 P450s, 1236 P450s belonging to the 35 P450 families were part of smBGCs (Figure 3 and Table 4 and Table S1). This means almost 78% of P450 families of Salinispora species are involved in secondary metabolism. Among the families that are part of smBGCs, CYP107 is dominant with 302 members (25%), followed by CYP105 with 220 members (18%), CYP208 with 87 members (7%), CYP244 with 79 members (7%), and CYP211 with 73 members (6%) (Figure 3 and Table S1). Analysis of the P450s part of smBGCs revealed a strong correlation between the dominant P450 families (Table 3) being dominant in smBGCs (Figure 3). This suggests that Salinispora species are enriched by blooming or expanding these P450 families (as discussed in the previous section) in their genome to produce secondary metabolites.
Analysis of P450 smBGCs revealed the presence of 18 types (Table 4 and Table S2). Among the types, Type I PKS (Polyketide synthase) (T1PKS) was dominant with 223 clusters, followed by nonribosomal peptides (NRPS) (205 clusters) and Type II PKS (T2PKS) (76 clusters) (Table 4 and Table S1). This suggests that most of the secondary metabolites produced by P450 smBGCs are T1PKS. When the P450 smBGCs were further analyzed for the number of P450s and P450 families, the dominant BGC type was not found to be dominant concerning the number of P450s being part of that smBGC type (Table 4 and Table S1). NRPS had the highest number of P450s (395 P450s), followed by T1PKS (275 P450s), oligosaccharide (121 P450s), and indole (105 P450s) (Table 4 and Table S1). The difference being not having more P450s despite being dominant smBGCs such as T1PKS is that the other smBGCs have more P450s per se more than one P450 being part of that type (Table 4 and Table S1). This phenomenon of more than one P450 being part of smBGCs has been reported earlier in other bacterial species [75]. However, having up to 6 P450s as part of smBGCs is unprecedented (Table 4), suggesting these clusters produce diverse secondary metabolites. The P450s co-present in different Salinispora species were part of the same cluster (Table 4). Based on the arrangement of P450s concerning their family/subfamily and the number of P450s in smBGCs, it is clear that these smBGCs are orthologs (Table 4). These smBGCs are passed into different Salinispora species from a single ancestor before diverging into S. arenicola, S. pacifica and S. tropica.

