Research Articles (Bioinformatics & Computational Biology Unit)

Permanent URI for this collectionhttp://hdl.handle.net/2263/3365

This collection contains some of the full text peer-reviewed/ refereed articles published by researchers from the Department of Biochemistry

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Now showing 1 - 11 of 11

Diversity analysis of southern African Artemisia afra using a single nucleotide polymorphism derived from diversity arrays
(Elsevier, 2024-02) Sedibe, Moosa Mahmood; Rafiri, Matumelo A.; Dikane, Goitsemang Mahlomola Hendry; Achilonu, Matthew Chilaka; Nkosi, S'busiso Mfan'vele; Ngubane, Xolile Veronica; Pierneef, Rian Ewald
Artemisia afra is an aromatic shrub used as a herbal remedy in southern Africa for various disorders, including coughs, colds, influenza, and, most notably, for the prophylaxis and treatment of Plasmodium falciparum infections. Modern high-throughput genotyping by sequencing, which combines next generation sequencing and diversity array technology (DArTseq) complexity reduction methods, allows for the generation of high-quality whole-genome profiles without any previous organismal genetic information that may hamper the diversity analyses. This study investigated the feasibility of incorporating DArTseq-derived single-nucleotide polymorphisms (SNPs) and bioactive compounds into a geographic information system to predict the spatial distribution of A. afra gene diversity in selected southern African environs. DNA extraction, sequencing, and SNP calling mineral analyses (using R Studio) were performed on a total of 80 genotypes collected around Roma and Mohale’s Hoek, Lesotho, and Wepener and Hobhouse, South Africa. The unweighted pair group method with arithmetic mean (UPGMA) and neighbour-joining dendrograms revealed three clusters of variation among genotypes; however, geographic distribution did not influence A. afra genetic diversity. The mean heterozygosity among genotypes was 7.7%. Genotypes collected in Roma and Mohale’s Hoek exhibited high levels of genetic diversity. Local A. afra genetic diversity was relatively low, indicating uniformity of subspecies per locality. The diversity among genotypes indicated that A. afra SNPs may occur despite the location. Given that genetic diversity enhances crop performance, our findings can be useful in germplasm management, industries producing by-products of A. afra, and plant breeding programs. For the long-term conservation of medicinal plants in South Africa, significant sampling and regional data are required. In addition to evaluating qualitative and quantitative assessments of phytochemicals, it is necessary to evaluate foliar mineral composition, as well as the agronomic and morphological characteristics of collected specimens from studied locations.
Whole-genome sequencing of Salmonella serotypes recovered longitudinally from broiler production, processing, and retailing in Trinidad and Tobago
(Springer, 2023-12) Khan, Anisa S.; Pierneef, Rian Ewald; Abebe, Woubit; Adesiyun, Abiodun Adewale
Please read abstract in the article.
Comparative genomics of Listeria species recovered from meat and food processing facilities
(American Society for Microbiology, 2022-09-06) Mafuna, T.; Matle, I.; Magwedere, K.; Pierneef, Rian Ewald; Reva, Oleg N.; oleg.reva@up.ac.za
Listeria species (spp.) are contaminants that can survive in food, on equipment, and on food processing premises if appropriate hygiene measures are not used. Homologous stress tolerance genes, virulence gene clusters such as the prfA cluster, and clusters of internalin genes that contribute to the pathogenic potential of the strains can be carried by both pathogenic and nonpathogenic Listeria spp. To enhance understanding of the genome evolution of virulence and virulence-associated properties, a comparative genome approach was used to analyze 41 genome sequences belonging to L. innocua and L. welshimeri isolated from food and food processing facilities. Genetic determinants responsible for disinfectant and stress tolerance were identified, including the efflux cassette bcrABC and Tn6188_qac_1 disinfectant resistance determinant, and stress survival islets. These disinfectant- resistant genes were more frequently found in L. innocua (12%) than in L. welshimeri (2%). Several isolates representing the presumed nonpathogenic L. innocua still carried virulence-associated genes, including LGI2, LGI3, LIPI-3, and LIPI-4 which were absent in all L. welshimeri isolates. The mobile genetic elements identified were plasmids (pLGUG1 and J1776) and prophages (PHAGE_Lister_vB_LmoS_188, PHAGE_Lister_LP_030_3, PHAGE_ Lister_A118, PHAGE_Lister_B054, and PHAGE_Lister_vB_LmoS_293). The results suggest that the presumed nonpathogenic isolates especially L. innocua can carry genes relevant to the strain’s virulence and stress tolerance in the food and food processing facilities. IMPORTANCE : This study provides genomic insights into the recently expanded genus in order to gain valuable information about the evolution of the virulence and stress tolerance properties of the genus Listeria and the distribution of these genetic elements pertinent to the pathogenic potential across Listeria spp. and clonal lineages in South Africa (SA).
