High-Throughput Sequencing and Expression Analysis Suggest the Involvement of <i>Pseudomonas putida</i> RA-Responsive microRNAs in Growth and Development of Arabidopsis
Beneficial soil microorganisms largely comprise of plant growth-promoting rhizobacteria (PGPR), which adhere to plant roots and facilitate their growth and development. <i>Pseudomonas putida</i> (RA) strain MTCC5279 is one such PGPR that exhibits several characteristics of plant growth p...
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MDPI AG
2020-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/15/5468 |
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| author | Ram Jatan Puneet Singh Chauhan Charu Lata |
| author_facet | Ram Jatan Puneet Singh Chauhan Charu Lata |
| author_sort | Ram Jatan |
| collection | DOAJ |
| description | Beneficial soil microorganisms largely comprise of plant growth-promoting rhizobacteria (PGPR), which adhere to plant roots and facilitate their growth and development. <i>Pseudomonas putida</i> (RA) strain MTCC5279 is one such PGPR that exhibits several characteristics of plant growth promotion, such as P-solubilization, and siderophores and IAA production. Plant–PGPR interactions are very complex phenomena, and essentially modulate the expression of numerous genes, consequently leading to changes in the physiological, biochemical, cellular and molecular responses of plants. Therefore, in order to understand the molecular bases of plant–PGPR interactions, we carried out the identification of microRNAs from the roots of <i>Arabidopsis</i> upon <i>P. putida</i> RA-inoculation, and analyses of their expression. MicroRNAs (miRNAs) are 20- to 24-nt non-coding small RNAs known to regulate the expression of their target genes. Small RNA sequencing led to the identification of 293 known and 67 putative novel miRNAs, from the control and RA-inoculated libraries. Among these, 15 known miRNAs showed differential expression upon RA-inoculation in comparison to the control, and their expressions were corroborated by stem-loop quantitative real-time PCR. Overall, 28,746 and 6931 mRNAs were expected to be the targets of the known and putative novel miRNAs, respectively, which take part in numerous biological, cellular and molecular processes. An inverse correlation between the expression of RA-responsive miRNAs and their target genes also strengthened the crucial role of RA in developmental regulation. Our results offer insights into the understanding of the RA-mediated modulation of miRNAs and their targets in <i>Arabidopsis</i>, and pave the way for the further exploitation and characterization of candidate RA-responsive miRNA(s) for various crop improvement strategies directed towards plant sustainable growth and development. |
| first_indexed | 2024-03-10T18:05:18Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T18:05:18Z |
| publishDate | 2020-07-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-86d021daa63f480598f98e9207aa9db22023-11-20T08:34:57ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-07-012115546810.3390/ijms21155468High-Throughput Sequencing and Expression Analysis Suggest the Involvement of <i>Pseudomonas putida</i> RA-Responsive microRNAs in Growth and Development of ArabidopsisRam Jatan0Puneet Singh Chauhan1Charu Lata2CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, IndiaCSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, IndiaCSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, IndiaBeneficial soil microorganisms largely comprise of plant growth-promoting rhizobacteria (PGPR), which adhere to plant roots and facilitate their growth and development. <i>Pseudomonas putida</i> (RA) strain MTCC5279 is one such PGPR that exhibits several characteristics of plant growth promotion, such as P-solubilization, and siderophores and IAA production. Plant–PGPR interactions are very complex phenomena, and essentially modulate the expression of numerous genes, consequently leading to changes in the physiological, biochemical, cellular and molecular responses of plants. Therefore, in order to understand the molecular bases of plant–PGPR interactions, we carried out the identification of microRNAs from the roots of <i>Arabidopsis</i> upon <i>P. putida</i> RA-inoculation, and analyses of their expression. MicroRNAs (miRNAs) are 20- to 24-nt non-coding small RNAs known to regulate the expression of their target genes. Small RNA sequencing led to the identification of 293 known and 67 putative novel miRNAs, from the control and RA-inoculated libraries. Among these, 15 known miRNAs showed differential expression upon RA-inoculation in comparison to the control, and their expressions were corroborated by stem-loop quantitative real-time PCR. Overall, 28,746 and 6931 mRNAs were expected to be the targets of the known and putative novel miRNAs, respectively, which take part in numerous biological, cellular and molecular processes. An inverse correlation between the expression of RA-responsive miRNAs and their target genes also strengthened the crucial role of RA in developmental regulation. Our results offer insights into the understanding of the RA-mediated modulation of miRNAs and their targets in <i>Arabidopsis</i>, and pave the way for the further exploitation and characterization of candidate RA-responsive miRNA(s) for various crop improvement strategies directed towards plant sustainable growth and development.https://www.mdpi.com/1422-0067/21/15/5468IAAmiRNAPGPRP-solubilizationsiderophorestarget gene |
| spellingShingle | Ram Jatan Puneet Singh Chauhan Charu Lata High-Throughput Sequencing and Expression Analysis Suggest the Involvement of <i>Pseudomonas putida</i> RA-Responsive microRNAs in Growth and Development of Arabidopsis International Journal of Molecular Sciences IAA miRNA PGPR P-solubilization siderophores target gene |
| title | High-Throughput Sequencing and Expression Analysis Suggest the Involvement of <i>Pseudomonas putida</i> RA-Responsive microRNAs in Growth and Development of Arabidopsis |
| title_full | High-Throughput Sequencing and Expression Analysis Suggest the Involvement of <i>Pseudomonas putida</i> RA-Responsive microRNAs in Growth and Development of Arabidopsis |
| title_fullStr | High-Throughput Sequencing and Expression Analysis Suggest the Involvement of <i>Pseudomonas putida</i> RA-Responsive microRNAs in Growth and Development of Arabidopsis |
| title_full_unstemmed | High-Throughput Sequencing and Expression Analysis Suggest the Involvement of <i>Pseudomonas putida</i> RA-Responsive microRNAs in Growth and Development of Arabidopsis |
| title_short | High-Throughput Sequencing and Expression Analysis Suggest the Involvement of <i>Pseudomonas putida</i> RA-Responsive microRNAs in Growth and Development of Arabidopsis |
| title_sort | high throughput sequencing and expression analysis suggest the involvement of i pseudomonas putida i ra responsive micrornas in growth and development of arabidopsis |
| topic | IAA miRNA PGPR P-solubilization siderophores target gene |
| url | https://www.mdpi.com/1422-0067/21/15/5468 |
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