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Global analyses of small interfering RNAs derived from Bamboo mosaic virus and its associated satellite RNAs in different plants.

Lin KY, Cheng CP, Chang BC, Wang WC, Huang YW, Lee YS, Huang HD, Hsu YH, Lin NS - PLoS ONE (2010)

Bottom Line: Most of the BaMV and satBaMV siRNAs were 21 or 22 nt, of both (+) and (-) polarities; however, a higher proportion of 22-nt BaMV and satBaMV siRNAs were generated in N. benthamiana than in A. thaliana.Furthermore, the proportion of non-viral 24-nt siRNAs was greatly increased in N. benthamiana after virus infection.DCL2 producing 24-nt siRNAs under biotic stresses may play a vital role in the antiviral mechanism in N. benthamiana.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan.

ABSTRACT

Background: Satellite RNAs (satRNAs), virus parasites, are exclusively associated with plant virus infection and have attracted much interest over the last 3 decades. Upon virus infection, virus-specific small interfering RNAs (vsiRNAs) are produced by dicer-like (DCL) endoribonucleases for anti-viral defense. The composition of vsiRNAs has been studied extensively; however, studies of satRNA-derived siRNAs (satsiRNAs) or siRNA profiles after satRNA co-infection are limited. Here, we report on the small RNA profiles associated with infection with Bamboo mosaic virus (BaMV) and its two satellite RNAs (satBaMVs) in Nicotiana benthamiana and Arabidopsis thaliana.

Methodology/principal findings: Leaves of N. benthamiana or A. thaliana inoculated with water, BaMV alone or co-inoculated with interfering or noninterfering satBaMV were collected for RNA extraction, then large-scale Solexa sequencing. Up to about 20% of total siRNAs as BaMV-specific siRNAs were accumulated in highly susceptible N. benthamiana leaves inoculated with BaMV alone or co-inoculated with noninterfering satBaMV; however, only about 0.1% of vsiRNAs were produced in plants co-infected with interfering satBaMV. The abundant region of siRNA distribution along BaMV and satBaMV genomes differed by host but not by co-infection with satBaMV. Most of the BaMV and satBaMV siRNAs were 21 or 22 nt, of both (+) and (-) polarities; however, a higher proportion of 22-nt BaMV and satBaMV siRNAs were generated in N. benthamiana than in A. thaliana. Furthermore, the proportion of non-viral 24-nt siRNAs was greatly increased in N. benthamiana after virus infection.

Conclusions/significance: The overall composition of vsiRNAs and satsiRNAs in the infected plants reflect the combined action of virus, satRNA and different DCLs in host plants. Our findings suggest that the structure and/or sequence demands of various DCLs in different hosts may result in differential susceptibility to the same virus. DCL2 producing 24-nt siRNAs under biotic stresses may play a vital role in the antiviral mechanism in N. benthamiana.

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The distribution of siRNAs on the BaMV (A) and satBaMV (B) genome from A. thaliana.The siRNAs are shown in red above (positive strand) or in green below (negative strand) the horizontal line. X axis represents the length of the genome, and Y axis represents the counts of the siRNAs.
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pone-0011928-g007: The distribution of siRNAs on the BaMV (A) and satBaMV (B) genome from A. thaliana.The siRNAs are shown in red above (positive strand) or in green below (negative strand) the horizontal line. X axis represents the length of the genome, and Y axis represents the counts of the siRNAs.

Mentions: Regarding the distribution of vsiRNAs, most of the BaMV siRNAs from A. thaliana were derived from the first 5′ half of the genome with or without BSF4 co-inoculation (Figure 7 and data not shown). This finding is in contrast to results of vsiRNAs from N. benthamiana being largely generated from the CP and 3′ UTR regions (Figure 5). However, the distribution patterns of BSF4 siRNAs on the satBaMV genome were similar in N. benthamiana and A. thaliana (Figures 5B and 7B). In A. thaliana, the mean GC % of BaMV siRNAs (50.84%) was comparable to that of the viral genome (50.53%), but that of satBaMV siRNAs (49.81%) was a bit lower.


