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

Characterization of RNA Helicase Genes in Ustilago maydis Reveals Links to Stress Response and Teliospore Dormancy

Fungi produce dormant structures that are responsible for protection during adverse environmental conditions and dispersal (disease spread). Ustilago maydis, a basidiomycete plant pathogen, is a model for understanding the molecular mechanisms of teliospore dormancy and germination. Dormant teliospores store components required for germination including mRNAs which may be stored as dsRNAs. RNA helicases are conserved enzymes that function to modulate, bind, and unwind RNA duplexes, and can displace other proteins. We hypothesize that RNA helicases function during teliospore dormancy to stabilize and/or modulate stored mRNAs. We identified the U. maydis udbp3 and uded1 as encoding RNA helicases of interest as they are upregulated in the dormant teliospore and decrease during germination. Experimental results suggest that udbp3 may function as a negative regulator of osmotic stress-responsive genes and that uded1 modulates stress response by repressing translation. The altered expression of uded1 also results in slow growth, polarized growth, and the formation of dsRNA. Together, the data support a role for both helicases modulating gene expression, in response to stress, leading to teliospore dormancy and also modulating responses for teliospore germination. Increasing our molecular understanding of these processes will aid in developing novel strategies to mitigate disease spread.

Correlation Between Effector Gene Expression Targeted by lncRNAs in the Oomycete Fish Pathogen, Saprolegnia parasitica

Saprolegniasis caused by Saprolegnia parasitica leads to significant economic losses in the aquaculture industry worldwide. Effector proteins secreted by pathogens are key molecules involved in their pathogenicity and long non-coding lncRNAs (lncRNAs) act as regulators in these processes. However, little is known about the lncRNAs and effector proteins in S. parasitica. Here, we first identified 1027 lncRNAs during the developmental stages and infection process of S. parasitica. Compared with mRNAs, these lncRNAs had shorter sequences and exon lengths and lower expression levels. In addition, their sequence conservation among other oomycete species was also low. The S. parasitica lncRNAs were characterized according to developmental stage and infection time point. We also identified effector proteins using a computational pipeline. In total, 131 S. parasitica effector proteins were identified and classified into 34 families. The 47 genes encoding effector genes were neighbors of 39 lncRNAs, and there was a correlation between the transcription level of lncRNAs and their neighboring genes. Gain- and loss-of-function experiments revealed that lncRNA8375.2 promoted the expression of a neighboring effector gene, SpCAP. Our results provide new data on S. parasitica lncRNAs and effector proteins, and provide insights into the lncRNA-effector module involved in S. parasitica.

Candidate effectors for leaf rust resistance gene Lr28 identified through transcriptome and in-silico analysis

Puccinia spp. causing rust diseases in wheat and other cereals secrete several specialized effector proteins into host cells. Characterization of these proteins and their interaction with host's R proteins could greatly help to limit crop losses due to diseases. Prediction of effector proteins by combining the transcriptome analysis and multiple in-silico approaches is gaining importance in revealing the pathogenic mechanism. The present study involved identification of 13 Puccinia triticina (Pt) coding sequences (CDSs), through transcriptome analysis, that were differentially expressed during wheat-leaf rust interaction; and prediction of their effector like features using different in-silico tools. NCBI-BLAST and pathogen-host interaction BLAST (PHI-BLAST) tools were used to annotate and classify these sequences based on their most closely matched counterpart in both the databases. Homology between CDSs and the annotated sequences in the NCBI database ranged from 79 to 94% and with putative effectors of other plant pathogens in PHI-BLAST from 24.46 to 54.35%. Nine of the 13 CDSs had effector-like features according to EffectorP 3.0 (≥0.546 probability of these sequences to be effector). The qRT-PCR expression analysis revealed that the relative expression of all CDSs in compatible interaction (HD2329) was maximum at 11 days post inoculation (dpi) and that in incompatible interactions (HD2329 + Lr28) was maximum at 3 dpi in seven and 9 dpi in five CDSs. These results suggest that six CDSs (>0.8 effector probability as per EffectorP 3.0) could be considered as putative Pt effectors. The molecular docking and MD simulation analysis of these six CDSs suggested that candidate Lr28 protein binds more strongly to candidate effector c14094_g1_i1 to form more stable complex than the remaining five. Further functional characterization of these six candidate effectors should prove useful for a better understanding of wheat-leaf rust interaction. In turn, this should facilitate effector-based leaf rust resistance breeding in wheat.

