The Full-Length Transcriptome of Spartina alterniflora Reveals the Complexity of High Salt Tolerance in Monocotyledonous Halophyte.

Spartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the molecular basis of its high salt tolerance remains elusive. In this study, we used Pacific Biosciences (PacBio) full-length single-molecule long-read sequencing and RNA-seq to elucidate the transcriptome dynamics of high salt tolerance in Spartina by salt gradient experiments. High-quality unigenes, transcription factors, non-coding RNA and Spartina-specific transcripts were identified. Co-expression network analysis found that protein kinase-encoding genes (SaOST1, SaCIPK10 and SaLRRs) are hub genes in the salt tolerance regulatory network. High salt stress induced the expression of transcription factors but repressed the expression of long non-coding RNAs. The Spartina transcriptome is closer to rice than Arabidopsis, and a higher proportion of transporter and transcription factor-encoding transcripts have been found in Spartina. Transcriptome analysis showed that high salt stress induced the expression of carbohydrate metabolism, especially cell-wall biosynthesis-related genes in Spartina, and repressed its expression in rice. Compared with rice, high salt stress highly induced the expression of stress response, protein modification and redox-related gene expression and greatly inhibited translation in Spartina. High salt stress also induced alternative splicing in Spartina, while differentially expressed alternative splicing events associated with photosynthesis were overrepresented in Spartina but not in rice. Finally, we built the SAPacBio website for visualizing full-length transcriptome sequences, transcription factors, ncRNAs, salt-tolerant genes and alternative splicing events in Spartina. Overall, this study suggests that the salt tolerance mechanism in Spartina is different from rice in many aspects and is far more complex than expected.

sRNA profiling in Aspergillus flavus reveals differentially expressed miRNA-like RNAs response to water activity and temperature.

Small non-coding RNA (sRNA) in various organisms remains a mysterious subject. Although microRNAs (miRNAs) have been intensively investigated in plants and animals, the study of miRNAs in fungi has been limited. Only microRNA-like RNAs (milRNAs) have been reported in several filamentous fungi. In this study, Illumina deep sequencing was performed to characterize the sRNA in Aspergillus flavus and to evaluate their responses to water activity and temperature. Global expression analysis showed an extensively differential expression of sRNA loci in A. flavus under different temperature or water activities. In addition, a total of 135 milRNAs were identified in A. flavus. The milRNA profiles obtained in deep sequencing were further validated by RT-qPCR assay. The presence and differential expression of milRNAs under different temperature or water activities in A. flavus imply that milRNAs might play important roles in the mycotoxin biosynthesis and mycelium growth in fungi A. flavus.

Characterization of the Bifunctional Enzyme BioDA Involved in Biotin Synthesis and Pathogenicity in Aspergillus flavus.

Biotin is an important enzyme cofactor that plays a key role in all three domains. The classical bifunctional enzyme BioDA in eukaryotes (such as Aspergillus flavus and Arabidopsis thaliana) is involved in the antepenultimate and penultimate steps of biotin biosynthesis. In this study, we identified a A. flavus bifunctional gene bioDA which could complement both Escherichia coli ΔEcbioD and ΔEcbioA mutants. Interestingly, the separated domain of AfBioD and AfBioA could, respectively, fuse with EcBioA and EcBioD well and work together. What is more, we found that BioDA was almost localized to the mitochondria in A. flavus, as shown by N-terminal red fluorescent protein tag fusion. Noteworthy, the subcellular localization of AfBioDA is never affected by common environmental stresses (such as hyperosmotic stress or oxidative stress). The knockout strategy demonstrated that the deletion of AfbioDA gene from the chromosome impaired the biotin de novo synthesis pathway in A. flavus. Importantly, this A. flavus mutant blocked biotin production and decreased its pathogenicity to infect peanuts. Based on the structural comparison, we found that two inhibitors (amiclenomycin and gemcitabine) could be candidates for antifungal drugs. Taken together, our findings identified the bifunctional AfbioDA gene and shed light on biotin biosynthesis in A. flavus.

Study on the bio-function of lipA gene in Aspergillus flavus.

Lipoic acid synthase (LipA) plays a role in lipoic acid synthesis and potentially affects the levels of acetyl-CoA, the critical precursor of tricarboxylic acid (TCA) cycle. Considering the potential effect of LipA on TCA cycle, whether the enzyme is involved in the growth and aflatoxin B1 (AFB1) biosynthesis, the significant events in Aspergillus flavus is yet known. The study was designed to explore the role of lipA gene in A. flavus, including growth rate, conidiation, sclerotia formation, and biosynthesis of AFB1. LipA coding lipoic acid synthetase was knocked out using homologous recombination. The role of lipA gene in A. flavus morphogenesis (including colony size, conidiation, and sclerotia formation) was explored on various media, and the bio-function of lipA gene in the biosynthesis of AFB1 was analyzed by thin layer chromatography analysis. The growth was suppressed in △lipA. The formation of conidia and sclerotia was also reduced when lipA gene was deleted. Moreover, AFB1 was down-regulated in ΔlipA compared with WT controls. LipA plays a role in the development of A. flavus and AFB1 biosynthesis, contributing to the full understanding of the lipA bio-function in A. flavus.

Inhibition of aflatoxin metabolism and growth of Aspergillus flavus in liquid culture by a DNA methylation inhibitor.

Aflatoxins (AFs) are a group of highly oxygenated polyketidese-derived toxins mainly produced by Aspergillus flavus and A. parasiticus, whose biosynthesis mechanisms are extremely sophisticated. Methylation is known as the major form of epigenetic regulation, which is correlated with gene expression. As the DNA methylation inhibitor 5-azacytidine (5-AC) blocks AF production, we studied AFB1 metabolism and morphological changes of A. flavus by treatment with 5-AC in liquid culture. The results show that 5-AC caused a decrease in AF production and concurrent changes in morphology. In addition, we isolated a non-aflatoxigenic mutant of A. flavus, showing a significant reduction in pigment production, after 5-AC treatment. This mutant showed significant reduction in the expression of genes in the AF biosynthesis pathway, and conidia formation. Furthermore, as AF biosynthesis and oxidative stress are intimately related events, we assessed the viability of A. flavus to oxidative stress after treatment with 5-AC, which showed that the mutant was more sensitive to the strong oxidant hydrogen peroxide. We found that the non-aflatoxigenic mutant showed a decrease in reactive oxygen species (ROS) and metabolites indicative of oxidative stress, which may be caused by the disruption of the defence system against excessive ROS formation after 5-AC treatment. These data indicate that 5-AC, as an inactivator of DNA methyltransferase, plays a very important role in AFB1 metabolism and the development of A. flavus, which might provide an effective strategy to pre- or post-harvest control of AFs.