Structural, functional, and phylogenetic studies of cytochrome P450 (CYP) enzyme in seed plants by bioinformatics tools

Darabi, Maryam; Seddigh, Samin; Abarshahr, Mina

doi:10.1080/00087114.2016.1274866

Cited by 10 publications

(8 citation statements)

References 45 publications

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“…In this present study, five motifs were found in most mammalian species according to the conserved motifs obtained by MEME and MAST tools (Figures 5 and 6). Similar findings were reported previously [61]; they made a comparison among six major P450s in humans (CYP3A4, CYP2D6, CYP2C9, CYP2C19, CYP1A2, and CYP2E1) to monitor its structural, functional, and evolutionary relationships [50]. According to motif analysis, they suggested eight motifs across these six CYPs identified by MEME and interpreted by MAST tools.…”

supporting

confidence: 74%

In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family

Ahmad

Afzal

Jamal

et al. 2021

BioMed Research International

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Cytochrome (CYP) enzymes catalyze the metabolic reactions of endogenous and exogenous compounds. The superfamily of enzymes is found across many organisms, regardless of type, except for plants. Information was gathered about CYP2D enzymes through protein sequences of humans and other organisms. The secondary structure was predicted using the SOPMA. The structural and functional study of human CYP2D was conducted using ProtParam, SOPMA, Predotar 1.03, SignalP, TMHMM 2.0, and ExPASy. Most animals shared five central motifs according to motif analysis results. The tertiary structure of human CYP2D, as well as other animal species, was predicted by Phyre2. Human CYP2D proteins are heavily conserved across organisms, according to the findings. This indicates that they are descended from a single ancestor. They calculate the ratio of alpha-helices to extended strands to beta sheets to random coils. Most of the enzymes are alpha-helix, but small amounts of the random coil were also found. The data were obtained to provide us with a better understanding of mammalian proteins’ functions and evolutionary relationships.

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supporting

confidence: 74%

In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family

Ahmad

Afzal

Jamal

et al. 2021

BioMed Research International

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“…In addition, CYPs are one of the largest superfamilies of enzyme proteins (Darabi, Seddigh, & Abarshahr, ). A large number of CYPs are involved in a wide range of biosynthetic reactions and biochemical pathways, leading to the synthesis of UV protectants (flavonoids and anthocyanins), defensive compounds (isoflavonoids, phytoalexins, hydroxamic acids, and terpenes), fatty acids, hormones (gibberellins and brassinosteroids), signaling molecules (oxylipins, salicylic acid, and jasmonic acid), accessory pigments (carotenoids), and structural polymers such as lignins (Darabi et al, ; Schuler & Werck‐Reichhart, ). In the present work, many CYP‐related unigenes were identified, such as CYP93A (e.g., CL361.Contig6_All, CL1330.Contig7_All, CL16738.Contig1_All), CYP76B (e.g., CL3689.Contig2_All, CL1852.Contig2_All), and CYP71 (e.g., CL6714.Contig2_All, Unigene23159_All, CL15279.Contig1_All), which respectively participated in the biosynthesis of isoflavonoids, flavonoids, and sesquiterpenoids and triterpenoids, which may act as defensive compounds that protect against oxidative damage under abiotic stress.…”

Section: Discussionmentioning

confidence: 99%

“…Based on the functional annotation of DEUs, a total of 120 core enzyme unigenes encoding CYPs were differentially expressed (Table A6 in Appendix). In addition, CYPs are one of the largest superfamilies of enzyme proteins (Darabi, Seddigh, & Abarshahr, ). A large number of CYPs are involved in a wide range of biosynthetic reactions and biochemical pathways, leading to the synthesis of UV protectants (flavonoids and anthocyanins), defensive compounds (isoflavonoids, phytoalexins, hydroxamic acids, and terpenes), fatty acids, hormones (gibberellins and brassinosteroids), signaling molecules (oxylipins, salicylic acid, and jasmonic acid), accessory pigments (carotenoids), and structural polymers such as lignins (Darabi et al, ; Schuler & Werck‐Reichhart, ).…”