Seryl-tRNA Synthetase Shows a Noncanonical Activity of Upregulating Laccase Transcription in Trametes hirsuta AH28-2 Exposed to Copper Ion

The function of Seryl-tRNA synthetase in fungi during gene transcription regulation beyond translation has not been reported. Here, we report a seryl-tRNA synthetase, ThserRS, which can negatively regulate laccase lacA transcription in Trametes hirsuta AH28-2 under exposure to copper ion. ThserRS was obtained through yeast one-hybrid screening using a bait sequence of lacA promoter (-502 to -372 bp). ThserRS decreased while lacA increased at the transcription level in T. hirsuta AH28-2 in the first 36 h upon CuSO4 induction. Then, ThserRS was upregulated, and lacA was downregulated. ThserRS overexpression in T. hirsuta AH28-2 resulted in a decrement in lacA transcription and LacA activity. By comparison, ThserRS silencing led to increased LacA transcripts and activity. A minimum of a 32-bp DNA fragment containing two putative xenobiotic response elements could interact with ThserRS, with a dissociation constant of 919.9 nM. ThserRS localized in the cell cytoplasm and nucleus in T. hirsuta AH28-2 and was heterologously expressed in yeast. ThserRS overexpression also enhanced mycelial growth and oxidative stress resistance. The transcriptional level of several intracellular antioxidative enzymes in T. hirsuta AH28-2 was upregulated. Our results demonstrate a noncanonical activity of SerRS that acts as a transcriptional regulation factor to upregulate laccase expression at an early stage after exposure to copper ions. IMPORTANCE Seryl-tRNA synthetase is well known for the attachment of serine to the corresponding cognate tRNA during protein translation. In contrast, its functions beyond translation in microorganisms are underexplored. We performed in vitro and cell experiments to show that the seryl-tRNA synthetase in fungi with no UNE-S domain at the carboxyl terminus can enter the nucleus, directly interact with the promoter of the laccase gene, and negatively regulate the fungal laccase transcription early upon copper ion induction. Our study deepens our understanding of the Seryl-tRNA synthetase noncanonical activities in microorganisms. It also demonstrates a new transcription factor for fungal laccase transcription.

Endophytic bacterium Pseudomonas protegens suppresses mycelial growth of Botryosphaeria dothidea and decreases its pathogenicity to postharvest fruits

Apple (Malus domestica Borkh.), one of the most economically important fruits widely consumed worldwide, has been suffering from apple ring rot caused by Botryosphaeria dothidea, which dramatically affects its quality and yield. In the present study, we demonstrated that Pseudomonas protegens, isolated from Chinese leek (Allium tuberosum), significantly suppressed the mycelial growth and propagation of B. dothidea, respectively, further displayed a considerably inhibitory effect on the apple ring rot of postharvest fruits. In addition, P. protegens significantly improved the total soluble solid/titrable acidity (TSS/TA) ratio and soluble sugar/titrable acidity (SS/TA) ratio and drastically maintained the fruit firmness. Further analysis manifested that P. protegens substantially induced the defense-related genes such as MdGLU, MdPAL, MdPOD, MdCAL, and transcription factors related to the resistance to B. dothidea, including MdWRKY15, MdPUB29, MdMyb73, and MdERF11 in apple fruits. Meanwhile, P. protegens considerably restrained the expressions of the pathogenicity-related genes in B. dothidea, including the BdCYP450, BdADH, BdGHY, BdATS, Bdα/β-HY, and BdSTR. By inference, P. protegens inhibited the apple ring rot on postharvest fruits by activating the defense system of apple fruit and repressing the pathogenic factor of B. dothidea. The study provided a theoretical basis and a potential alternative to manage the apple ring rot on postharvest fruits.

lncRsp1, a long noncoding RNA, influences Fgsp1 expression and sexual reproduction in Fusarium graminearum

