Research Articles (Biochemistry, Genetics and Microbiology (BGM))

Permanent URI for this collectionhttp://hdl.handle.net/2263/87805

Browse

Now showing 1 - 20 of 685

Oxalate content of vegetation and termite frass in western South Africa
(Wiley, 2025-05) Nel, T.; Clarke, C.E.; Francis, M.L.; Babenko, D.; Breecker, D.; Cowan, Don A.; Gallagher, T.; McAuliffe, J.R.; Trindade, M.
Please read abstract in the article.
Investigating the antimicrobial and anticancer potential of culturable fungal endophytes isolated from the stems of Kirkia acuminata Oliv
(BioMed Central, 2025-05) Magagula, Mfundo; Motaung, Thabiso Eric; Mbita, Zukile; Dithebe, Khumiso
BACKGROUND : Fungal endophytes produce various structurally and chemically diverse bioactive secondary metabolites including those that are similar to their host plants. However, fungal endophytes from South African medicinal plants are relatively under-explored. The medicinal plant, Kirkia acuminata Oliv., is on the decline in the natural environment due to overharvesting. This necessitates the search for novel alternatives to sustainably obtain the plant’s bioactive metabolites. Thus, fungal endophytes may serve as suitable candidates as they can produce host-similar bioactive compounds. RESULTS : Eighteen morphologically distinct fungal endophytes were isolated from the surface-sterilised stems of K. acuminata Oliv. Sequencing of the internal transcribed spacer (ITS) region revealed that the isolates were distributed among three genera, namely Diaporthe, Neofusicoccum and Pseudofusicoccum. The broth micro-dilution assay showed that 17 of the 18 ethyl acetate crude extracts exhibited inhibitory activity with minimum inhibitory concentration (MIC) values ranging from 0.31 to 2.5 mg/mL and 1.25 to 2.5 mg/mL against bacterial pathogens and Candida albicans, respectively. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay revealed that most of the crude extracts had dose-dependent cytotoxicity against non-cancerous human embryonic kidney (HEK-293) cells, with the crude extracts of the N. parvum KaS-3, D. macadamiae KaS-4, P. olivaceum KaS-5 and D. neotheicola KaS-6 isolates demonstrating safety against the non-cancerous cells. The alamarBlue assay revealed that the four non-cytotoxic crude extracts had moderate anticancer activity against cervical cancer ME-180 and melanoma A375 cancerous cell lines. Moreover, mycochemical analysis of the non-cytotoxic crude extracts using colourimetric quantification methods revealed that the observed cytotoxic effect could be attributed to the high total phenolic content in the crude extracts. CONCLUSION : The study highlights that the fungal endophytes inhabiting the stems of K. acuminata Oliv. produce secondary metabolites that may serve as leads for novel antimicrobial and non-toxic anticancer agents.
The root rot pathogen Phytophthora cinnamomi : a long-overlooked threat to the Cape Floristic Region of South Africa
(Springer, 2025-04) Paap, Trudy; Balocchi, Felipe; Wingfield, Michael J.; trudy.paap@fabi.up.ac.za
The globally important plant pathogen Phytophthora cinnamomi was first reported in South Africa in 1931, where it caused substantial damage to avocado orchards. Surprisingly, 40 years passed before the pathogen was recognised as a significant threat to South Africa’s natural ecosystems. This first became evident when P. cinnamomi caused a “quick decline” of the iconic silver trees (Leucadendron argenteum) in the Cape Floristic Region (CFR) of the Western Cape Province. Subsequent research has underscored the role of P. cinnamomi as a major root rot pathogen affecting numerous native species. Despite these findings, there has been limited research on the extent of the threat P. cinnamomi poses to Cape flora, leaving the risk of extinction for many species largely unknown. A recent observation of P. cinnamomi causing rapid mortality in Sorocephalus imbricatus, a Critically Endangered Proteaceae, underscores the urgent need for a comprehensive evaluation of this pathogen’s impact on Cape flora and the associated extinction risks. Given the high number of rare and threatened species in the CFR, many of which belong to families known to be vulnerable to P. cinnamomi, there is a pressing need to initiate an intensive local research programme to fill this critical gap. To address this, we propose a structured research programme that will guide targeted mitigation efforts against P. cinnamomi. Enhancing our understanding of P. cinnamomi’s threat to the CFR, a global biodiversity hotspot, will be essential to inform conservation strategies and to set restoration priorities in the region.
