Ribonuclease D Processes a Small RNA Regulator of Multicellular Development in Myxobacteria
By targeting mRNA transcripts, non-coding small RNAs (sRNAs) regulate the expression of genes governing a wide range of bacterial functions. In the social myxobacterium <i>Myxococcus xanthus</i>, the sRNA Pxr serves as a gatekeeper of the regulatory pathway controlling the life-cycle tra...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/5/1061 |
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| author | Sarah M. Cossey Gregory J. Velicer Yuen-Tsu Nicco Yu |
| author_facet | Sarah M. Cossey Gregory J. Velicer Yuen-Tsu Nicco Yu |
| author_sort | Sarah M. Cossey |
| collection | DOAJ |
| description | By targeting mRNA transcripts, non-coding small RNAs (sRNAs) regulate the expression of genes governing a wide range of bacterial functions. In the social myxobacterium <i>Myxococcus xanthus</i>, the sRNA Pxr serves as a gatekeeper of the regulatory pathway controlling the life-cycle transition from vegetative growth to multicellular fruiting body development. When nutrients are abundant, Pxr prevents the initiation of the developmental program, but Pxr-mediated inhibition is alleviated when cells starve. To identify genes essential for Pxr function, a developmentally defective strain in which Pxr-mediated blockage of development is constitutively active (strain “OC”) was transposon-mutagenized to identify suppressor mutations that inactivate or bypass Pxr inhibition and thereby restore development. One of the four loci in which a transposon insertion restored development is <i>rnd</i>, encoding the Ribonuclease D protein (RNase D). RNase D is an exonuclease important for tRNA maturation. Here, we show that disruption of <i>rnd</i> abolishes the accumulation of Pxr-S, the product of Pxr processing from a longer precursor form (Pxr-L) and the active inhibitor of development. Additionally, the decrease in Pxr-S caused by <i>rnd</i> disruption was associated with increased accumulation primarily of a longer novel Pxr-specific transcript (Pxr-XL) rather than of Pxr-L. The introduction of a plasmid expressing <i>rnd</i> reverted cells back to OC-like phenotypes in development and Pxr accumulation, indicating that a lack of RNase D alone suppresses the developmental defect of OC. Moreover, an in vitro Pxr-processing assay demonstrated that RNase D processes Pxr-XL into Pxr-L; this implies that overall, Pxr sRNA maturation requires a sequential two-step processing. Collectively, our results indicate that a housekeeping ribonuclease plays a central role in a model form of microbial aggregative development. To our knowledge, this is the first evidence implicating RNase D in sRNA processing. |
| first_indexed | 2024-03-11T03:43:05Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T03:43:05Z |
| publishDate | 2023-05-01 |
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| record_format | Article |
| series | Genes |
| spelling | doaj.art-daaee9578aa84ea9b27b2cab75ff58282023-11-18T01:29:56ZengMDPI AGGenes2073-44252023-05-01145106110.3390/genes14051061Ribonuclease D Processes a Small RNA Regulator of Multicellular Development in MyxobacteriaSarah M. Cossey0Gregory J. Velicer1Yuen-Tsu Nicco Yu2Institute for Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zurich, SwitzerlandInstitute for Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zurich, SwitzerlandInstitute for Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zurich, SwitzerlandBy targeting mRNA transcripts, non-coding small RNAs (sRNAs) regulate the expression of genes governing a wide range of bacterial functions. In the social myxobacterium <i>Myxococcus xanthus</i>, the sRNA Pxr serves as a gatekeeper of the regulatory pathway controlling the life-cycle transition from vegetative growth to multicellular fruiting body development. When nutrients are abundant, Pxr prevents the initiation of the developmental program, but Pxr-mediated inhibition is alleviated when cells starve. To identify genes essential for Pxr function, a developmentally defective strain in which Pxr-mediated blockage of development is constitutively active (strain “OC”) was transposon-mutagenized to identify suppressor mutations that inactivate or bypass Pxr inhibition and thereby restore development. One of the four loci in which a transposon insertion restored development is <i>rnd</i>, encoding the Ribonuclease D protein (RNase D). RNase D is an exonuclease important for tRNA maturation. Here, we show that disruption of <i>rnd</i> abolishes the accumulation of Pxr-S, the product of Pxr processing from a longer precursor form (Pxr-L) and the active inhibitor of development. Additionally, the decrease in Pxr-S caused by <i>rnd</i> disruption was associated with increased accumulation primarily of a longer novel Pxr-specific transcript (Pxr-XL) rather than of Pxr-L. The introduction of a plasmid expressing <i>rnd</i> reverted cells back to OC-like phenotypes in development and Pxr accumulation, indicating that a lack of RNase D alone suppresses the developmental defect of OC. Moreover, an in vitro Pxr-processing assay demonstrated that RNase D processes Pxr-XL into Pxr-L; this implies that overall, Pxr sRNA maturation requires a sequential two-step processing. Collectively, our results indicate that a housekeeping ribonuclease plays a central role in a model form of microbial aggregative development. To our knowledge, this is the first evidence implicating RNase D in sRNA processing.https://www.mdpi.com/2073-4425/14/5/1061sRNAribonucleasedevelopment<i>Myxococcus xanthus</i> |
| spellingShingle | Sarah M. Cossey Gregory J. Velicer Yuen-Tsu Nicco Yu Ribonuclease D Processes a Small RNA Regulator of Multicellular Development in Myxobacteria Genes sRNA ribonuclease development <i>Myxococcus xanthus</i> |
| title | Ribonuclease D Processes a Small RNA Regulator of Multicellular Development in Myxobacteria |
| title_full | Ribonuclease D Processes a Small RNA Regulator of Multicellular Development in Myxobacteria |
| title_fullStr | Ribonuclease D Processes a Small RNA Regulator of Multicellular Development in Myxobacteria |
| title_full_unstemmed | Ribonuclease D Processes a Small RNA Regulator of Multicellular Development in Myxobacteria |
| title_short | Ribonuclease D Processes a Small RNA Regulator of Multicellular Development in Myxobacteria |
| title_sort | ribonuclease d processes a small rna regulator of multicellular development in myxobacteria |
| topic | sRNA ribonuclease development <i>Myxococcus xanthus</i> |
| url | https://www.mdpi.com/2073-4425/14/5/1061 |
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