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Uncovering miRNAs involved in crosstalk between nutrient deficiencies in Arabidopsis.

Liang G, Ai Q, Yu D - Sci Rep (2015)

Bottom Line: In particular, the miRNAs that are induced specifically by a certain nutrient deficiency are often suppressed by other nutrient deficiencies.Further investigation indicated that the modulation of nutrient-responsive miRNA abundance affects the adaptation of plants to nutrient starvation conditions.This study revealed that miRNAs function as important regulatory nodes of different nutrient metabolic pathways.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.

ABSTRACT
Integrating carbon (C), nitrogen (N), and sulfur (S) metabolism is essential for the growth and development of living organisms. MicroRNAs (miRNAs) play key roles in regulating nutrient metabolism in plants. However, how plant miRNAs mediate crosstalk between different nutrient metabolic pathways is unclear. In this study, deep sequencing of Arabidopsis thaliana small RNAs was used to reveal miRNAs that were differentially expressed in response to C, N, or S deficiency. Comparative analysis revealed that the targets of the differentially expressed miRNAs are involved in different cellular responses and metabolic processes, including transcriptional regulation, auxin signal transduction, nutrient homeostasis, and regulation of development. C, N, and S deficiency specifically induced miR169b/c, miR826 and miR395, respectively. In contrast, miR167, miR172, miR397, miR398, miR399, miR408, miR775, miR827, miR841, miR857, and miR2111 are commonly suppressed by C, N, and S deficiency. In particular, the miRNAs that are induced specifically by a certain nutrient deficiency are often suppressed by other nutrient deficiencies. Further investigation indicated that the modulation of nutrient-responsive miRNA abundance affects the adaptation of plants to nutrient starvation conditions. This study revealed that miRNAs function as important regulatory nodes of different nutrient metabolic pathways.

No MeSH data available.


Related in: MedlinePlus

Expression of miRNAs and their targets in response to nutrient deficiencies.RNA was isolated from 10-day-old seedlings. Relative expression was indicated by the log2 value. Student’s t test indicated that the values marked by one asterisk are significantly different from the corresponding full nutrient value (P < 0.01; n = 3).
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f3: Expression of miRNAs and their targets in response to nutrient deficiencies.RNA was isolated from 10-day-old seedlings. Relative expression was indicated by the log2 value. Student’s t test indicated that the values marked by one asterisk are significantly different from the corresponding full nutrient value (P < 0.01; n = 3).

Mentions: Plant miRNAs mediate target mRNA cleavage or translation inhibition; therefore, the expression of plant miRNAs is usually negatively correlated with that of their targets. To test this, the expression patterns of miRNAs and their targets were compared using quantitative RT-PCR assays. As expected, most targets displayed the opposite expression trends compared with the corresponding miRNAs. For example, miR169b/c, miR826, and miR395a/d/e were induced by –C, –N, and –S, respectively, and their targets were repressed correspondingly, with the exception of APS3 (Fig. 3A–C). The expression patterns of miR826-AOP2 in –N and miR395-APS1/3/4 in –S agreed with the previous reports212641. miR397 and miR408 are involved in the copper starvation response. Consistent with the sequencing data, their expression was downregulated by –C, –N, and –S. Among the six target genes examined, the expressions of LAC4 and LAC17 were inversely related to miR397b (Fig. 3D), as were those of LAC3 and LAC13 to miR408 (Fig. 3G). Both miR399 and miR827 were suppressed by –C, –N, and –S, and their targets, PHO2 and NLA, were induced correspondingly (Fig. 3E,H). miR160 and miR167 are involved in the auxin pathway by targeting ARF genes. miR160 was induced whereas miR167a/b was repressed by –C, –N, and –S. In contrast, the targets of miR160, ARF10 and ARF16, were repressed, whereas the target of miR167, ARF8, was induced by –C, –N, and –S (Fig. 3F,I). In addition, some miRNAs were positively correlated with their targets, such as miR395-APS3 in –S, miR397-LAC2 in –C, and miR160-ARF17 in –C and –S. It is likely that these targets are also regulated by other transcription factors or their expression does not completely overlap with miRNAs spatiotemporally.