Long noncoding RNAs (lncRNAs) are crucial regulators of gene expression in many biological processes, but their biological functions remain largely unknown, especially in fungi. Fusarium graminearum is an important pathogen that causes the destructive disease Fusarium head blight (FHB) or head scab disease on wheat and barley. In our previous RNA sequencing (RNA-Seq) study, we discovered that lncRsp1 is an lncRNA that is located +99 bp upstream of a putative sugar transporter gene, Fgsp1, with the same transcription direction. Functional studies revealed that ΔlncRsp1 and ΔFgsp1 were normal in growth and conidiation but had defects in ascospore discharge and virulence on wheat coleoptiles. Moreover, lncRsp1 and Fgsp1 were shown to negatively regulate the expression of several deoxynivalenol (DON) biosynthesis genes, TRI4, TRI5, TRI6, and TRI13, as well as DON production. Further analysis showed that the overexpression of lncRsp1 enhanced the ability of ascospore release and increased the mRNA expression level of the Fgsp1 gene, while lncRsp1-silenced strains reduced ascospore discharge and inhibited Fgsp1 expression during the sexual reproduction stage. In addition, the lncRsp1 complementary strains lncRsp1-LC-1 and lncRsp1-LC-2 restored ascospore discharge to the level of the wild-type strain PH-1. Taken together, our results reveal the distinct and specific functions of lncRsp1 and Fgsp1 in F. graminearum and principally demonstrate that lncRsp1 can affect the release of ascospores by regulating the expression of Fgsp1.

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

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.

A novel antisense long non-coding RNA participates in asexual and sexual reproduction by regulating the expression of GzmetE in Fusarium graminearum

Fusarium graminearum is an important worldwide pathogen that causes Fusarium head blight in wheat, barley, maize and other grains. LncRNAs play important roles in many biological processes, but little is known about their functions and mechanisms in filamentous fungi. Here, we report that a natural antisense RNA, GzmetE-AS, is transcribed from the opposite strand of GzmetE. GzmetE encodes a homoserine O-acetyltransferase, which is important for sexual development and plant infection. The expression of GzmetE-AS was increased significantly during the conidiation stage, while GzmetE was upregulated in the late stage of sexual reproduction. Overexpression of GzmetE-AS inhibited the transcription of GzmetE. In contrast, the expression of GzmetE was significantly increased in GzmetE-AS transcription termination strain GzmetE-AS-T. Furthermore, GzmetE-AS-T produced more perithecia and facilitated the ascospore discharge, resembling the phenotype of GzmetE overexpressing strains. However, overexpression of GzmetE-AS in ∆dcl1/2 strain cannot inhibit the expression of GzmetE, and the GzmetE nat-siRNA is also significantly reduced in ∆dcl1/2 mutant. Taken together, we have identified a novel antisense lncRNA GzmetE-AS, which is involved in asexual and sexual reproduction by regulating its antisense gene GzmetE through RNAi pathway. Our findings reveal that the lncRNA plays critical roles in the development of F. graminearum.

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

Biotrophic basidiomycete plant pathogens cause billions of dollars in losses to cereal crops annually. The model for this group of fungi is the corn smut pathogen Ustilago maydis. Annotation of its genome identified antisense RNAs (asRNAs) complementary to over half of the coded mRNAs, some of which are present at high levels in teliospores but detected at very low levels or not at all in other cell types, suggesting they have a function in the teliospore or during teliospore formation. Expression of three such asRNAs (as-UMAG_02150, ncRNA1, and as-UMAG_02151) is controlled by two adjacent genomic regions. Deletion of these regions increased transcript levels of all three asRNAs and attenuated pathogenesis. This study investigated the reason for this marked reduction in pathogenesis by: (1) using deletion analyses to assess the involvement of genes, complementary to the asRNAs, in pathogenesis; (2) determining that one of the linked genes encodes a putative xylitol dehydrogenase; and (3) identifying and functionally characterizing asRNAs that could influence expression of protein-coding genes. The results presented suggest that the influence of the asRNAs on pathogenesis occurs through their action at unlinked loci.