Differences in precipitation regime shape microbial community composition and functional potential in Namib Desert soils
(Springer, 2022-04) Naidoo, Yashini; Valverde, Angel; Pierneef, Rian Ewald; Cowan, Don A.
Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and ‘resistance to antibiotics and toxic compounds’ related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.
Genetic diversity and population structure analysis reveals the unique genetic composition of South African selected macadamia accessions
(Springer, 2022-03) Ranketse, Mary; Hefer, Charles A.; Pierneef, Rian Ewald; Fourie, Gerda; Myburg, Alexander Andrew; zander.myburg@fabi.up.ac.za
Macadamia nuts are known globally for their high quality and economic value. Global macadamia commercial nut production amounts to 60,000 metric tonnes and is increasing steadily. South Africa is the leading producer with 29% of worldwide kernel production. Commercial macadamia germplasm was originally selected from a small genepool (mainly Macadamia integrifolia species) from a limited geographic distribution in Australia. These accessions were subsequently bred, cloned and exported across the world to start local macadamia industries. The South African macadamia industry was established with pre-commercial and commercial macadamia from different parts of the world, and local selections were also performed. Many of these accessions have unique genetic compositions that have not been characterized yet. We used 13 nuclear microsatellite markers to study the genetic diversity and structure of macadamia germplasm cultivated in South Africa. We compared four groups of accessions including 31 originating from the Hawaiian Agricultural Experimental Station (HAES), 19 from Australia (AUS), two from California and one from Israel (OTH), 31 from South Africa’s locally selected accessions (SA) and 26 from two local Farmers (FARM). We used STRUCTURE, PCoA and neighbour-joining phylogenetic analyses to show that the South African selected accessions include diverse hybrid genotypes with strong Macadamia tetraphylla composition, unlike the Hawaiian commercially released and Australian representative collections that mostly have M. integrifolia or hybrid composition. Our results suggest that the South African selections represent a unique and diverse set of germplasm for future macadamia improvement efforts that will benefit from genomic breeding technologies.
Phylogenetic analyses of Salmonella detected along the broiler production chain in Trinidad and Tobago
(Elsevier, 2023-02) Khan, Anisa S.; Pierneef, Rian Ewald; Gonzalez-Escalona, Narjol; Maguire, Meghan; Georges, Karla; Abebe, Woubit; Adesiyun, Abiodun Adewale
This study was conducted to determine the phylogenies of Salmonella strains isolated from cross-sectional studies conducted at hatcheries, broiler farms, processing plants, and retail outlets (broiler production chain) in Trinidad and Tobago over 4 yr (2016–2019). Whole-genome sequencing (WGS) was used to characterize Salmonella isolates. Core genome phylogenies of 8 serovars of public health significance were analyzed for similarities in origin and relatedness. In addition, Salmonella strains isolated from human salmonellosis cases in Trinidad were analyzed for their relatedness to the isolates detected along the broiler production chain. The common source of these isolates of diverse serovars within farms, within processing plants, between processing plants and retail outlets, and among farm-processing plant-retail outlet continuum was well-supported (bootstrap value >70%) by the core genome phylogenies for the respective serovars. Also, genome analyses revealed clustering of Salmonella serovars of regional (intra-Caribbean) and international (extra-Caribbean) origin. Similarly, strains of S. Enteritidis and S. Infantis isolated from human clinical salmonellosis in 2019 from Trinidad and Tobago clustered with our processing plant isolates recovered in 2018. This study is the first phylogenetic analysis of Salmonella isolates using WGS from the broiler industry in the Caribbean region. The use of WGS confirmed the genetic relatedness and transmission of Salmonella serovars contaminating chickens in broiler processing, and retailing in the country, with zoonotic and food safety implications for humans.