Uncovering miRNAs involved in crosstalk between nutrient deficiencies in Arabidopsis.

Liang G, Ai Q, Yu D - Sci Rep (2015)

Expression of miRNAs and their targets in response to nutrient deficiencies.RNA was isolated from 10-day-old seedlings. Relative expression was indicated by the log2 value. Student’s t test indicated that the values marked by one asterisk are significantly different from the corresponding full nutrient value (P < 0.01; n = 3).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4488870&req=5

f3: Expression of miRNAs and their targets in response to nutrient deficiencies.RNA was isolated from 10-day-old seedlings. Relative expression was indicated by the log2 value. Student’s t test indicated that the values marked by one asterisk are significantly different from the corresponding full nutrient value (P < 0.01; n = 3).
Mentions: Plant miRNAs mediate target mRNA cleavage or translation inhibition; therefore, the expression of plant miRNAs is usually negatively correlated with that of their targets. To test this, the expression patterns of miRNAs and their targets were compared using quantitative RT-PCR assays. As expected, most targets displayed the opposite expression trends compared with the corresponding miRNAs. For example, miR169b/c, miR826, and miR395a/d/e were induced by –C, –N, and –S, respectively, and their targets were repressed correspondingly, with the exception of APS3 (Fig. 3A–C). The expression patterns of miR826-AOP2 in –N and miR395-APS1/3/4 in –S agreed with the previous reports212641. miR397 and miR408 are involved in the copper starvation response. Consistent with the sequencing data, their expression was downregulated by –C, –N, and –S. Among the six target genes examined, the expressions of LAC4 and LAC17 were inversely related to miR397b (Fig. 3D), as were those of LAC3 and LAC13 to miR408 (Fig. 3G). Both miR399 and miR827 were suppressed by –C, –N, and –S, and their targets, PHO2 and NLA, were induced correspondingly (Fig. 3E,H). miR160 and miR167 are involved in the auxin pathway by targeting ARF genes. miR160 was induced whereas miR167a/b was repressed by –C, –N, and –S. In contrast, the targets of miR160, ARF10 and ARF16, were repressed, whereas the target of miR167, ARF8, was induced by –C, –N, and –S (Fig. 3F,I). In addition, some miRNAs were positively correlated with their targets, such as miR395-APS3 in –S, miR397-LAC2 in –C, and miR160-ARF17 in –C and –S. It is likely that these targets are also regulated by other transcription factors or their expression does not completely overlap with miRNAs spatiotemporally.

Bottom Line: In particular, the miRNAs that are induced specifically by a certain nutrient deficiency are often suppressed by other nutrient deficiencies.Further investigation indicated that the modulation of nutrient-responsive miRNA abundance affects the adaptation of plants to nutrient starvation conditions.This study revealed that miRNAs function as important regulatory nodes of different nutrient metabolic pathways.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.

ABSTRACT
Integrating carbon (C), nitrogen (N), and sulfur (S) metabolism is essential for the growth and development of living organisms. MicroRNAs (miRNAs) play key roles in regulating nutrient metabolism in plants. However, how plant miRNAs mediate crosstalk between different nutrient metabolic pathways is unclear. In this study, deep sequencing of Arabidopsis thaliana small RNAs was used to reveal miRNAs that were differentially expressed in response to C, N, or S deficiency. Comparative analysis revealed that the targets of the differentially expressed miRNAs are involved in different cellular responses and metabolic processes, including transcriptional regulation, auxin signal transduction, nutrient homeostasis, and regulation of development. C, N, and S deficiency specifically induced miR169b/c, miR826 and miR395, respectively. In contrast, miR167, miR172, miR397, miR398, miR399, miR408, miR775, miR827, miR841, miR857, and miR2111 are commonly suppressed by C, N, and S deficiency. In particular, the miRNAs that are induced specifically by a certain nutrient deficiency are often suppressed by other nutrient deficiencies. Further investigation indicated that the modulation of nutrient-responsive miRNA abundance affects the adaptation of plants to nutrient starvation conditions. This study revealed that miRNAs function as important regulatory nodes of different nutrient metabolic pathways.

No MeSH data available.


Related in: MedlinePlus