Biochemistry and Microbiology

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Browsing Biochemistry and Microbiology by Subject "Alphaproteobacteria"

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    In silico genome-wide analysis of P450s, their redox partners and secondary metabolite gene-clusters in the bacterial class Alphaproteobacteria
    (University of Zululand, 2021) Nzuza, Nomfundo
    Cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins, are well-known players in the generation of secondary metabolites that are valuable to humans. With the exception of self-sufficient P450s, all P450s need electrons to perform their enzymatic reactions and these electrons are supplied by redox proteins such as ferredoxins, iron-sulfur (Fe-S) cluster proteins. However, to date, comprehensive comparative analysis of P450s, their redox proteins and secondary metabolite gene clusters in the ancient group of bacterial class Alphaproteobacteria has not been reported. Thus, this study aimed to address this research gap. In this study, comprehensive analysis of P450s, ferredoxins and P450s’ role in generation of secondary metabolites in Alphaproteobacteria has been carried out. This study also proposes a subtype classification and nomenclature for ferredoxins based on the characteristic spacing between the cysteine amino acids of the Fe-S binding motif as a subtype signature to assess diversity and lateral gene transfer (LGT) of ferredoxins across the living organisms. Genome data-mining and annotation of P450s in 599 alphaproteobacterial species belonging to 164 genera revealed the presence of P450s in only 241 species belonging to 82 genera that are grouped into 143 P450 families and 214 P450 subfamilies, including 77 new P450 families. Alphaproteobacterial species have the highest average number of P450s compared to Firmicutes species and cyanobacterial species. The lowest percentage of alphaproteobacterial species in P450s (2.4%) was found to be part of secondary metabolite biosynthetic gene clusters (BGCs) compared with other bacterial species, indicating that during evolution large numbers of P450s became part of BGCs in other bacterial species. The study revealed that some of the P450 families found in alphaproteobacterial species were passed on to other bacterial species. This is the first study to report on the identification of CYP125 P450, cholesterol and cholest-4-en-3-one hydroxylase in alphaproteobacterial species (Phenylobacterium zucineum) and to predict cholesterol side-chain oxidation capability (based on homolog proteins) by P. zucineum. Genome wide analysis of ferredoxins revealed presence of 1306 ferredoxins in 241 alphaproteobacterial species. The 2[4Fe-4S] cluster type was found to be the most abundant with 711 ferredoxins followed by 2Fe-2S with 490 ferredoxins, 3Fe-4S with 60 ferredoxins, 2[4Fe-4S]Alv with 31 ferredoxins, 7Fe-8S with 12 ferredoxins and 4Fe-4S with two ferredoxins. To assess the diversity and LGT of ferredoxins, ferredoxins collected from Alphaproteobacteria and from species of different domains of life that are reported in the literature were grouped into different subtypes based on the cysteine binding motif. A large number of alphaproteobacterial species ferredoxin subtypes were found across the species of 3 Bacteria, Archaea and Eukarya, suggesting common evolutionary origin of ferredoxins between Archaea and Bacteria and LGT of ferredoxins between prokaryotes (Archaea/ Bacteria) and eukaryotes.
University of Zululand