Molecular mechanisms underlying tree host-pathogen interactions under drought stress and subsequent rewatering in Eucalyptus grandis
(Elsevier, 2024-12-02) Teshome, Demissew Tesfaye; Zharare, Godfrey Elijah; Ployet, Raphael; Naidoo, Sanushka; sanushka.naidoo@up.ac.za
Abiotic stresses such as drought change plant-pathogen interactions by affecting both hosts and pathogens. Here, we aimed to unravel the molecular mechanisms underlying forest tree-pathogen interactions under drought stress and subsequent rewatering. We conducted glasshouse experiments involving infection by the stem canker-causing fungal pathogen Chrysoporthe austroafricana under drought stress and rewatering in Eucalyptus grandis and investigated host and pathogen transcriptomic changes using RNA-seq data from our current combined stress experiment as well as previous single stress studies. We found that mild drought stress enhances disease progression while, upon rewatering, pathogen infection delays recovery of leaf stomatal conductance. Transcriptomic changes in the host support increased susceptibility to the pathogen while the in planta fungal transcriptome suggests prioritization of survival in the drought-stressed host. Upon rewatering, changes in the host transcriptome suggest allocation of resources to stress responses at the expense of growth and carbohydrate storage while that of the pathogen indicate downregulation of some fungal metabolic pathways potentially because the pathogen takes advantage of changes in the host. Our study identified key molecular processes and genes that provide mechanistic insights into tree-pathogen interactions under abiotic stresses. This enables prediction of tree resilience under a changing climate and contributes towards future tree health improvement endeavours.
Mulching of post-harvest residues and delayed planting improves fungal biodiversity in South African Eucalyptus plantations and enhances plantation productivity
(Elsevier, 2025-06) Bose, Tanay; Roux, Jolanda; Titshall, Louis; Dovey, Steven B.; Hammerbacher, Almuth; tanay.bose@fabi.up.ac.za
Short-rotation Eucalyptus plantations provide essential forest products, with productivity and soil health influenced by residue management and planting strategies. This study examined the effects of burning or mulching post-harvest residue followed by immediate versus delayed planting on soil fungal biodiversity, soil properties, and tree growth across four sites in KwaZulu-Natal, South Africa. Plots were planted either three months ('immediate') or six months ('delayed') after treatment implementation. Volume measurements assessed tree growth, and soil attributes, including moisture, temperature, and nutrient levels, were analyzed. Soil samples were collected in November 2019 and March 2022, and fungal communities were analyzed through high-throughput sequencing targeting the internal transcribed spacer 1 (ITS1) region. Data emerging from this study showed mulched plots had significantly higher tree volume, with delayed planting increasing productivity by 13.6 % at 24–36 months and 25 % at 36–48 months post-planting. Soil moisture was 1.3–2 times higher in mulched plots than in burnt plots. Mulching significantly reduced the maximum soil temperatures by 4.5–6.8 °C. Four months after treatment, burnt plots had higher pH (1.1-fold), carbon (2.2-fold), phosphate (1.6-fold) and manganese (2.5-fold). Initially, mulched plots had lower fungal biodiversity (0.81-fold) than burnt plots but surpassed them after 28 months (1.28-fold increase). Fungal community overlap declined from 83.28 % to 40.64 %, with mulching supporting higher saprotroph (1.3-fold) and symbiotroph (1.25-fold) abundances, while delayed planting increased pathotroph presence by 1.5-fold in burnt plots. These findings highlight the long-term benefits of mulching and delayed planting in enhancing fungal biodiversity, promoting beneficial microbial communities, and improving tree growth, contributing to more sustainable Eucalyptus plantation management.