Global analyses of small interfering RNAs derived from Bamboo mosaic virus and its associated satellite RNAs in different plants.

Lin KY, Cheng CP, Chang BC, Wang WC, Huang YW, Lee YS, Huang HD, Hsu YH, Lin NS - PLoS ONE (2010)

The distribution of siRNAs on the BaMV (A) and satBaMV (B) genome from A. thaliana.The siRNAs are shown in red above (positive strand) or in green below (negative strand) the horizontal line. X axis represents the length of the genome, and Y axis represents the counts of the siRNAs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2914070&req=5

pone-0011928-g007: The distribution of siRNAs on the BaMV (A) and satBaMV (B) genome from A. thaliana.The siRNAs are shown in red above (positive strand) or in green below (negative strand) the horizontal line. X axis represents the length of the genome, and Y axis represents the counts of the siRNAs.
Mentions: Regarding the distribution of vsiRNAs, most of the BaMV siRNAs from A. thaliana were derived from the first 5′ half of the genome with or without BSF4 co-inoculation (Figure 7 and data not shown). This finding is in contrast to results of vsiRNAs from N. benthamiana being largely generated from the CP and 3′ UTR regions (Figure 5). However, the distribution patterns of BSF4 siRNAs on the satBaMV genome were similar in N. benthamiana and A. thaliana (Figures 5B and 7B). In A. thaliana, the mean GC % of BaMV siRNAs (50.84%) was comparable to that of the viral genome (50.53%), but that of satBaMV siRNAs (49.81%) was a bit lower.

Bottom Line: Most of the BaMV and satBaMV siRNAs were 21 or 22 nt, of both (+) and (-) polarities; however, a higher proportion of 22-nt BaMV and satBaMV siRNAs were generated in N. benthamiana than in A. thaliana.Furthermore, the proportion of non-viral 24-nt siRNAs was greatly increased in N. benthamiana after virus infection.DCL2 producing 24-nt siRNAs under biotic stresses may play a vital role in the antiviral mechanism in N. benthamiana.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan.

ABSTRACT

Background: Satellite RNAs (satRNAs), virus parasites, are exclusively associated with plant virus infection and have attracted much interest over the last 3 decades. Upon virus infection, virus-specific small interfering RNAs (vsiRNAs) are produced by dicer-like (DCL) endoribonucleases for anti-viral defense. The composition of vsiRNAs has been studied extensively; however, studies of satRNA-derived siRNAs (satsiRNAs) or siRNA profiles after satRNA co-infection are limited. Here, we report on the small RNA profiles associated with infection with Bamboo mosaic virus (BaMV) and its two satellite RNAs (satBaMVs) in Nicotiana benthamiana and Arabidopsis thaliana.

Methodology/principal findings: Leaves of N. benthamiana or A. thaliana inoculated with water, BaMV alone or co-inoculated with interfering or noninterfering satBaMV were collected for RNA extraction, then large-scale Solexa sequencing. Up to about 20% of total siRNAs as BaMV-specific siRNAs were accumulated in highly susceptible N. benthamiana leaves inoculated with BaMV alone or co-inoculated with noninterfering satBaMV; however, only about 0.1% of vsiRNAs were produced in plants co-infected with interfering satBaMV. The abundant region of siRNA distribution along BaMV and satBaMV genomes differed by host but not by co-infection with satBaMV. Most of the BaMV and satBaMV siRNAs were 21 or 22 nt, of both (+) and (-) polarities; however, a higher proportion of 22-nt BaMV and satBaMV siRNAs were generated in N. benthamiana than in A. thaliana. Furthermore, the proportion of non-viral 24-nt siRNAs was greatly increased in N. benthamiana after virus infection.

Conclusions/significance: The overall composition of vsiRNAs and satsiRNAs in the infected plants reflect the combined action of virus, satRNA and different DCLs in host plants. Our findings suggest that the structure and/or sequence demands of various DCLs in different hosts may result in differential susceptibility to the same virus. DCL2 producing 24-nt siRNAs under biotic stresses may play a vital role in the antiviral mechanism in N. benthamiana.

Show MeSH
Related in: MedlinePlus