Bacterial profiling of Haemonchus contortus gut microbiome infecting Dohne Merino sheep in South Africa
(Nature Research, 2021-03) Mafuna, Thendo; Soma, P.; Tsotetsi‑Khambule, A.M.; Hefer, C.A.; Muchadeyi, F.C.; Thekisoe, O.M.M.; Pierneef, Rian Ewald
A metagenomic approach was used to study the gut microbiome of Haemonchus contortus feld strains and that of its predilection site, the abomasum of Dohne Merino sheep. The abomasum contents and H. contortus were collected from 10 naturally infected Dohne Merino sheep. The H. contortus specimens were classifed and sexually diferentiated using morphometric characters and was further confrmed through molecular identifcation. We investigated diferences and similarities between the bacterial composition of the adult male and female H. contortus gut microbiomes, which were both dominated by bacteria from the Escherichia, Shigella, Vibrio and Halomonas genera. Major abundance variations were identifed between the shared adult male and female H. contortus microbiomes. The results also revealed that Succiniclasticum, Rikenellaceae RC9 gut group and Candidatus Saccharimonas were the predominant genera in the Dohne Merino abomasum. This study provides insight into the highly diverse bacterial composition of the H. contortus gut microbiome and the Dohne Merino abomasum which needs to be studied further to explore the complex interactions of diferent gastrointestinal nematode microbiomes with the host.
Draft genome sequence of Thermoactinomyces sp. strain AS95 isolated from a Sebkha in Thamelaht, Algeria
(Genomic Standards Consortium, 2016-09-09) Bezuidt, Keoagile Ignatius Oliver; Gomri, Mohamed A.; Pierneef, Rian Ewald; Van Goethem, Marc W.; Kharroub, Karima; Cowan, Don A.; Makhalanyane, Thulani Peter; thulani.makhalanyane@up.ac.za
The members of the genus Thermoactinomyces are known for their protein degradative capacities. Thermoactinomyces sp. strain AS95 is a Gram-positive filamentous bacterium, isolated from moderately saline water in the Thamelaht region of Algeria. This isolate is a thermophilic aerobic bacterium with the capacity to produce extracellular proteolytic enzymes. This strain exhibits up to 99 % similarity with members of the genus Thermoactinomyces, based on 16S rRNA gene sequence similarity. Here we report on the phenotypic features of Thermoactinomyces sp. strain AS95 together with the draft genome sequence and its annotation. The genome of this strain is 2,558,690 bp in length (one chromosome, but no plasmid) with an average G + C content of 47.95 %, and contains 2550 protein-coding and 60 RNA genes together with 64 ORFs annotated as proteases.