Mesorhizobium salmacidum sp. nov. and Mesorhizobium argentiipisi sp. nov. are symbionts of the dry-land forage legumes Lessertia diffusa and Calobota sericea
(Springer, 2025-03) Muema, Esther K.; Van Lill, Melandre; Venter, S.N. (Stephanus Nicolaas); Chan, Wai Yin; Claassens, Ricu; Steenkamp, Emma Theodora
Legumes Lessertia diffusa and Calobota sericea, indigenous to South Africa, are commonly used as fodder crops with potential for sustainable livestock pasture production. Rhizobia were isolated from their root nodules grown in their respective soils from the Succulent Karoo biome (SKB) in South Africa, identified and characterized using a polyphasic approach. Sequence analysis of the 16S rRNA gene confirmed all isolates as Mesorhizobium members, which were categorized into two distinct lineages using five housekeeping protein-coding genes. Lineage I included 14 strains from both legumes, while Lineage II comprised a single isolate from C. sericea. Differences in phenotypic traits were observed between the lineages and corroborated by average nucleotide identity analyses. While all strains nodulated their original hosts, strains from C. sericea failed to effectively nodulate L. diffusa and vice versa. Phylogenetic analyses of nitrogen fixation (nifH) and nodulation (nodA, nodC) loci grouped all strains in a single clade, suggesting that unique symbiotic loci determine nodulation of these legumes. We designated Lineage I and II as Mesorhizobium salmacidum sp. nov. (Ld1326Ts; GCA_037179605.1Ts) and Mesorhizobium argentiipisi sp. nov. (Cs1330R2N1Ts; GCA_037179585.1Ts), using genome sequences as nomenclatural types according to the Nomenclatural Code for Prokaryotes using Sequence Data, thus avoiding complications with South Africa's biodiversity regulations. Identifying effective microsymbionts of L. diffusa and C. sericea is essential for conservation of Succulent Karoo Biome, where indigenous invasive species like Vachellia karroo and non-native Australian acacia species are present. Furthermore, targeted management practices using effective symbionts of the studied legumes can sustain the biome's socio-economic contribution through fodder provision.
Establishing African genomics and bioinformatics programs through annual regional workshops
(Nature Research, 2024-08) Sharaf, Abdoallah; Nesengani, Lucky Tendani; Hayah, Ichrak; Kuja, Josiah Ochieng; Mdyogolo, Sinebongo; Omotoriogun, Taiwo Crossby; Odogwu, Blessing Adanta; Beedessee, Girish; Smith, Rae Marvin; Barakat, Abdelhamid; Moila, Acclaim M.; El Hamouchi, Adil; Benkahla, Alia; Boukteb, Amal; Elmouhtadi, Amine; Mafwila, Antoine Lusala; Abushady, Asmaa Mohammed; Elsherif, Assem Kadry; Ahmed, Bulbul; Wairuri, Charles; Ndiribe, Charlotte C.; Ebuzome, Chukwuike; Kinnear, Craig J.; Ndlovu, Deborah-Fay; Iraqi, Driss; El Fahime, Elmostafa; Assefa, Ermias; Ouardi, Faissal; Belharfi, Fatima Zohra; Tmimi, Fatim Zohra; Markey, Fatu Badiane; Radouani, Fouzia; Zeukeng, Francis; Mvumbi, Georges Lelo; Ganesan, Hamilton; Hanachi, Mariem; Nigussie, Helen; Charoute, Hicham; Benamri, Ichrak; Mkedder, Ikram; Haddadi, Imane; Meftah-Kadmiri, Issam; Mubiru, Jackson Franco; Domelevo Entfellner, Jean-Baka Kodjo; Rokani, Joan Bayowa; Ogwang, Joel; Daiga, Jude Bigoga; Omumbo, Judy; Ideozu, Justin Eze; Errafii, Khaoula; Labuschagne, Kim; Komi, Komi Koukoura; Tonfack, Libert Brice; Hadjeras, Lydia; Ramantswana, Madeleine; Chaisi, Mamohale; Botes, Marietjie W.; Kilian, Mariette; Kvas, Marija; Melloul, Marouane; Chaouch, Melek; Khyatti, Meriem; Abdo, Michael; Phasha-Muchemenye, Mmatshepho; Hijri, Mohamed; Mediouni, Mohammed Rida; Hassan, Mohammed Ahmed; Piro, Mohammed; Mwale, Monica; Maaloum, Mossaab; Mavhunga, Mudzuli; Olivier, Nicholas Abraham; Aminou, Oumaima; Arbani, Oumayma; Souiai, Oussema; Djocgoue, Pierre Francois; Mentag, Rachid; Zipfel, Renate Dorothea; Tata, Rolland Bantar; Megnekou, Rosette; Muzemil, Sadik; Paez, Sadye; Salifu, Samson Pandam; Kagame, Samuel Paul; Selka, Sarra; Edwards, Sean; Gaouar, Semir Bechir Suheil; Reda, Shaimaa Roshdy Abdullah; Fellahi, Siham; Khayi, Slimane; Ayed, Soumia; Madisha, Thabang; Sahil, Tulsi; Udensi, Ogbuagu Ugorji; Ras, Verena; Ezebuiro, Victor; Duru, Vincent C.; David, Xavier; Geberemichael, Yonas; Tchiechoua, Yves H.; Mungloo-Dilmohamud, Zahra; Chen, Zhiliang; Happi, Christian; Kariuki, Thomas; Ziyomo, Cathrine; Djikeng, Appolinaire; Badaoui, Bouabid; Mapholi, Ntanganedzeni; Muigai, Anne; Osuji, Julian O.; Ebenezer, ThankGod Echezona
The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.