3.5. Functional Prediction of Salinispora Species P450s

Most of the Salinispora species P450s are orphans without an assigned biological function. Based on the homolog P450s from other organisms and being part of smBGCs, some P450 functions can be predicted. CYP105 and CYP107 members are involved in the degradation/biotransformation of xenobiotics and biosynthesis of secondary metabolites [76,77,78,79,80]. CYP107 from S. arenicola CNS-205 is involved in secondary metabolite biosynthesis [53]. It catalyzes multiple oxidative rearrangement reactions in the biosynthesis of saliniketal and rifampin [53]. CYP105 and CYP107 members’ enzymatic functions could help Salinispora species utilize diverse compounds as carbon sources, detoxify toxic compounds, or kill other bacterial species to thrive in the environment. It is no doubt that due to these beneficial properties, Salinispora species enriched these family members in their genomes. CYP125 members conserved in Salinispora species are cholesterol and cholest-4-en-3-one hydroxylases [81,82]. One can assume that CYP125 members possibly help Salinispora species utilize cholesterol or cholesterol-like molecules as carbon sources. Growth of S. arenicola CNS-205 on cholesterol where complete degradation of cholesterol was observed [83] strongly supports this assumption considering these species do have CYP125 in their genome.
Interestingly, the presence of CYP125 members as part of smBGCs as observed in Salinispora species (Table 4) is also observed in mycobacterial species [75], indicating CYP125 members do have other functions apart from cholesterol oxidation. CYP146 members are involved in β-hydroxytyrosine formation, a precursor for the biosynthesis of vancomycin antibiotics [84]. Interestingly, only a single member was found in Salinispora species (Table 3) and is not part of smBGCs, complicating predicting its role in these species.
CYP154 members are involved in regio- and stereo-selective hydroxylation of different steroids [85,86]. CYP154 from Nocardia farcinica IFM10152 is a bifunctional enzyme with O-dealkylation and ortho-hydroxylation activities [87]. This P450 converts formononetin, an isoflavone compound, into ortho-dihydroxy-isoflavone [87]. In Salinispora species, CYP154 members are dominant, indicating they may attribute the above-said activities to these species. However, the role of CYP154 in the generation of secondary metabolites and these compounds’ properties concerning Salinispora species is of future interest (Figure 3 and Table 4).
CYP163A and CYP163B members produce novobiocin, aminocoumarin antibiotic [88], and skyllamycin, a potent inhibitor of the platelet-derived growth factor [89]. CYP162A members are involved in peptidyl nucleoside antibiotic nikkomycin synthesis [90,91]. CYP161A members are involved in the biosynthesis of antibiotics, pimaricin [92], and amphotericin [93]. CYP113 members are involved in the production a variety of antibiotics erythromycin [94,95], tylosin [96,97] and himastatin [98,99]. The presence of the CYP161-CYP163 and CYP113 members as part of smBGCs in Salinispora species (Figure 3 and Table 4) suggests that these members are certainly involved in the production of secondary metabolites in these species.
CYP244 and CYP245 members are involved in the biosynthesis of antibiotic rapamycin [100,101]. These two P450s together as part of smBGCs clusters in Salinispora species (Table 4) indicate they are working together in producing secondary metabolite. CYP248A members are involved in the production of antibiotic aureothin [102]. Salinispora species have 63 CYP248A members (Table 3), and 40 of them are part of smBGC (Figure 3 and Table 4), indicating their prominent role in secondary metabolites production. CYP124 members are known for their terminal hydroxylation of methyl branched-lipids in M. tuberculosis [103]. None of these members were found as part of smBGCs in Salinispora species (Table 4), indicating their limited role possibly in the oxidation of different methylated-aliphatic lipids in these species.
It is evident from the data presented in this article that close to half of Salinispora species P450s (1236 P450s) are part of smBGCs. Thus, we predict that these P450s play a role in producing different secondary metabolites characteristic of smBGC types (Table 4 and Table S2). The detailed information on species name, list of P450s part of smBGCs, their cluster information, and BGC type is presented in Table S1.

4. Conclusions

Salinispora species being marine organisms within the phylum Actinomycetes, are considered model organisms for studying bacterial diversity and secondary metabolite production. Compared to the genera Streptomyces and Mycobacterium, the genus Salinispora has an unprecedented number of P450s as part of secondary metabolite biosynthetic gene clusters (smBGCs), indicating a great diversity of secondary metabolites produced by these species. The presence of up to six P450s as part of smBGCs is unusual and not observed in other bacterial species. Future functional characterization of P450s sheds lighter on the untapped secondary metabolite biotechnological potentials from Salinispora species. Based on the data presented in this article and the literature published on P450s function, we predict that Salinispora species enriched or expanded specific P450s in their genome to utilize diverse compounds as carbon sources to detoxify toxic compounds or kill other bacterial species to thrive in the environment.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/microorganisms10050871/s1. Figure S1: Phylogenetic analysis of Salinispora species P450s. 2643 P450s were used to construct the tree, and the members of the eight most abundant P450 families are highlighted in different colors and indicated in the figure. P450 protein sequences used to build the tree are listed in Table S2. Table S1: Identification of P450s that are part of secondary metabolite biosynthesis tic gene clusters (smBGCs) in Salinispora species. Cluster-ID and BGC type is retrieved from Integrated Microbial Genomes & Microbiomes (IMG/M) database [54,55]. BGC Type was indicated for consistency with the standard BGC Type name terminology available in the anti-SMASH database [74]. Table S2: P450 sequences identified and annotated in Salinispora species. Each P450 is presented with its assigned name followed by gene ID (in parenthesis) and species name.

Author Contributions

Conceptualization, K.S.; methodology, N.A.M., N.N., T.P., P.R.S., R.K., D.G., D.R.N. and K.S.; software, N.A.M., N.N., T.P., P.R.S., R.K., D.G., D.R.N. and K.S.; validation, N.A.M., N.N., T.P., P.R.S., R.K., D.G., D.R.N. and K.S.; formal analysis, N.A.M., N.N., T.P., P.R.S., R.K., D.G., D.R.N. and K.S.; investigation, N.A.M., N.N., T.P., P.R.S., R.K., D.G., D.R.N. and K.S.; resources, N.A.M., N.N., T.P., P.R.S., R.K., D.G., D.R.N. and K.S.; data curation, N.A.M., N.N., T.P., P.R.S., R.K., D.G., D.R.N. and K.S.; writing—original draft preparation, N.A.M., N.N., T.P., P.R.S., R.K., D.G., D.R.N. and K.S.; writing—review and editing, N.A.M., N.N., T.P., P.R.S., R.K., D.G., D.R.N. and K.S.; visualization, N.A.M., N.N., T.P., P.R.S., R.K., D.G., D.R.N. and K.S.; supervision, K.S.; project administration, K.S.; funding acquisition, K.S. All authors have read and agreed to the published version of the manuscript.

