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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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Size distribution of total small RNAs isolated from A. thaliana.Total sRNAs ranging from 17 to 28 nt are shown on the X axis, and relative percentages are shown on the Y axis. The percentages of sRNAs of different lengths of mock (♦), BaMV (■), and BaMV co-inoculated with BSF4 (▲) or BSL6 (×) plants are shown.
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pone-0011928-g006: Size distribution of total small RNAs isolated from A. thaliana.Total sRNAs ranging from 17 to 28 nt are shown on the X axis, and relative percentages are shown on the Y axis. The percentages of sRNAs of different lengths of mock (♦), BaMV (■), and BaMV co-inoculated with BSF4 (▲) or BSL6 (×) plants are shown.

Mentions: Analysis of the whole set of siRNAs, including the endogenous siRNAs, from A. thaliana revealed the 24-nt siRNAs the most predominant [23], and 21-nt siRNAs were the second highest in all treatments, including mock, BaMV, BaMV+BSF4 or +BSL6 infection (Figure 6). However, siRNAs matched to BaMV or satBaMVs were mainly 21 nt (Figure S4). This result differs from that of siRNAs from infected N. benthamiana. Most of the siRNAs isolated from mock-inoculated N. benthamiana were 22 nt but decreased in level after BaMV inoculation or co-inoculation with satBaMVs, which was followed by accumulation of the 24-nt siRNAs (Figure 3).


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)

Size distribution of total small RNAs isolated from A. thaliana.Total sRNAs ranging from 17 to 28 nt are shown on the X axis, and relative percentages are shown on the Y axis. The percentages of sRNAs of different lengths of mock (♦), BaMV (■), and BaMV co-inoculated with BSF4 (▲) or BSL6 (×) plants are shown.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0011928-g006: Size distribution of total small RNAs isolated from A. thaliana.Total sRNAs ranging from 17 to 28 nt are shown on the X axis, and relative percentages are shown on the Y axis. The percentages of sRNAs of different lengths of mock (♦), BaMV (■), and BaMV co-inoculated with BSF4 (▲) or BSL6 (×) plants are shown.
Mentions: Analysis of the whole set of siRNAs, including the endogenous siRNAs, from A. thaliana revealed the 24-nt siRNAs the most predominant [23], and 21-nt siRNAs were the second highest in all treatments, including mock, BaMV, BaMV+BSF4 or +BSL6 infection (Figure 6). However, siRNAs matched to BaMV or satBaMVs were mainly 21 nt (Figure S4). This result differs from that of siRNAs from infected N. benthamiana. Most of the siRNAs isolated from mock-inoculated N. benthamiana were 22 nt but decreased in level after BaMV inoculation or co-inoculation with satBaMVs, which was followed by accumulation of the 24-nt siRNAs (Figure 3).

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