Genome-wide identification of long non-coding RNAs suggests a potential association with effector gene transcription in Phytophthora sojae

Numerous long non-coding RNAs (lncRNAs) identified and characterized in mammals, plants and fungi have been found to play critical regulatory roles in biological processes. However, little is known about the role of lncRNAs in oomycete plant pathogens, which cause devastating damage to the economy and ecosystems. We used strand-specific RNA sequencing (RNA-seq) to generate a computational pipeline to identify lncRNAs in Phytophthora sojae, a model oomycete plant pathogen. In total, 940 lncRNAs with 1010 isoforms were identified from RNA-seq data obtained from four representative stages of P. sojae. The lncRNAs had shorter transcript lengths, longer exon lengths, fewer numbers of exons, lower GC content and higher minimum free energy values compared with protein-coding genes. lncRNAs in P. sojae exhibited low sequence conservation amongst oomycetes and P. sojae isolates. Transcriptional data indicated that P. sojae lncRNAs tended to be transcribed in a stage-specific manner; representative lncRNAs were validated by semi-quantitative reverse transcription-polymerase chain reaction. Phytophthora sojae lncRNAs were concentrated in gene-sparse regions, and lncRNAs were associated with secreted protein and effector coding genes. The neighbouring genes of lncRNAs encoded various effector family members, and RNA-seq data revealed a correlation between the transcription level of lncRNAs and their neighbouring genes. Our results provide the first comprehensive identification of lncRNAs in oomycetes and suggest a potential association between lncRNAs and effector genes.

Investigating Teliospore Germination Using Microrespiration Analysis and Microdissection

Smut fungi are the etiological agents of several devastating agricultural diseases. They are characterized by the production of teliospores, which are thick-walled dispersal agents. Teliospores can remain dormant for decades. The dormancy is characterized by low metabolic rates, paused macromolecular biosynthesis and greatly reduced levels of respiration. Upon receiving required environmental signals, teliospores germinate to produce haploid cells, which can initiate new rounds of infection. Teliospore germination is characterized by the resumption of macromolecular biosynthesis, increased respiration and dramatic morphological changes. In order to precisely measure changes in cellular respiration during the early stages of germination, we have developed a simple protocol employing a Clark-type respirometer. The later stages of germination are distinguished by specific morphological changes, but germination is asynchronous. We developed a microdissection technique that enables us to collect teliospores at distinct germination stages.

Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

Background

Biotrophic fungal plant pathogens cause billions of dollars in losses to North American crops annually. The model for functional investigation of these fungi is Ustilago maydis. Its 20.5 Mb annotated genome sequence has been an excellent resource for investigating biotrophic plant pathogenesis. Expressed-sequence tag libraries and microarray hybridizations have provided insight regarding the type of transcripts produced by U. maydis but these analyses were not comprehensive and there were insufficient data for transcriptome comparison to other smut fungi. To improve transcriptome annotation and enable comparative analyses, comprehensive strand-specific RNA-seq was performed on cell-types of three related smut species: U. maydis (common smut of corn), Ustilago hordei (covered smut of barley), and Sporisorium reilianum (head smut of corn).

Results

In total, >1 billion paired-end sequence reads were obtained from haploid cell, dikaryon and teliospore RNA of U. maydis, haploid cell RNA of U. hordei, and haploid and dikaryon cell RNA of S. reilianum. The sequences were assembled into transfrags using Trinity, and updated gene models were created using PASA and categorized with Cufflinks Cuffcompare. Representative genes that were predicted for the first time with these RNA-seq analyses and genes with novel annotation features were independently assessed by reverse transcriptase PCR. The analyses indicate hundreds more predicted proteins, relative to the previous genome annotation, could be produced by U. maydis from altered transcript forms, and that the number of non-coding RNAs produced, including transcribed intergenic sequences and natural antisense transcripts, approximately equals the number of mRNAs. This high representation of non-coding RNAs appears to be a conserved feature of the smut fungi regardless of whether they have RNA interference machinery. Approximately 50% of the identified NATs were conserved among the smut fungi.

Conclusions

Overall, these analyses revealed: 1) smut genomes encode a number of transcriptional units that is twice the number of annotated protein-coding genes, 2) a small number of intergenic transcripts may encode proteins with characteristics of fungal effectors, 3) the vast majority of intergenic and antisense transcripts do not contain ORFs, 4) a large proportion of the identified antisense transcripts were detected at orthologous loci among the smut fungi, and 5) there is an enrichment of functional categories among orthologous loci that suggests antisense RNAs could have a genome-wide, non-RNAi-mediated, influence on gene expression in smut fungi.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3720-8) contains supplementary material, which is available to authorized users.