Funding

Khajamohiddin Syed expresses sincere gratitude to the University of Zululand (Grant number C686). Doctoral students Nomfundo Nzuza, Tiara Padayachee, and Puleng Rosinah Syed thank the National Research Foundation (NRF), South Africa, for postgraduate scholarships (Grant numbers MND210615611861, MND210504599108, and MND190606443406, respectively). Research in Dominik Gront’s laboratory is funded by the National Science Centre (Poland) 2018/29/B/ST6/01989.

Data Availability Statement

The authors confirm that the data supporting the findings of this study are available within the article and its Supplementary Materials.

Conflicts of Interest

The authors declare no conflict of interest, and the funders had no role in the study’s design, in the collection, analyses, or interpretation of data, in the writing of the manuscript, or in the decision to publish the results.

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Figure 1. Phylogenetic analysis of Salinispora species P450s. 2643 P450s were used to construct the tree, and the members of the eight most abundant P450 families are highlighted in different colors and indicated in the figure. P450 protein sequences used to build the tree are listed in Table S2. A high-resolution phylogenetic tree is provided in Figure S1.
Figure 1. Phylogenetic analysis of Salinispora species P450s. 2643 P450s were used to construct the tree, and the members of the eight most abundant P450 families are highlighted in different colors and indicated in the figure. P450 protein sequences used to build the tree are listed in Table S2. A high-resolution phylogenetic tree is provided in Figure S1.
Microorganisms 10 00871 g001
Microorganisms 10 00871 g002 550
Figure 2. Heat-map of P450 family conservation or co-presence analysis in Salinispora species. In the heat-map, the presence and absence of P450 families are indicated in red and green colors. The horizontal axis represents P450 families, and the vertical axis represents Salinispora species.
Figure 2. Heat-map of P450 family conservation or co-presence analysis in Salinispora species. In the heat-map, the presence and absence of P450 families are indicated in red and green colors. The horizontal axis represents P450 families, and the vertical axis represents Salinispora species.
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Microorganisms 10 00871 g003 550
Figure 3. Comparative analysis of P450s associated with secondary metabolism in Salinispora species. The P450 family name, number of P450s, and the percentage of the total number of P450s that are part of secondary metabolite biosynthetic gene clusters (smBGCs) are presented in the figure. Detailed information on secondary metabolite clusters, species, and P450s are shown in Table S1.
Figure 3. Comparative analysis of P450s associated with secondary metabolism in Salinispora species. The P450 family name, number of P450s, and the percentage of the total number of P450s that are part of secondary metabolite biosynthetic gene clusters (smBGCs) are presented in the figure. Detailed information on secondary metabolite clusters, species, and P450s are shown in Table S1.
Microorganisms 10 00871 g003
Table
Table 1. Comparative analysis of key features of P450s and their association with secondary metabolism between Salinispora species and different bacterial species. Abbreviation: No., number of; BGCs: biosynthetic gene clusters.