A revision of the family Cucurbitariaceae with additional new taxa from forest trees in Iran
(Springer, 2024-02) Eisvand, Payam; Mehrabi-Koushki, Mehdi; Crous, Pedro W.
The family Cucurbitariaceae is rich in species diversity and has a wide host range and geographic distribution. In this study, we identified 12 Cucurbitariaceae isolates which were obtained from disease symptoms in two forest trees in Khuzestan province, Iran. In addition, this family is reassessed using phylogenetic analyses based on DNA sequences from five nuclear regions (ITS, LSU, TUB2, TEF1α, and RPB2). The phylogenetic analyses showed that the present isolates represent one new genus, Nothocucurbitaria, and three new species, Allocucurbitaria galinsogisoli, Nothocucurbitaria izehica, and Parafenestella quercicola, which are described and illustrated. Furthermore, the genus Allocucurbitaria is emended to accommodate Seltsamia ulmi that grouped with the type species of Allocucurbitaria. Parafenestella pittospori and A. prunicola are recombined into the genera Neocucurbitaria and Nothocucurbitaria, respectively. Comparative analysis of single-locus trees revealed that the TUB2 and TEF1α can distinguish most genera and species in Cucurbitariaceae, while the ITS and LSU phylogenies show low resolution at both generic and species level. The best single-locus marker, RPB2, was able to distinguish all generic and most species lineages in Cucurbitariaceae.
A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts
(Nature Research, 2024-07) Graham, Emily B.; Camargo, Antonio Pedro; Wu, Ruonan; Neches, Russell Y.; Nolan, Matt; Paez-Espino, David; Kyrpides, Nikos C.; Jansson, Janet K.; McDermott, Jason E.; Hofmockel, Kirsten S.; Blanchard, Jeffrey L.; Liu, Xiao Jun A.; Rodrigues, Jorge L. Mazza; Freedman, Zachary B.; Baldrian, Petr; Stursova, Martina; DeAngelis, Kristen M.; Lee, Sungeun; Godoy-Vitorino, Filipa; Yeoh, Yun Kit; Cadillo-Quiroz, Hinsby; Tringe, Susannah G.; Chauhan, Archana; Cowan, Don A.; Van Goethem, Marc W.; Woyke, Tanja; Dove, Nicholas C.; Konstantinidis, Konstantinos T.; Juenger, Thomas E.; Hart, Stephen C.; Myrold, David D.; Onstott, Tullis C.; Bohannan, Brendan J.M.; Schmer, Marty R.; Palmer, Nathan A.; Nusslein, Klaus; Makhalanyane, Thulani P.; Dynarski, Katherine A.; Nas, Neslihan; Nicol, Graeme W.; Hazard, Christina; Scully, Erin D.; Jain, Kunal R.; Madamwar, Datta; Bissett, Andrew; Constant, Philippe; Oliveira, Rafael S.; Takacs-Vesbach, Cristina; Cregger, Melissa A.; Carrell, Alyssa A.; Klingeman, Dawn M.; Pietrasiak, Nicole
Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.
A comprehensive molecular phylogeny of Cephalotrichum and Microascus provides novel insights into their systematics and evolutionary history
(Naturalis Biodiversity Center and Centraalbureau voor Schimmelcultures, 2024-06) Wei, T.P.; Wu, Y.M.; Zhang, X.; Zhang, H.; Crous, Pedro W.; Jiang, Y.L.
