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SCIENCE CHINA Life Sciences, https://doi.org/10.1007/s11427-018-9437-7

The lifestyle transition of Arthrobotrys oligospora is mediated by microRNA-like RNAs

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  • ReceivedNov 29, 2018
  • AcceptedDec 27, 2018
  • PublishedApr 15, 2019

Abstract

The lifestyle transition of fungi, defined as switching from taking organic material as nutrients to pathogens, is a fundamental phenomenon in nature. However, the mechanisms of such transition remain largely unknown. Here we show microRNA-like RNAs (milRNAs) play a key role in fungal lifestyle transition for the first time. We identified milRNAs by small RNA sequencing in Arthrobotrys oligospora, a known nematode-trapping fungus. Among them, 7 highly expressed milRNAs were confirmed by northern-blot analysis. Knocking out two milRNAs significantly decreased A. oligospora’s ability to switch lifestyles. We further identified that two of these milRNAs were associated with argonaute protein QDE-2 by RNA-immunoprecipitation (RIP) analysis. Three of the predicted target genes of milRNAs were found in immunoprecipitation (IP) products of QDE-2. Disruption of argonaute gene qde-2 also led to serious defects in lifestyle transition. Interestingly, knocking out individual milRNAs or qde-2 lead to diverse responses under different conditions, and qde-2 itself may be targeted by the milRNAs. Collectively, it indicates the lifestyle transition of fungi is mediated by milRNAs through RNA interference (RNAi) machinery, revealing the wide existence of miRNAs in fungi kingdom and providing new insights into understanding the adaptation of fungi from scavengers to predators and the mechanisms underlying fungal infections.


Funded by

the National Basic Research Program of China(2013CB127500)

the National Natural Science Foundation of China(31160021,31270131,U1502262)

sponsored by the Nanjing University of Posts and Telecommunications Scientific Foundation(NUPTSF)

a grant(2018KF003)


Acknowledgment

This work was supported by the National Basic Research Program of China (2013CB127500), the National Natural Science Foundation of China (31160021, 31270131 and U1502262) and sponsored by the Nanjing University of Posts and Telecommunications Scientific Foundation (NUPTSF) (NY218140) and a grant (2018KF003) from YNCUB. We thank BGI-Shenzhen who contributed to the small RNA sequencing projects. We thank H. Yin for comments and discussion.


Interest statement

The author(s) declare that they have no conflict of interest.


Supplement

SUPPORTING INFORMATION

Fugure S1 Core component genes of RNAi machinery in genome of A. oligospora.

Figure S2 Gene expression of qde-2.

Figure S3 Position distribution of predicted milRNAs.

Figure S4 Structures of milRNAs.

Figure S5 Disruption of milRNAs.

Figure S6 Myc-tagged QDE-2.

Figure S7 Disruption of qde-2.

Figure S8 Venn diagrams of target prediction of milRNAs.

Figure S9 Flowchart of small RNA analysis.

Figure S10 Target prediction of putative milRNAs.

Table S1 List of core component genes of RNAi machinery in genome of A. oligospora

Table S2 Small RNA sequencing

Table S3 Confirmed milRNAs

Table S4 Comparative analysis in M. haptotylum

The supporting information is available online at http://life.scichina.com and https://link.springer.com. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.


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  • Figure 1

    MilRNAs exist in A. oligospora. A, A. oligospora develops adhesive networks to trap nematode. B, Length distribution of small RNAs. C, 5′-distribution of predicted milRNAs. D, MilRNAs were confirmed by RT-PCR. E, MilRNAs were confirmed by northern blot analysis. F, Stem-loop structure of mil-289. Seed region was shown in yellow; 5′-U was marked in red circle; mature sequence was shown in blue. AN, adhesive network; WT, wildtype; W, water; M, marker; nt, nucleotide; U6, U6 snRNA.

  • Figure 2

    MilRNAs function in trap induction and are associated with QDE-2. A, mil-289, mil-764 and mil-799 showed up-regulation during trap induction. “X” represents no expression detected. B, Ability of mil-289 deletion strains to develop traps was reduced on induction of urea. C, Ability of mil-799 deletion strains to develop traps was reduced on induction of urea. D, Immunoprecipitation of QDE-2 was confirmed by western blot analysis. E, mil-764 and mil-289 can be detected in immunoprecipitated Myc-QDE-2 by qPCR analysis. WT, wild type; AN, adhesive network; U6, U6 snRNA; IP, immunoprecipitation; kD, kilo dalton; AoΔmyc-qde-2, myc-tagged strain.

  • Figure 3

    QDE-2 functions in trap induction. A, Nematode capturing was seriously interfered in qde-2 deletion strain. Photos were taken 14, 26, 38 and 48 h after induced by live nematode. B, Trap formation was seriously interfered in qde-2 deletion strain induced by nematode extracts. After 48 h induction, compared with WT (top), almost no traps (bottom left) or much less traps (bottom right) were observed in deletion strain. C, Knockout of qde-2 disables trap formation on induction of urea. WT, wild type; AoΔqde-2, qde-2 deletion strain; AN, adhesive network.

  • Figure 4

    Target analysis provides clues to mechanisms for milRNAs in pathogenic adaptation of nematode-trapping fungi. A, Three putative target mRNAs of mil-289 were detected in RIP products of QDE-2. B, qPCR analysis showed that the two genes were up-regulated in mil-289 deletion strain. C, Qde-2 was down-regulated during trap induction and recovered after trap formation. D, Predicted interaction between mil-289 and qde-2 mRNA. E, Western blot analysis showed the expression of QDE-2 in transient gene expression system in tobacco and non-expression by mil-289. F, Both green and red florescence were detected in guard cells. The green fluorescence showed expression of QDE-2. The red fluorescence showed chloroplast. G, Only red florescence was detected in the guard cells after injection of mil-289. The expression of QDE-2 was inhibited by mil-289. H, The milRNAs interfere with targets with the aid of QDE-2 and regulate the pathogenic transition of nematode-trapping fungi on induction of different inducers, including live nematodes, nematode extracts and urea. The milRNAs could be generated via multiple pathways. The argonaute gene qde-2 itself could be regulated by milRNAs and achieves a dynamic balance through regulatory loops. WT, wild type; M, marker; GFP, green fluorescent protein; AoΔmil-289, mil-289 deletion strain; =, wild type with immunoprecipitation; *, tagged strain AoΔmyc-qde-2 with immunoprecipitation; CP, chloroplast; AN, adhesive network; RISC, RNA-induced silencing complex.

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