Table 1. Comparative analysis of key features of P450s and their association with secondary metabolism between Salinispora species and different bacterial species. Abbreviation: No., number of; BGCs: biosynthetic gene clusters.
CategorySalinispora SpeciesStreptomyces SpeciesMycobacterial SpeciesCyanobacterial SpeciesFirmicutes SpeciesAlphaproteobacterial SpeciesGammaproteobacterial Species
Species analysed126203601149725991261
Species without P450s00007433701091
Species with P450s12620360114229229169
Percentage of species with P450s100100100100243813
No. of P450s264354601784341712873277
No. of families4525377361414381
No. of subfamilies1036981327953214102
Dominant P450 familyCYP105CYP107CYP125CYP110CYP107CYP202CYP133 & CYP107
Average No. of P450s2127303342
P450 diversity percentage0.010.020.070.090.010.070.17
No. of P450s part of BGCs12361231204271262149
No. of P450 families part of BGCs35135316101622
Percentage of P450s part of BGCs472311818218
Reference(s)This study[56,72][72,73][71][70][64][68]
Table
Table 2. Genome-wide data mining and annotation of P450s in 126 Salinispora species. Abbreviation, No. indicates the number in the table.
Table 2. Genome-wide data mining and annotation of P450s in 126 Salinispora species. Abbreviation, No. indicates the number in the table.
Species NameNo. of P450sNo. of P450 FragmentsNo. of P450 FamiliesNo. of Subfamilies
Salinispora arenicola CNH9962661425
Salinispora arenicola CNH996B27 1425
Salinispora arenicola CNY28035 1832
Salinispora arenicola CNH87734 1530
Salinispora arenicola CNS84832 1629
Salinispora arenicola CNT79831 1427
Salinispora arenicola CNH6433111428
Salinispora arenicola CNS-99131 1528
Salinispora arenicola CNT79931 1428
Salinispora arenicola CNY6793111427
Salinispora arenicola CNT85031 1327
Salinispora arenicola CNT80031 1428
Salinispora arenicola CNY01131 1426
Salinispora arenicola CNY23030 1730
Salinispora arenicola CNH71330 1427
Salinispora arenicola CNH9053111428
Salinispora arenicola CNT85730 1428
Salinispora arenicola CNY2812911729
Salinispora arenicola CNH94129 1426
Salinispora arenicola CNB5272941527
Salinispora arenicola CNT85929 1326
Salinispora arenicola CNT00528 1628
Salinispora arenicola CNH9642811424
Salinispora arenicola CNP19328 1426
Salinispora arenicola CNP1052821425
Salinispora arenicola CNH64628 1426
Salinispora arenicola CNR42528 1528
Salinispora arenicola CNS-2052811528
Salinispora arenicola ATCC BAA-91727131121
Salinispora arenicola CNY6852661426
Salinispora arenicola CNS32526 1326
Salinispora arenicola CNS74426 1326
Salinispora arenicola CNY6942661326
Salinispora arenicola CNY26026 1426
Salinispora arenicola CNT-0882611324
Salinispora arenicola CNB4582641326
Salinispora arenicola CNS2962511425
Salinispora arenicola CNY23125 1426
Salinispora arenicola CNY28225 1325
Salinispora arenicola CNS2992511425
Salinispora arenicola CNQ74825 1325
Salinispora arenicola CNY24425 1325
Salinispora arenicola CNS82025 1325
Salinispora arenicola CNS67325 1325
Salinispora arenicola CNY23724 1224
Salinispora arenicola CNS3422411324
Salinispora arenicola CNH7182411324
Salinispora arenicola CNX8912431524
Salinispora arenicola CNY25624 1325
Salinispora arenicola CNS2432411324
Salinispora arenicola CNY2342411324