The genera Cephalotrichum and Microascus contain ecologically, morphologically and lifestyle diverse fungi in Microascaceae (Microascales, Sordariomycetes) with a world-wide distribution. Despite previous studies having elucidated that Cephalotrichum and Microascus are highly polyphyletic, the DNA phylogeny of many traditionally morphology-defined species is still poorly resolved, and a comprehensive taxonomic overview of the two genera is lacking. To resolve this issue, we integrate broad taxon sampling strategies and the most comprehensive multi-gene (ITS, LSU, tef1 and tub2) datasets to date, with fossil calibrations to address the phylogenetic relationships and divergence times among major lineages of Microascaceae. Two previously recognised main clades, Cephalotrichum (24 species) and Microascus (49 species), were re-affirmed based on our phylogenetic analyses, as well as the phylogenetic position of 15 genera within Microascaceae. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of species belonging to Cephalotrichum and Microascus, as well as detailed descriptions and illustrations of 21 species of which eight are newly described. Furthermore, the divergence time estimates indicate that the crown age of Microascaceae was around 210.37 Mya (95 % HPD: 177.18–246.96 Mya) in the Late Triassic, and that Cephalotrichum and Microascus began to diversify approximately 27.07 Mya (95 % HPD: 20.47–34.37 Mya) and 70.46 Mya (95 % HPD: 56.96–86.24 Mya), respectively. Our results also demonstrate that multigene sequence data coupled with broad taxon sampling can help elucidate previously unresolved clade relationships.
Several Seiridium species (Sporocadaceae: Xylariales) cause cypress canker in South Africa
(Elsevier, 2025-02) Aylward, Janneke; Atkins, Sydney; Roets, Francois; Wingfield, Brenda D.; Wingfield, Michael J.; janneke.aylward@fabi.up.ac.za
Cypress canker is an important fungal disease caused by at least seven different Seiridium species. The disease has been known on Cupressaceae trees in South Africa since the 1980's, but its relevance was recently accentuated with an outbreak on native Widdringtonia nodiflora trees in the Western Cape. The causal agent, S. neocupressi, was previously unknown in the country, highlighting a lack of information regarding the disease in South Africa. The aim of this study was to investigate the occurrence of cypress canker and its causal agents across the country by sampling diseased Cupressaceae trees and reconsidering the identity of Seiridium strains previously collected in the country. Phylogenetic analyses revealed five known cypress canker pathogens and two putatively novel species. Seiridium cardinale was the most frequently isolated species in the Western Cape. Only two isolates of S. neocupressi were found outside the outbreak on Widdringtonia. Seiridium unicorne was most frequently isolated in the Gauteng and Free State provinces. Seiridium cancrinum, S. kenyanum and the two undescribed species were each recovered only in localised areas. Stem inoculations on x Hesperotropsis leylandii using S. cardinale, S. neocupressi and S. unicorne strains confirmed the pathogenicity of S. cardinale and S. neocupressi. In contrast, S. unicorne strains exhibited variable levels of aggressiveness. This study represents the first extensive consideration of cypress canker in South Africa and one of few studies on this important disease in the Southern Hemisphere
Production of fusel alcohols and fusel acetates by pathogenic fungi in the Ceratocystidaceae
(Elsevier, 2025-08) Mailula, Dineo M.; Wingfield, Brenda D.; Van der Nest, Magrieta Aletta; Hammerbacher, Almuth; almuth.hammerbacher@fabi.up.ac.za
The family Ceratocystidaceae includes economically important plant pathogens that vary in host preference and lifestyle. These fungi are believed to attract insect vectors, for their dispersal through their floral and fruity scents. This study aimed to identify the volatiles produced by a subset of fungi within the Ceratocystidaceae using gas chromatography coupled with mass spectrometry. The primary volatiles produced by most genera in the family were fusel alcohols and fusel acetates, but their emission rates differed significantly between genera and isolates from a single species. Ceratocystis albifundus collected from Protea cynaroides produced higher levels of fusel acetates compared to isolates from Terminalia sericea. In addition, significant differences in volatile biosynthesis were observed between isolates grown under different temperatures. Results of this study demonstrate that Ceratocystidaceae exhibit varied volatile profiles, but further research is needed to understand the ecological and physiological mechanisms underlying this plasticity.
