Ustilago maydis natural antisense transcript expression alters mRNA stability and pathogenesis

Abstract

Ustilago maydis infection of Zea mays leads to the production of thick-walled diploid teliospores that are the dispersal agent for this pathogen. Transcriptome analyses of this model biotrophic basidiomycete fungus identified natural antisense transcripts (NATs) complementary to 247 open reading frames. The U. maydis NAT cDNAs were fully sequenced and annotated. Strand-specific RT-PCR screens confirmed expression and identified NATs preferentially expressed in the teliospore. Targeted screens revealed four U. maydis NATs that are conserved in a related fungus. Expression of NATs in haploid cells, where they are not naturally occurring, resulted in increased steady-state levels of some complementary mRNAs. The expression of one NAT, as-um02151, in haploid cells resulted in a twofold increase in complementary mRNA levels, the formation of sense–antisense double-stranded RNAs, and unchanged Um02151 protein levels. This led to a model for NAT function in the maintenance and expression of stored teliospore mRNAs. In testing this model by deletion of the regulatory region, it was determined that alteration in NAT expression resulted in decreased pathogenesis in both cob and seedling infections. This annotation and functional analysis supports multiple roles for U. maydis NATs in controlling gene expression and influencing pathogenesis.

Natural antisense transcripts are linked to the modulation of mitochondrial function and teliospore dormancy in Ustilago maydis

“…The data presented here have allowed us to refine the model of NAT‐mediated mRNA stability during teliospore dormancy first proposed in Donaldson and Saville (). In the new model (Fig.…”

“…Inter‐species conservation of NAT expression is often another indicator of functionality (Ling et al ., ). A characterized NAT to the human hypoxia‐inducible factor subunit‐α (HIFα) is conserved in rodent species, with similar functional roles as the human counterpart (Rossignol et al ., ), and a NAT to the U. maydis UMAG_02151 is conserved in Ustilago hordei (Donaldson and Saville, ). The presence of a NAT to the ssm1 ortholog in U. hordei was not thoroughly assessed (data not shown), however RNA‐seq and RT‐PCR indicate that there is a NAT complementary to the S. reilianum ssm1 ortholog and that it is preferentially expressed in the teliospore (Fig.…”

“…These complexes block translation, inhibiting mitochondria function. This model is modified from a model proposed by Donaldson and Saville ().…”

Non-coding RNAs in the development and pathogenesis of eukaryotic microbes

“…Thus, lncRNAs, similar to many fast evolving proteins, are likely involved in species-specific or even strain specific virulence functions. Recently another lncRNA antisense to gene um02151 was found to be essential for Ustilago virulence (Donaldson and Saville 2013). The expression of this antisense transcript and the RNA hybrid it formed with its sense strand is high in resting spores and teliospores of U. maydis .…”

RNA Biology in Fungal Phytopathogens

“…This is supported by the observation that Khd4 localizes to processing bodies (unpublished observation), which are known centers for mRNA degradation (Figure 1, #3). The importance of regulating mRNA stability was recently further underlined by showing that natural antisense transcripts might also be important for the regulation of mRNA stability and pathogenicity (Figure 1, #4) [11].…”