Salinispora arenicola CNY6902441324
Salinispora arenicola CNQ8842311325
Salinispora arenicola CNR10722 1222
Salinispora arenicola CNR92122 1222
Salinispora arenicola CNH9622211222
Salinispora arenicola CNX4812221222
Salinispora arenicola CNH9632211222
Salinispora arenicola CNX8142211221
Salinispora arenicola CNY4862211324
Salinispora arenicola CNX5082111221
Salinispora arenicola CNX4822111221
Salinispora pacifica CNS9962111521
Salinispora pacifica CNS2372011219
Salinispora pacifica CNY6462011319
Salinispora tropica CNT2612021018
Salinispora pacifica DSM 4554819 710
Salinispora pacifica CNT0451911319
Salinispora pacifica CNT12419 1319
Salinispora pacifica DSM 4554319 1218
Salinispora tropica CNB53619 1119
Salinispora tropica CNH8981811120
Salinispora pacifica CNT4031811217
Salinispora pacifica CNS8601821116
Salinispora pacifica CNS8631821217
Salinispora tropica CNY0121821018
Salinispora pacifica CNT58417 1117
Salinispora pacifica DSM 455491711116
Salinispora pacifica CNR1141711317
Salinispora tropica CNR6991721016
Salinispora pacifica CNT85418 1318
Salinispora pacifica CNT1501711116
Salinispora pacifica CNT1311711115
Salinispora pacifica DSM 4554416 1116
Salinispora pacifica CNT0031611015
Salinispora tropica CNY6811611016
Salinispora tropica CNS1971611016
Salinispora tropica CNY6781611016
Salinispora tropica CNT2501611016
Salinispora tropica CNB-4401611016
Salinispora tropica CNS41615 915
Salinispora pacifica CNT0011511115
Salinispora pacifica CNY4981511115
Salinispora pacifica CNR9091511015
Salinispora tropica CNB476151915
Salinispora pacifica CNR89415 1115
Salinispora pacifica CNY36315 1115
Salinispora pacifica CNS05515 915
Salinispora pacifica CNT6031511115
Salinispora pacifica CNT13814 1014
Salinispora pacifica DSM 455471411014
Salinispora pacifica CNH7321411014
Salinispora pacifica CNY70314 913
Salinispora pacifica CNQ7681411014
Salinispora pacifica CNY67314 1014
Salinispora pacifica CNT85514 914
Salinispora pacifica CNY2391411014
Salinispora pacifica CNR9421411014
Salinispora pacifica DSM 455461411014
Salinispora pacifica CNT6091411014
Salinispora pacifica CNY33114 1014
Salinispora tropica CNR41614 914
Salinispora pacifica CNY33013 913
Salinispora pacifica CNT851131913
Salinispora pacifica CNT796131913
Salinispora pacifica CNS10313 913
Salinispora pacifica CNY202131913
Salinispora pacifica CNT133A13 913
Salinispora arenicola CNY666135813
Salinispora pacifica CNT029 131913
Salinispora pacifica CNT08413 913
Salinispora pacifica CNR51013 913
Salinispora pacifica CNT569121913
Salinispora pacifica CNT-133111179
Salinispora pacifica CNS80110 710
Salinispora pacifica CNT14810 710
Table
Table 3. Comparative analysis of P450 families and subfamilies in Salinispora species.
Table 3. Comparative analysis of P450 families and subfamilies in Salinispora species.
P450 FamilyP450 CountPercentage CountSubfamilyCountPercentage Count
CYP1004341.29%A170.64
B170.64
CYP10051274.81%A1274.79
CYP103720.08%B20.08
CYP1051602.27%A602.26
CYP105620.08%B20.08
CYP10560022.70%AB1244.67
AH40.15
B10.04
BL782.94
BN10.04
CH441.66
CN622.34
CP622.34
CT411.55
EJ30.11
G622.34
H30.11
J521.96
W632.37
CYP10755120.85%AW652.45
AX752.83
AY1164.37
CL30.11
CT60.23
E381.43
EP20.08
EU441.66
FH250.94
FJ200.75
FS612.30
GU10.04
HF20.08
LA60.23
N20.08
NE20.08
NF20.08
NG40.15
NH80.30
Q632.37
Z60.23
CYP111410.04%C10.04
CYP113240.91%B60.23
D10.04