Section: Discussionmentioning

confidence: 99%

Molecular basis underlying the successful invasion of hexaploid cytotypes of Solidago canadensis L.: Insights from integrated gene and miRNA expression profiling

Chen

Wang

2019

Ecology and Evolution

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Dissecting complex connections between cytogenetic traits (ploidy levels) and plant invasiveness has emerged as a popular research subject in the field of invasion biology. Although recent work suggests that polyploids are more likely to be invasive than their corresponding diploids, the molecular basis underlying the successful invasion of polyploids remains largely unexplored. To this end, we adopted an RNA‐seq and sRNA‐seq approach to describe how polyploids mediate invasiveness differences in two contrasting cytotypes of Solidago canadensis L., a widespread wild hexaploid invader with localized cultivated diploid populations. Our analysis of the leaf transcriptome revealed 116,801 unigenes, of which 12,897 unigenes displayed significant differences in expression levels. A substantial number of these differentially expressed unigenes (DEUs) were significantly associated with the biosynthesis of secondary metabolites, carbohydrate metabolism, lipid metabolism, and environmental adaptation pathways. Gene Ontology term enrichment‐based categorization of DEU‐functions was consistent with this observation, as terms related to single‐organism, cellular, and metabolic processes including catalytic, binding, transporter, and enzyme regulator activity were over‐represented. Concomitantly, 186 miRNAs belonging to 44 miRNA families were identified in the same leaf tissues, with 59 miRNAs being differentially expressed. Furthermore, we discovered 83 miRNA‐target interacting pairs that were oppositely regulated, and a meticulous study of these targets depicted that several unigenes encoding transcription factors, DNA methyltransferase, and leucine‐rich repeat receptor‐like kinases involved in the stress response were greatly influenced. Collectively, these transcriptional and epigenetic data provide new insights into miRNA‐mediated gene expression regulatory mechanisms that may operate in hexaploid cytotypes to favor successful invasion.

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“…Bioinformatic tools have been routinely used to search for new enzymes and for conducting analysis of the similarity among already available enzymes [15][16][17]. Previously, the CYP153A from Marinobacter aquaeolei (CYP153AM.aq.)…”

Section: Construction Of a Cyp153a Three-component Systemmentioning

confidence: 99%

Enzymatic Synthesis of ω-Hydroxydodecanoic Acid By Employing a Cytochrome P450 from Limnobacter sp. 105 MED

et al. 2019

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ω-Hydroxylated fatty acids are valuable and versatile building blocks for the production of various adhesives, lubricants, cosmetic intermediates, etc. The biosynthesis of ω-hydroxydodecanoic acid from vegetable oils is one of the important green pathways for their chemical-based synthesis. In the present study, the novel monooxygenase CYP153AL.m from Limnobacter sp. 105 MED was used for the whole-cell biotransformations. We constructed three-component system that was comprised of CYP153AL.m, putidaredoxin and putidaredoxin reductase from Pseudomonas putida. This in vivo study demonstrated that CYP153AL.m is a powerful catalyst for the biosynthesis of ω-hydroxydodecanoic acid. Under optimized conditions, the application of a solid-state powdered substrate rather than a substrate dissolved in DMSO significantly enhanced the overall reaction titer of the process. By employing this efficient system, 2 g/L of 12-hydroxydodecanoic acid (12-OHDDA) was produced from 4 g/L of its corresponding fatty acid, which was namely dodecanoic acid. Furthermore, the system was extended to produce 3.28 g/L of 12-OHDDA using 4 g/L of substrate by introducing native redox partners. These results demonstrate the utility of CYP153AL.m-catalyzed biotransformations in the industrial production of 12-OHDDA and other valuable building blocks.

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Structural, functional, and phylogenetic studies of cytochrome P450 (CYP) enzyme in seed plants by bioinformatics tools

Cited by 10 publications

References 45 publications

In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family

In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family

Molecular basis underlying the successful invasion of hexaploid cytotypes of Solidago canadensis L.: Insights from integrated gene and miRNA expression profiling

Enzymatic Synthesis of ω-Hydroxydodecanoic Acid By Employing a Cytochrome P450 from Limnobacter sp. 105 MED

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