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...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.展开更多
Synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU). Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have be...Synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU). Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have been calculated, and codon-anticodon binding strength has been estimated by the stacking energies of codon-anticodon bases in Watson-Crick pairs. The data show common features in synonymous codon bias for all codon families in human genes: all C-ending codons, which possess the strongest codon-anticodon binding energies, are the most favored codons in almost all codon families, and those codons with medium codon-anticodon binding energies are avoided. Data analysis suggests that besides isochore and genome signature, codon-anticodon binding strength may be closely related to synonymous codon choice in human genes. The join-effect of these factors on human genes results in the common features in codon bias.展开更多
基金This work was supported by the National Basic Research Program of China(2013CB127500)the National Natural Science Foundation of China(31160021,31270131 and U1502262)+1 种基金sponsored by the Nanjing University of Posts and Telecommunications Scientific Foundation(NUPTSF)(NY218140)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.
文摘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.
基金This work was supported by the National Natural Science Foundation of China (Grant No. 39970412) and the sub-project of the "95" Key Project of the Chinese Academy of Sciences.
文摘Synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU). Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have been calculated, and codon-anticodon binding strength has been estimated by the stacking energies of codon-anticodon bases in Watson-Crick pairs. The data show common features in synonymous codon bias for all codon families in human genes: all C-ending codons, which possess the strongest codon-anticodon binding energies, are the most favored codons in almost all codon families, and those codons with medium codon-anticodon binding energies are avoided. Data analysis suggests that besides isochore and genome signature, codon-anticodon binding strength may be closely related to synonymous codon choice in human genes. The join-effect of these factors on human genes results in the common features in codon bias.