E100.38
R20.08
S20.08
T10.04
X20.08
CYP119710.04%A10.04
CYP1198431.63%B431.62
CYP120740.15%A40.15
CYP122360.23%D20.08
A40.15
CYP122620.08%A20.08
CYP124150.57%M150.57
CYP1251646.21%A1284.82
G361.36
CYP126920.08%A20.08
CYP1278110.42%A50.19
B60.23
CYP143710.04%C10.04
CYP14610.04%A10.04
CYP152210.04%A10.04
CYP1541555.86%AJ40.15
J10.04
M1505.65
CYP161110.04%B10.04
CYP161281.06%N230.87
0.00%T50.19
CYP162391.48%A110.41
B20.08
G20.08
H10.04
J10.04
K10.04
L10.04
M10.04
N10.04
P180.68
CYP163391.48%A20.08
B371.39
CYP16440.15%C40.15
CYP166622.35%A622.34
CYP17310.04%K10.04
CYP190220.08%A20.08
CYP2054220.83%A220.83
CYP20510.04%A10.04
CYP2081264.77%A1264.75
CYP209110.04%A10.04
CYP209820.08%A20.08
CYP2112258.51%B1244.67
C1013.81
CYP229610.04%A10.04
CYP2441074.05%A1074.03
CYP245833.14%A833.13
CYP247210.79%A210.79
CYP248632.38%A632.37
CYP261110.04%B10.04
CYP28310.04%A10.04
CYP28540.15%A20.08
D20.08
CYP294A420.08%A20.08
Table
Table 4. Secondary metabolite biosynthetic gene cluster (smBGC) types and P450s are part of the cluster in Salinispora species. smBGC types were again classified into different varieties based on the P450s. The smBGCs type count and the total number of P450s in the cluster variety are also presented. The same smBGCs type names listed in the antibiotics and secondary metabolite analysis shell (anti-SMASH) database [74] were used in the table. Detailed information on secondary metabolite clusters, species, and P450s are shown in Table S1.
Table 4. Secondary metabolite biosynthetic gene cluster (smBGC) types and P450s are part of the cluster in Salinispora species. smBGC types were again classified into different varieties based on the P450s. The smBGCs type count and the total number of P450s in the cluster variety are also presented. The same smBGCs type names listed in the antibiotics and secondary metabolite analysis shell (anti-SMASH) database [74] were used in the table. Detailed information on secondary metabolite clusters, species, and P450s are shown in Table S1.
smBGC TypesmBGC Type CountsmBGC Type VarietyP450sP450 Count
Bacteriocin4746CYP107AW46
1CYP283A1
betalactone21CYP162A6,CYP107HF12
1CYP113S11
butyrolactone11CYP105CT1,CYP154M52
Indole5451CYP244A,CYP245A102
3CYP244A3
ladderane184CYP154M15,CYP125G6,CYP107FS2,CYP105CN1,CYP105CP220
8CYP107AX-fragment8
6CYP107AX6
lanthipeptide21CYP1223A51
1CYP105CP2,CYP105CN1,CYP107FS2,CYP248A2,CYP105W25
LAP11CYP154AJ21
lipolanthine22CYP1223A52
NRPS2051CYP1004B1,CYP1004A12
8CYP1004B,CYP1004A,CYP125G24
1CYP105CH2-fragment,CYP105CH1-fragment2
1CYP105CN11
1CYP105CN1,CYP105CP22
1CYP105CN1,CYP107FS2,CYP125G6,CYP154M154
1CYP105CN1,CYP107FS2,CYP247A73
1CYP105CP21
7CYP105CP2,CYP105CN1,CYP107FS221
10CYP105CP2,CYP105CN1,CYP107FS2,CYP125G6,CYP154M1550
2CYP105CP2,CYP105CN1,CYP107FS2,CYP248A28
1CYP105CP2,CYP105CN1,CYP107FS2,CYP248A2,CYP105W25
3CYP105W3
38CYP107AY38
1CYP107AY14,CYP244A-fragment22
6CYP107AY2,CYP105CT1,CYP154M518
1CYP107AY2,CYP163B162
1CYP107AY7,CYP244A5,CYP245A113
1CYP107AY9,CYP162B32
1CYP107AY9,CYP244A102
2CYP107CL2,CYP1056B24
5CYP107CT35
1CYP107CT3,CYP107AY72
1CYP107FS21
6CYP107FS2,CYP105CN1,CYP105CP218
2CYP107NH1,CYP247A8,CYP107Z276
1CYP107Z27,CYP247A8,CYP107NH13
1CYP113D13,CYP163B222
1CYP1196A21
1CYP1198B11
1CYP1198B1,CYP107AY22
2CYP1207A122
1CYP125G1,CYP1004A1,CYP1004B13
1CYP125G6,CYP154M152
4CYP1278A44
1CYP1437C11
1CYP154AJ31