CRISPR-Cas9 genome editing reveals that the Pgs gene of Fusarium circinatum is involved in pathogenicity, growth and sporulation
(Elsevier, 2025-03) Van Dijk, Alida; Wilson, Andi M.; Marx, Bianke; Hough, Bianca; Swalarsk-Parry, Benedicta S.; De Vos, Lieschen; Wingfield, Michael J.; Wingfield, Brenda D.; Steenkamp, Emma Theodora; alida.vandijk@up.ac.za
Fusarium circinatum, the causal agent of pine pitch canker, is one of the most destructive pathogens of Pinus species worldwide. Infections by this pathogen result in serious mortality of seedlings due to root and root collar disease, and growth reduction in trees due to canker formation and dieback. Although much is known about the population biology, genetics, and genomics of F. circinatum, relatively little is known regarding the molecular basis of pathogenicity in F. circinatum. In this study, a protoplast-based transformation using CRISPR-Cas9-mediated genome editing was utilized to functionally characterize a putative pathogenicity gene in three different strains of the fungus. In silico analyses suggested the gene likely encodes a small secreted protein, and all isolates in which it was deleted displayed significantly reduced vegetative growth and asexual spore production compared to the wild-type isolates. In pathogenicity tests, lesions induced by the deletion mutants on detached Pinus patula branches were significantly shorter than those produced by the wild-types. The putative pathogenicity gene was named Pgs reflecting its role in pathogenicity, growth, and sporulation. Future research will seek to explore the molecular mechanisms underlying the mutant phenotypes observed. Overall, this study represents a significant advance in F. circinatum research as the development and application of a Cas9-mediated gene deletion process opens new avenues for functional gene characterization underlying many of the pathogen's biological traits.
In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomi
(Frontiers Media, 2025-01) Harvey, Aaron Thomas; Van den Berg, Noelani; Swart, Velushka; velushka.swart@up.ac.za
The avocado industry faces a significant threat from the hemibiotrophic oomycete pathogen Phytophthora cinnamomi. A variably expressed defence gene during an avocado infection trial was a Wall-associated kinase (WAK). WAK and WAK-Like (WAKL) proteins are known to bind to fragmented pectin (oligogalacturonides) produced during pathogen penetration, thereby activating downstream defence-related pathways. To better understand the P. cinnamomi-avocado defence interaction, this gene family was assessed using in silico methods. In this study, previously generated RNA-sequencing data were used to associate genes with the defence response, followed by promoter- and phylogenetic analysis of these genes/proteins. The predicted proteins from these genes were modelled with AlphaFold2, and structural similarity across different rootstocks, as well as their binding affinity for oligogalacturonides, were assessed. The analysis identified 14 Persea americana (Pa)WAKs and 62 PaWAKLs across the West-Indian (pure accession reference), Dusa®, Leola™ and R0.12 avocado rootstock genomes. These genes showed distribution across the West-Indian genome’s chromosomes, with MCScanX analyses predicting tandem duplications. PaWAK/WAKL expression profiles were compared, implicating five PaWAK/WAKLs in defence. Phylogenetic and promoter analyses were conducted to predict associated defence-related pathways, focusing on stress and phytohormone-responsive pathways. Structural differences and varying oligogalacturonide binding affinities of PaWAK/WAKLs were predicted across rootstocks. These defence-related genes could be incorporated into a molecular screening tool to improve the development of resistant avocado rootstocks.
Flavonoids and anthocyanins in seagrasses : implications for climate change adaptation and resilience
(Frontiers Media, 2025-01) Botes, Jana; Ma, Xiao; Chang, Jiyang; Van de Peer, Yves; Berger, David Kenneth
Seagrasses are a paraphyletic group of marine angiosperms and retain certain adaptations from the ancestors of all embryophytes in the transition to terrestrial environments. Among these adaptations is the production of flavonoids, versatile phenylpropanoid secondary metabolites that participate in a variety of stress responses. Certain features, such as catalytic promiscuity and metabolon interactions, allow flavonoid metabolism to expand to produce novel compounds and respond to a variety of stimuli. As marine environments expose seagrasses to a unique set of stresses, these plants display interesting flavonoid profiles, the functions of which are often not completely clear. Flavonoids will likely prove to be effective and versatile agents in combating the new host of stress conditions introduced to marine environments by anthropogenic climate change, which affects marine environments differently from terrestrial ones. These new stresses include increased sulfate levels, changes in salt concentration, changes in herbivore distributions, and ocean acidification, which all involve flavonoids as stress response mechanisms, though the role of flavonoids in combatting these climate change stresses is seldom discussed directly in the literature. Flavonoids can also be used to assess the health of seagrass meadows through an interplay between flavonoid and simple phenolic levels, which may prove to be useful in monitoring the response of seagrasses to climate change. Studies focusing on the genetics of flavonoid metabolism are limited for this group, but the large chalcone synthase gene families in some species may provide an interesting topic of research. Anthocyanins are typically studied separately from other flavonoids. The phenomenon of reddening in certain seagrass species typically focuses on the importance of anthocyanins as a UV-screening mechanism, while the role of anthocyanins in cold stress is discussed less often. Both of these stress response functions would be useful for adaptation to climate change-induced deviations in tidal patterns and emersion. However, ocean warming will likely lead to a decrease in anthocyanin content, which may impact the performance of intertidal seagrasses. This review highlights the importance of flavonoids in angiosperm stress response and adaptation, examines research on flavonoids in seagrasses, and hypothesizes on the importance of flavonoids in these organisms under climate change.
