Exploring links between antisense RNAs and pathogenesis in Ustilago maydis through transcript and gene characterization

Goulet, Kristi M.; Storfie, Emilee R. M.; Saville, Barry J.

doi:10.1016/j.fgb.2019.103283

Cited by 6 publications

(4 citation statements)

References 22 publications

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“…Disease symptoms were scored at 5, 7, 10, 14, and 21 days post-infection (DPI), using the 0–8 scoring scale for U. maydis from Gold et al [ 35 ] as amended by Goulet et al [ 36 ]. The score of each plant was used to calculate an average, which was reported as the disease index (DI).…”

Section: Methodsmentioning

confidence: 99%

Fungal Pathogen Emergence: Investigations with an Ustilago maydis × Sporisorium reilianum Hybrid

Storfie

Saville

2021

JoF

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The emergence of new fungal pathogens threatens sustainable crop production worldwide. One mechanism by which new pathogens may arise is hybridization. To investigate hybridization, the related smut fungi, Ustilago maydis and Sporisorium reilianum, were selected because they both infect Zea mays, can hybridize, and tools are available for their analysis. The hybrid dikaryons of these fungi grew as filaments on plates but their colonization and virulence in Z. mays were reduced compared to the parental dikaryons. The anthocyanin induction caused by the hybrid dikaryon infections was distinct, suggesting its interaction with the host was different from that of the parental dikaryons. Selected virulence genes previously characterized in U. maydis and their predicted S. reilianum orthologs had altered transcript levels during hybrid infection of Z. mays. The downregulated U. maydis effectors, tin2, pit2, and cce1, and transcription factors, rbf1, hdp2, and nlt1, were constitutively expressed in the hybrid. Little impact was observed with increased effector expression; however, increased expression of rbf1 and hdp2, which regulate early pathogenic development by U. maydis, increased the hybrid’s capacity to induce symptoms including the rare induction of small leaf tumors. These results establish a base for investigating molecular aspects of smut fungal hybrid pathogen emergence.

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Section: Methodsmentioning

confidence: 99%

Fungal Pathogen Emergence: Investigations with an Ustilago maydis × Sporisorium reilianum Hybrid

Storfie

Saville

2021

JoF

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“…In addition, the percentage of CIMG-unique genes with significant sense transcription was only half of that in the total CIMG gene predictions, while the percentage of genes with significant antisense expressions was twice as high. Antisense expression occurs in all types of organisms and plays a variety of roles, including regulation of transcription and translation [31,34,35]. Nonetheless, the difference in the antisense prediction of CIMG-unique gene predictions and all genes predicted by the CIMG method is striking.…”

Section: Discussionmentioning

confidence: 99%

“…The number of CIMG-unique ortho genes with significant sense-strand RNA-seq counts was substantially lower than was seen in the total set of CIMG transcripts in both the mycelial and spherule phases of the organism (Figure 3). Transcription from both the sense and antisense strands occurs in many fungi [31][32][33], including C. immitis [24]. Antisense transcripts play a role in gene regulation via several mechanisms.…”

Section: Comparing All Cimg-predicted Genes To Cimg-unique Genesmentioning

confidence: 99%

“…The percentages of genes with significant sense and antisense expression in the predicted CIMG-unique ortho and total CIMG gene sets are shown in Figure 4. Transcription from both the sense and antisense strands occurs in many fungi [31][32][33], including C. immitis [24]. Antisense transcripts play a role in gene regulation via several mechanisms.…”

Section: Comparing All Cimg-predicted Genes To Cimg-unique Genesmentioning

confidence: 99%

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Evaluation of Different Gene Prediction Tools in Coccidioides immitis

Kirkland,

Beyhan,

Stajich

2023

JoF

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Gene prediction is required to obtain optimal biologically meaningful information from genomic sequences, but automated gene prediction software is imperfect. In this study, we compare the original annotation of the Coccidioides immitis RS genome (the reference strain of C. immitis) to annotations using the Funannotate and Augustus genome prediction pipelines. A total of 25% of the originally predicted genes (denoted CIMG) were not found in either the Funannotate or Augustus predictions. A comparison of Funannotate and Augustus predictions also found overlapping but not identical sets of genes. The predicted genes found only in the original annotation (referred to as CIMG-unique) were less likely to have a meaningful functional annotation and a lower number of orthologs and homologs in other fungi than all CIMG genes predicted by the original annotation. The CIMG-unique genes were also more likely to be lineage-specific and poorly expressed. In addition, the CIMG-unique genes were found in clusters and tended to be more frequently associated with transposable elements than all CIMG-predicted genes. The CIMG-unique genes were more likely to have experimentally determined transcription start sites that were further away from the originally predicted transcription start sites, and experimentally determined initial transcription was less likely to result in stable CIMG-unique transcripts. A sample of CIMG-unique genes that were relatively well expressed and differentially expressed in mycelia and spherules was inspected in a genome browser, and the structure of only about half of them was found to be supported by RNA-seq data. These data suggest that some of the CIMG-unique genes are not authentic gene predictions. Genes that were predicted only by the Funannotate pipeline were also less likely to have a meaningful functional annotation, be shorter, and express less well than all the genes predicted by Funannotate. C. immitis genes predicted by more than one annotation are more likely to have predicted functions, many orthologs and homologs, and be well expressed. Lineage-specific genes are relatively uncommon in this group. These data emphasize the importance and limitations of gene prediction software and suggest that improvements to the annotation of the C. immitis genome should be considered.

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Past, present and future of glycolipids from Ustilaginaceae – A review on cellobiose lipids and mannosylerythritol lipids

Münßinger,

Beck,

Oraby

et al. 2024

J Surfact & Detergents

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The glycolipids cellobiose lipids (CL) and mannosylerythritol lipids (MEL) are biosurfactants mainly synthesized by microorganisms of the Ustilaginaceae family. They have a large structural diversity, varying in their sugar moieties and the attached fatty acids, resulting in a prospectively broad range of applications. This literature review provides a detailed overview of known microbial producers of CL and MEL, and their respective metabolic pathways that result in different molecular structures. Further, current advances in the aerobic fermentative synthesis of the glycolipids and their purification methods are illustrated. All influencing factors identified to date with regard to the fermentation are highlighted in detail: For CL synthesis usually hydrophilic carbon sources are used as substrate, whereas hydrophobic carbon sources are usually metabolized to MEL. Nitrogen limitation was described as a major trigger for glycolipid synthesis and an acidic pH range was favored for increased CL production. An overview of applied fermentation parameters in recent publications (e.g., substrate‐concentrations, feeding approaches) demonstrates the future potential of CL and MEL production optimization. Foaming during fermentation is either combated or exploited by foam fractionation as the first purification step. The current purification processes focus on solvent extractions and chromatography in the laboratory scale and a need for development was identified for future scale‐up. Finally, environmental hotspots during CL and MEL production are presented and future optimization potentials are highlighted.

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Exploring links between antisense RNAs and pathogenesis in Ustilago maydis through transcript and gene characterization

Cited by 6 publications

References 22 publications

Fungal Pathogen Emergence: Investigations with an Ustilago maydis × Sporisorium reilianum Hybrid

Fungal Pathogen Emergence: Investigations with an Ustilago maydis × Sporisorium reilianum Hybrid

Evaluation of Different Gene Prediction Tools in Coccidioides immitis

Past, present and future of glycolipids from Ustilaginaceae – A review on cellobiose lipids and mannosylerythritol lipids

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