Browse
Recent Submissions
- ItemGenome data mining, annotation, and phylogenetic analysis of cytochrome P450 monooxygenases in the fungal class Pezizomycetes(University of Zululand, 2022) Nsele, Nomfundo NtombizinhleCytochrome P450 monooxygenases (CYPs/P450s) are heme proteins that play a role in organisms’ primary and secondary metabolism. P450s play an important role in organism adaptation since lifestyle influences P450 composition in their genome. This phenomenon is well-documented in bacteria but less so in fungi. This study observed this phenomenon where diverse P450 complements were identified in saprophytic and ectomycorrhizal Pezizomycetes. Genome-wide data mining, annotation, and phylogenetic analysis of P450s in 19 Pezizomycetes revealed 668 P450s that can be grouped into 153 P450 families and 245 P450 subfamilies. Only four P450 families, namely, CYP51, CYP61, CYP5093, and CYP6001, are conserved across 19 Pezizomycetes, indicating their important role in these species. A total of 5 saprophyte Pezizomycetes have 103 P450 families, whereas 14 ectomycorrhizal Pezizomycetes have 89 P450 families. Only 39 P450 families were common, and 50 and 64 P450 families, respectively, were unique to ectomycorrhizal and saprophytic Pezizomycetes. These findings suggest that the switch from a saprophytic to an ectomycorrhizal lifestyle led to both the development of diverse P450 families as well as the loss of P450s, which led to the lowest P450 family diversity, despite the emergence of novel P450 families in ectomycorrhizal Pezizomycetes.
- ItemAnnotation and comparative analysis of P450s, their redox partners and secondary metabolite gene clusters in the bacterial phylum Bacteroidetes(2022-09) Nkosi, Bridget Valeria ZinhleSpecies belonging to the bacterial phyla Bacteroidetes and Firmicutes represent over 90% of the gastrointestinal microbiota. Changes in the ratio of these two bacterial groups were found to have contrasting health effects, including obesity and inflammatory diseases. Despite the availability of many bacterial genomes, comparative genomic studies on the gene pools of these two bacterial groups concerning cytochrome P450 monooxygenases (P450s), ferredoxins, and secondary metabolite biosynthetic gene clusters (smBGCs) are not reported. Recently, an analysis of P450s, ferredoxins, and smBGCs in Firmicutesspecies has been reported. However, such studies on Bacteroidetes species have not been performed. This study is aimed to address this research gap. In this study, a thorough comparative analysis of P450s in the phylum Bacteroidetes has been carried out. P450 data mining and annotation of P450s in this phylum displayed 98 P450s in 77 species. It consisted of 130 genera, the Hymenobacter genus having the most P450s. Twenty-one P450 families were discovered, with CYP1103 dominating. Cluster analysis revealed 1298 smBGCs, with terpene being the most dominant. Out of the 98 P450s found in 334 Bacteroidetes species, only eight P450s (8.2 %) of seven Bacteroidetes species were found as part of the secondary metabolite BGCs. Genome data mining and annotation of ferredoxins in 104 Bacteroidetes species revealed the presence of 269 ferredoxins in their genomes. Among the Bacteroidetes species, Tenacibaculum jejuense had the highest number of ferredoxins (six). The 269 ferredoxins found in Bacteroidetes species can be grouped into five iron-sulfur (Fe-S) cluster types: 2Fe-2S, 3Fe-4S, 4Fe-4S, 2[4Fe-4S], and 2[4Fe-4S]Alv. The 7Fe-8S cluster-type ferredoxins were not found in the Bacteroidetesspecies analyzed in this study. Based on the amino acid spacing pattern analysis between the cysteine amino acids of the Fe-S cluster binding motif, 136 2Fe-2S ferredoxins of Bacteroidetes can be grouped into five subtypes. Eleven 4Fe-4S ferredoxins found in Bacteroidetes species can be grouped into three subtypes. The study revealed the presence of diverse sets of P450s, ferredoxins, and smBGCs in Bacteroidetes species genomes. Bacteroidetes species have the highest number of P450 families, ferredoxin cluster-types, and smBGCs compared to Firmicutes species. Only four P450 families, three ferredoxin cluster types, and five smBGCs are commonly shared between these two bacterial groups. Considering the above facts, we propose that the contrasting effects of these two bacterial groups on the host are partly due to the distinct nature of secondary metabolites produced by these organisms. Thus, the cause of the contrasting health effects of these two bacterial groups lies in their gene pools.
- ItemComprehensive comparative analysis of cytochrome P450s and those associated with secondary metabolism in Salinispora species(2022) Malinga, Nsikelelo AllisonCytochrome 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 the 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. Thus, P450s analysis in 126 strains from three different species Salinispora arenicola, S. pacifica, and S. tropica is carried out in this study. 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
- ItemAn in silico approach to understanding the role of P450s involved in secondary metabolites production in mycobacterial species(University of Zululand, 2022-09) Zondo, Ntokozo MinenhleCytochrome P450 monooxygenases (P450s/CYPs) are ubiquitous enzymes with unique regio- and stereo-selective oxidation activities. Due to these properties, P450s play a key role in the biosynthesis of natural metabolites. Mycobacterial species are well-known producers of complex metabolites that help them survive in diverse ecological niches, including in the host. In this study, a comprehensive analysis of P450s and their role in natural metabolite synthesis in 2666 mycobacterial species have been carried out. The study revealed the presence of 62815 P450s that can be grouped into 182 P450 families and 345 subfamilies. Blooming (presence of more than one copy of the same gene) and expansion (presence of the same gene in many species) were observed at the family and subfamily levels. CYP135 was the dominant family in mycobacterial species. The mycobacterial species have distinct P450 profiles, indicating lifestyle impacts P450 content in their genome vis a vis P450s play a key role in organisms' adaptation. Analysis of the P450 profile revealed a gradual loss of P450s from non-pathogenic to pathogenic mycobacteria. Pathogenic mycobacteria have more P450s in biosynthetic gene clusters that produce natural metabolites. This indicates that P450s are recruited for the biosynthesis of unique metabolites, thus helping these pathogens survive in their niches. This study is the first to analyze P450s and their role in natural metabolite synthesis in many mycobacterial species.
- ItemInvestigation of the prevalence of antibiotic resistant bacteria and their genes in wastewater(University of Zululand, 2020) Ndhlovu, Tshepo InnocenAntibiotics are therapeutic agents commonly used in the treatment of infections caused by microorganisms. Due to the increased demand of antibiotics, they have become environmental pollutant to both water and soil. This have caused adverse effects to human, animals, aquatic ecosystem and in the environment in general. These effects includes the development of antibiotic resistant microorganisms, which in turn makes the selection of appropriate antibiotics for particular infections difficult. Therefore, the presence and the prevalence of antibiotics in wastewater were investigated in this study and resistant microorganism and their resistant genes were identified. Gas chromatography with tandem mass spectrum was used to determine the presence of antibiotics in domestic wastewater. Resistance capabilities were detected using the disk diffusion method and resistance isolates were identified using the 16S rDNA sequencing. Polymerase chain reaction (PCR) with specific primers was used to detect resistant genes. Penicillin, ampicillin, meropenem and imipenem traces were determined in domestic wastewater and Bacillus cereus isolates were identified. CTX M, TEM and SHV resistant genes were detected. These genes are commonly found in water and are implicated in numerous diseases such as gastrointestinal infections including diarrhoea, abdominal pains, fever, etc. It is essential to track the pattern of antibiotic resistance because this has a potential in controlling the spread of these genes, thus preventing infections caused resistant microorganisms.