Antibiotic resistance profiles and mutations that might affect drug susceptibility in metagenome-assembled genomes of Legionella pneumophila and Aeromonas species from municipal wastewater
(BioMed Central, 2025-04) Poopedi, Evida; Pierneef, Rian Ewald; Singh, Tanusha; Gomba, Annancietar
Please read abstract in the article.
A potent and selective reaction hijacking inhibitor of Plasmodium falciparum tyrosine tRNA synthetase exhibits single dose oral efficacy in vivo
(Public Library of Science, 2024-12-09) Xie, Stanley C.; Tai, Chia-Wei; Morton, Craig J.; Ma, Liting; Huang, Shih-Chung; Wittlin, Sergio; Du, Yawei; Hu, Yongbo; Dogovski, Con; Salimimarand, Mina; Griffin, Robert; England, Dylan; De la Cruz, Elisa; Yeo, Tomas; Burkhard, Anna Y.; Striepen, Josefine; Schindler, Kyra A.; Crespo, Benigno; Gamo, Francisco J.; Khandokar, Yogesh; Hutton, Craig A.; Rabie, Tayla Anne; Birkholtz, Lyn-Marie; Famodimu, Mufuliat T.; Delves, Michael J.; Bolsher, Judith; Koolen, Karin M.J.; Van der Laak, Rianne; Aguiar, Anna C.C.; Pereira, Dhelio B.; Guido, Rafael V.C.; Creek, Darren J.; Fidock, David A.; Dick, Lawrence R.; Brand, Stephen L.; Gould, Alexandra E.; Langston, Steven; Griffin, Michael D.W.; Tilley, Leann
The Plasmodium falciparum cytoplasmic tyrosine tRNA synthetase (PfTyrRS) is an attractive drug target that is susceptible to reaction-hijacking by AMP-mimicking nucleoside sulfamates. We previously identified an exemplar pyrazolopyrimidine ribose sulfamate, ML901, as a potent reaction hijacking inhibitor of PfTyrRS. Here we examined the stage specificity of action of ML901, showing very good activity against the schizont stage, but lower trophozoite stage activity. We explored a series of ML901 analogues and identified ML471, which exhibits improved potency against trophozoites and enhanced selectivity against a human cell line. Additionally, it has no inhibitory activity against human ubiquitin-activating enzyme (UAE) in vitro. ML471 exhibits low nanomolar activity against asexual blood stage P. falciparum and potent activity against liver stage parasites, gametocytes and transmissible gametes. It is fast-acting and exhibits a long in vivo half-life. ML471 is well-tolerated and shows single dose oral efficacy in the SCID mouse model of P. falciparum malaria. We confirm that ML471 is a reaction hijacking inhibitor that is converted into a tight binding Tyr-ML471 conjugate by the PfTyrRS enzyme. A crystal structure of the PfTyrRS/ Tyr-ML471 complex offers insights into improved potency, while molecular docking into UAE provides a rationale for improved selectivity.