TULIP software and web server : automatic classification of protein sequences based on pairwise comparisons and Z-value statistics
(Bentham Science, 2009-03) Grando, Delphine; Ortet, Philippe; Joubert, Fourie; Marechal, Eric; Bastien, Olivier
A configuration space of homologous protein sequences (or CSHP) has been recently constructed based on pairwise comparisons, with probabilities deduced from Z-value statistics (Monte Carlo methods applied to pairwise comparisons) and following evolutionary assumptions. A Z-value cut-off is applied so as proteins are placed in the CSHP only when the similarity of pairs of sequences is significant following the Theorem of the Upper Limit of a score Probability (TULIP theorem). Based on the positions of similar protein sequences in the CSHP, a classification can be deduced, which can be visualized as trees, called TULIP trees. In previous case studies, TULIP trees where shown to be consistent with phylogenetic trees. To date, no tool has been made available to allow the computation of TULIP trees following this model. The availability of methods to cluster proteins based on pairwise comparisons and following evolutionary assumptions should be useful for evaluation and for the future improvements they might inspire. We developed a web server allowing the local or online computation of TULIP trees based on the CSHP probabilities. The input is a set of homologous protein sequences in multi-FASTA format. Pairwise comparisons are conducted using the Smith-Waterman method, with 100-1,000 sequence shuffling to estimate pairwise Z-values. Obtained Z-value matrix is used to infer a tree which is then written to a file. Output consists therefore of a Z-value matrix, a distance matrix, a TULIP treefile in NEWICK format, and a TULIP tree visualisation. The TULIP server provides an easy-to-use interface to the TULIP software, and allows a classification of protein sequences based on pairwise alignments and following evolutionary assumptions. TULIP trees are consistent with phylogenies in numerous cases, but they can be inconsistent for multi-domain proteins in which some domains have been conserved in all branches. Thus TULIP trees cannot be considered as conventional phylogenetic trees, following the MIAPA (Minimum Information About a Phylogenetic Analysis) recommendations. A major strength of the TULIP classification is its statistical validity when analysing samples including compositionally unbiased and biased sequences (i.e. with biased amino acid distributions), like sequences from Plasmodium falciparum. The TULIP web server is a service of the Malaria Portal of the University of Pretoria, South Africa, and is available at http://malport.bi.up.ac.za/TULIP/
The SeqWord Genome Browser : an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
(BioMed Central, 2008-08) Ganesan, Hamilton; Rakitianskaia, A.S. (Anastassia Sergeevna); Davenport, Colin F.; Tummler, Burkhard; Reva, Oleg N.; annar@cs.up.ac.za
BACKGROUND: Data mining in large DNA sequences is a major challenge in microbial genomics and bioinformatics. Oligonucleotide usage (OU) patterns provide a wealth of information for large scale sequence analysis and visualization. The purpose of this research was to make OU statistical analysis available as a novel web-based tool for functional genomics and annotation. The tool is also available as a downloadable package. RESULTS: The SeqWord Genome Browser (SWGB) was developed to visualize the natural compositional variation of DNA sequences. The applet is also used for identification of divergent genomic regions both in annotated sequences of bacterial chromosomes, plasmids, phages and viruses, and in raw DNA sequences prior to annotation by comparing local and global OU patterns. The applet allows fast and reliable identification of clusters of horizontally transferred genomic islands, large multi-domain genes and genes for ribosomal RNA. Within the majority of genomic fragments (also termed genomic core sequence), regions enriched with housekeeping genes, ribosomal proteins and the regions rich in pseudogenes or genetic vestiges may be contrasted. CONCLUSION: The SWGB applet presents a range of comprehensive OU statistical parameters calculated for a range of bacterial species, plasmids and phages.
Structural and mechanistic insights into the action of Plasmodium falciparum spermidine synthase
(Elsevier, 2007-02) Burger, Pieter Buys; Birkholtz, Lyn-Marie; Joubert, Fourie; Haider, Nashya; Walter, Rolf D.; Louw, Abraham Izak
Spermidine synthase is currently considered as a promising drug target in the malaria parasite, Plasmodium falciparum, due to the vital role of spermidine in the activation of the eukaryotic translation initiation factor (eIF5A) and cell proliferation. However, very limited information was available regarding the structure and mechanism of action of the protein at the start of this study. Structural and mechanistic insights of the P. falciparum spermidine synthase (PfSpdSyn) were obtained utilizing molecular dynamics simulations of a homology model based on the crystal structures of the Arabidopsis thaliana and Thermotoga maritima homologues. Our data are supported by in vitro site-directed mutagenesis of essential residues as well as by a crystal structure of the protein that became available recently. We provide, for the first time, dynamic evidence for the mechanism of the aminopropyltransferase action of PfSpdSyn. This characterization of the structural and mechanistic properties of the PfSpdSyn as well as the elucidation of the active site residues involved in substrate, product, and inhibitor interactions paves the way toward inhibitor selection or design of parasite-specific inhibitors.

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