Annotation and comparative analysis of P450s, their redox partners and secondary metabolite gene clusters in the bacterial phylum Firmicutes
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Date
2021-11
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University of Zululand
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s), heme thiolate proteins, are well known for their role in organisms’ primary and secondary metabolism. P450s are also involved in the generation of secondary metabolites with biotechnological value. P450s require electrons to perform their function, and these electrons are provided by iron-sulfur (Fe-S) cluster proteins known as ferredoxins. However, to date, comparative analysis of P450s, redox proteins and P450s involved in secondary metabolite production is not reported in the bacterial phylum Firmicutes. This study aimed to address this research gap. 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, except for 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. A total of 281 ferredoxins were found amongst 227 Firmicutes species. Four types of ferredoxins were found in this phylum, namely, 2Fe-2S, 4Fe-4S, 7Fe-8S and 2[4Fe-4S]. The dominant type found amongst this phylum was 4Fe-4S with 140 ferredoxins followed by 2Fe-2S with 97 ferredoxins, 7Fe-8S with 32 ferredoxins and 2[4Fe-4S] with 12 ferredoxins. To date, evolutionary analysis of these proteins across the domains of life is confined to observing the abundance of Fe-S cluster types and the diversity of ferredoxins within a type is not reported. To address this research gap, here 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 was proposed. To test this hypothesis, comparative analysis of ferredoxins between Firmicutes and ferredoxins collected from species of different domains of life that are reported in the literature has been carried out. Various ferredoxin subtypes were found amongst Firmicutes species. Eleven different subtypes were found amongst 2Fe-2S ferredoxins with subtype 20 being the dominant subtype. 4Fe-4S had five subtypes with subtype 2 being dominant, and 2[4Fe-4S] had three subtypes with subtype 9 being dominant. It is interesting to note that 7Fe-8S only had one subtype showing a preference to that specific ferredoxin subtype. Three subtypes of 2Fe-2S and two subtypes of
2[4Fe-4S] were found to be common between the Archaea and Firmicutes species, indicating their shared common ancestral origin.
Overall, the study results supported the hypothesis proposed by our laboratory that organisms’ lifestyles impact P450 repertoire in their genomes. This is clearly evident in the bacterial phylum Firmicutes where a pathogenic or commensal lifestyle resulted in complete or nearly loss of P450s in the species. This study also is the first to propose ferredoxin subtype classification and identification of ferredoxins that have common ancestor origin (between Archean and Bacteria) and those are subjected to lateral gene transfer from prokaryotes (Archean/Bacteria) to eukaryotes.
Description
A thesis submitted to the Faculty of Science, Agriculture and Engineering in fulfilment of the requirements for the Degree of Master of Science in the Department of Biochemistry and Microbiology at the University of Zululand, South Africa, 2021.
Keywords
P450s, Redox partners, Secondary metabolites gene clusters, Bacterial phylum Firmicutes