Development of a molecular genetics and cell biology toolbox for the filamentous fungus Diplodia sapinea
(Public Library of Science, 2024-12-27) Oostlander, Anne Geertje; Brodde, Laura; Von Bargen, Miriam; Slippers, Bernard; Becker, Yvonne; Brandt, Ulrike; Klawonn, Frank; Grobler, Christiaan; Well, Lucas; Stenlid, Jan; Oliva, Jonas; Elfstrand, Malin; Fleissner, Andre
Diplodia sapinea (Fr.) Fuckel is a widespread fungal pathogen affecting conifers worldwide. Infections can lead to severe symptoms, such as shoot blight, canker, tree death, or blue stain in harvested wood, especially in Pinus species. Its impact on forest health is currently intensified, likely due to climate change, posing an increasing threat to global ecosystems and forestry. Despite extensive and successful research on this pathogen system, fundamental questions about its biology and plant-associated lifestyle remain unanswered. Addressing these questions will necessitate the development of additional experimental tools, including protocols for molecular genetics and cell biology approaches. In this study, we continue to address this need by establishing an Agrobacterium-mediated genetic transformation protocol for D. sapinea, enabling targeted mutagenesis and heterologous gene expression. We utilized this methodology to localize the histone H2B by tagging it with the fluorescent protein mCherry. Additionally, we established a time- and space-efficient laboratory-scale infection assay using two-week-old Pinus sylvestris seedlings. Integrating these tools in a proof-of-concept study enabled the visualization of D. sapinea in planta growth through the fluorescently labeled reporter strain.
Bacterial Isolation from natural grassland on nitrogen-free agar yields many strains without nitrogenase
(MDPI, 2025-01) Koirala, Amrit; Alshibli, Nabilah Ali; Das, Bikram K.; Brözel, Volker Siegfried
Nitrogen inputs for sustainable crop production for a growing population require the enhancement of biological nitrogen fixation. Efforts to increase biological nitrogen fixation include bioprospecting for more effective nitrogen-fixing bacteria. As bacterial nitrogenases are extremely sensitive to oxygen, most primary isolation methods rely on the use of semisolid agar or broth to limit oxygen exposure. Without physical separation, only the most competitive strains are obtained. The distance between strains provided by plating on solid media in reduced oxygen environments has been found to increase the diversity of culturable potential diazotrophic bacteria. To obtain diverse nitrogen-fixing isolates from natural grasslands, we plated soil suspensions from 27 samples onto solid nitrogen-free agar and incubated them under atmospheric and oxygen-reducing conditions. Putative nitrogen fixers were confirmed by subculturing in liquid nitrogen-free media and PCR amplification of the nifH genes. Streaking of the 432 isolates on nitrogen-rich R2A revealed many cocultures. In most cases, only one community member then grew on NFA, indicating the coexistence of nonfixers in coculture with fixers when growing under nitrogen-limited conditions. To exclude isolates able to scavenge residual nitrogen, such as that from vitamins, we used a stringent nitrogen-free medium containing only 6.42 μmol/L total nitrogen and recultured them in a nitrogen-depleted atmosphere. Surprisingly, PCR amplification of nifH using various primer pairs yielded amplicons from only 17% of the 442 isolates. The majority of the nifH PCR-negative isolates were Bacillus and Streptomyces. It is unclear whether these isolates have highly effective uptake systems or nitrogen reduction systems that are not closely aligned with known nitrogenase families. We advise caution in determining the nitrogen fixation ability of plants from growth on nitrogen-free media, even where the total nitrogen is very limited.
Associating serum testosterone levels with African ancestral prostate cancer health disparities
(Nature Research, 2025-04) Lebelo, Maphuti Tebogo; Mmekwa, Naledi; Louw, Melanie; Jaratlerdsiri, Weerachai; Mutambirwa, Shingai B.A.; Loda, Massimo; Hayes, Vanessa M.; Bornman, Maria S. (Riana); riana.bornman@up.ac.za
Serum testosterone levels decrease in the aging male, while the risk for prostate cancer (PCa) increases concomitantly. Higher levels in younger men have been linked with racially driven PCa disparities, with African men disproportionately impacted. In turn, higher levels of serum lipids have been associated with aggressive disease, while racial disparity between serum testosterone, cholesterol and cancer mortality has been suggested. Having previously reported a 2.1-fold increased age-adjusted risk for aggressive PCa in Black South African over Black American men, we determined the serum testosterone and associated lipid levels in 250 Black South African men either with or without clinicopathologically diagnosed disease. Observing no associations with serum lipid levels, Black South Africans presented with testosterone levels between 1.24 (< 60 years) and 1.3-fold (≥ 60 years) greater than Black Americans. Notably, a rapid drop in total-, bioavailable- and free testosterone levels in men 65 years or older was significantly associated with PCa risk (P = 0.0057, 0.009 and 0.005, respectively), while irrespective of age, further associated with advanced disease (P = 0.004, 0.0012 and 0.0036, respectively). These preliminary data provide insights into the potential role of androgens in driving PCa health disparities, with important consequence for tailoring treatment for Black men.

Browse

Recent Submissions