1CYP154J2,CYP244A5,CYP245A113
5CYP154M1,CYP208A410
6CYP154M6
3CYP154M,CYP208A6
1CYP154M16,CYP211C62
1CYP154M21,CYP154M132
1CYP154M21,CYP154M13,CYP105W2,CYP248A24
3CYP154M21,CYP154M13,CYP105W2,CYP248A2,CYP154M2015
1CYP154M21,CYP154M13,CYP105W2,CYP248A2,CYP154M20,CYP162P16
12CYP16212
1CYP163A10,CYP162K12
15CYP163B15
3CYP164C23
5CYP208A21,CYP154M1610
2CYP208A4,CYP154M14
8CYP244A,CYP107AY16
5CYP244A5,CYP245A1110
2CYP244A,CYP107AY4
2CYP244A2
1CYP245A111
3CYP247A3
1CYP247A8,CYP107NH12
1CYP247A8,CYP107Z272
1CYP248A21
1CYP248A2,CYP105W22
1CYP285D21
NRPS-like305CYP107EU5
1CYP107EU1,CYP1198B1,CYP105CH13
1CYP107FH3,CYP161N4,CYP107AY93
7CYP107FH3,CYP2054A3,CYP161N421
2CYP161N4,CYP2054A3,CYP107FH36
6CYP162A86
6CYP166A46
1CYP166A4,CYP107Q4,CYP105G53
1CYP285A9-fragment,CYP285A9-fragment2
oligosaccharide351CYP105CP21
1CYP105W2,CYP107FS2,CYP105CN1,CYP105CP24
1CYP105W2,CYP107NH12
1CYP105W2,CYP154M20,CYP154M13,CYP154M21,CYP248A25
5CYP105W2,CYP248A210
1CYP105W2,CYP248A2,CYP107FS23
9CYP105W2/3,CYP248A2,CYP107FS2,CYP105CN1,CYP105CP245
1CYP1269A21
8CYP154M20,CYP248A2,CYP105W2,CYP154M13,CYP154M2140
1CYP2091A11
3CYP248A23
3CYP248A2,CYP105W2/36
other42CYP247A72
2CYP105AH42
1CYP1004A3,CYP1004B4,CYP113E2,CYP163B184
T1PKS2231CYP105AH41
1CYP105BN41
17CYP105CH1/217
1CYP105CN11
4CYP105G54
16CYP105G5,CYP107Q432
2CYP105H112
1CYP107AY131
24CYP107E24
1CYP107E3,CYP125G1,CYP1004A1,CYP1004B14
8CYP107EU18
2CYP107FH42
1CYP107NE11
3CYP107Q43
17CYP107Q4,CYP105G534
6CYP113E1/26
1CYP113E2,CYP107EP22
2CYP1198B22
1CYP125G11
1CYP1278B-fragment21
5CYP154M5,CYP105CT110
1CYP154M5,CYP105CT1,CYP105G5,CYP105CP24
1CYP154M5,CYP105CT1,CYP107AY2-fragment3
1CYP154M5,CYP105CT22
1CYP1611B1,CYP2098A12
29CYP166A429
1CYP166A4,CYP107Q4,CYP105G53
70CYP208A70
1CYP208A28,CYP154M182
1CYP211C51
2CYP294A42
T2PKS762CYP107NG12
1CYP107NH11
1CYP125G41
1CYP161T11
69CYP211C69
1CYP2296A2,CYP166A4,CYP173K13
1CYP244A5,CYP211C62
T3PKS87CYP161N4,CYP2054A3,CYP107FH321
1CYP107FH31
Terpene6139CYP1051A39
2CYP105CT12
7CYP105CT1,CYP154M514
6CYP107AY6
4CYP107AY9,CYP244A108
1CYP107E371
1CYP154AJ21
1CYP154M51
transAT-PKS11CYP113 × 11
transAT-PKS-like88CYP163B8
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Malinga, N.A.; Nzuza, N.; Padayachee, T.; Syed, P.R.; Karpoormath, R.; Gront, D.; Nelson, D.R.; Syed, K. An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species. Microorganisms 2022, 10, 871. https://doi.org/10.3390/microorganisms10050871

AMA Style

Malinga NA, Nzuza N, Padayachee T, Syed PR, Karpoormath R, Gront D, Nelson DR, Syed K. An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species. Microorganisms. 2022; 10(5):871. https://doi.org/10.3390/microorganisms10050871

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Malinga, Nsikelelo Allison, Nomfundo Nzuza, Tiara Padayachee, Puleng Rosinah Syed, Rajshekhar Karpoormath, Dominik Gront, David R. Nelson, and Khajamohiddin Syed. 2022. "An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species" Microorganisms 10, no. 5: 871. https://doi.org/10.3390/microorganisms10050871

APA Style

Malinga, N. A., Nzuza, N., Padayachee, T., Syed, P. R., Karpoormath, R., Gront, D., Nelson, D. R., & Syed, K. (2022). An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species. Microorganisms, 10(5), 871. https://doi.org/10.3390/microorganisms10050871

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