An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans

Recent biochemical studies of the AAA ATPase, katanin, provide a foundation for understanding how microtubules might be severed along their length. These in vitro studies are complemented by a series of recent reports of direct in vivo observation of microtubule breakage, which indicate that the in vitro phenomenon of catalysed microtubule severing is likely to be physiological. There is also new evidence that microtubule severing by katanin is important for the production of non-centrosomal microtubules in cells such as neurons and epithelial cells. Although it has been difficult to establish the role of katanin in mitosis, new genetic evidence indicates that a katanin-like protein, MEI-1, plays an essential role in meiosis in C. elegans. Finally, new proteins involved in the severing of axonemal microtubules have been discovered in the deflagellation system of Chlamydomonas.

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picd-1, a gene that encodes CABIN1 domain-containing protein, interacts with pry-1/Axin to regulate multiple processes in Caenorhabditis elegans

10.1101/2021.09.27.462077 ◽

2021 ◽

Author(s):

Avijit Mallick ◽

Shane K. B. Taylor ◽

Sakshi Mehta ◽

Bhagwati P. Gupta

Keyword(s):

Stress Response ◽

Essential Role ◽

Family Members ◽

Transcriptome Profiling ◽

Scaffolding Protein ◽

Dependent Manner ◽

C Elegans ◽

Downstream Effectors ◽

Cellular Components

ABSTRACTAXIN family members control diverse biological processes in eukaryotes. As a scaffolding protein, AXIN facilitates interactions between cellular components and provides specificity to signaling pathways. Despite its crucial roles in metazoans and discovery of a large number of family members, the mechanism of AXIN function is not very well understood. The C. elegans AXIN homolog PRY-1 provides a powerful tool to identify interacting genes and downstream effectors that function in a conserved manner to regulate AXIN-mediated signaling. Previous work demonstrated pry-1’s essential role in developmental processes such as reproductive system, seam cells, and a P lineage cell P11.p. More recently, our lab carried out a transcriptome profiling of pry-1 mutant and uncovered the essential role of the gene in lipid metabolism, stress response, and aging. In this study, we have extended the work on pry-1 by reporting a novel interacting gene picd-1 (pry-1-interacting CABIN1 domain containing). Our findings have revealed that picd-1 plays an essential role in C. elegans and is involved in several pry-1-mediated processes including regulation of stress response and lifespan maintenance. In support of this, picd-1 expression overlaps with pry-1 in multiple tissues throughout the lifespan of animals. Further experiments showed that picd-1 inhibits CREB-regulated transcriptional coactivator homolog CRTC-1 function, which promotes longevity in a calcineurin-dependent manner. These data provide evidence for an essential role of the CABIN1 domain protein PICD-1 in mediating PRY-1 signaling in C. elegans.

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An optimized ribodepletion approach for C. elegans RNA-sequencing libraries

10.1101/2021.01.04.425342 ◽

2021 ◽

Author(s):

Alec Barrett ◽

Rebecca McWhirter ◽

Seth R Taylor ◽

Alexis Weinreb ◽

David M Miller ◽

...

Keyword(s):

Ribosomal Rna ◽

Noncoding Rnas ◽

Rrna Gene ◽

Library Preparation ◽

C Elegans ◽

Pcr Duplicates ◽

Rrna Depletion ◽

Dissociated Cells ◽

Probe Set ◽

Long Genes

ABSTRACTA recent and powerful technique is to obtain transcriptomes from rare cell populations, such as single neurons in C. elegans, by enriching dissociated cells using fluorescent sorting. However, these cell samples often have low yields of RNA that present challenges in library preparation. This can lead to PCR duplicates, noisy gene expression for lowly expressed genes, and other issues that limit endpoint analysis. Further, some common resources, such as sequence specific kits for removing ribosomal RNA, are not optimized for non-mammalian samples. To optimize library construction for such challenging samples, we compared two approaches for building RNAseq libraries from less than 10 nanograms of C. elegans RNA: SMARTSeq V4 (Takara), a widely used kit for selecting poly-adenylated transcripts; and SoLo Ovation (Tecan Genomics), a newly developed ribodepletion-based approach. For ribodepletion, we used a custom kit of 200 probes designed to match C. elegans rRNA gene sequences. We found that SoLo Ovation, in combination with our custom C. elegans probe set for rRNA depletion, detects an expanded set of noncoding RNAs, shows reduced noise in lowly expressed genes, and more accurately counts expression of long genes. The approach described here should be broadly useful for similar efforts to analyze transcriptomics when RNA is limiting.

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DER containing two consecutive GTP-binding domains plays an essential role in chloroplast ribosomal RNA processing and ribosome biogenesis in higher plants

Journal of Experimental Botany ◽

10.1093/jxb/ert360 ◽

2013 ◽

Vol 65 (1) ◽

pp. 117-130 ◽

Cited By ~ 15

Author(s):

Young Jeon ◽

Chang Sook Ahn ◽

Hyun Ju Jung ◽

Hunseung Kang ◽

Guen Tae Park ◽

...

Keyword(s):

Ribosomal Rna ◽

Rna Processing ◽

Ribosome Biogenesis ◽

Essential Role ◽

Higher Plants ◽

Binding Domains ◽

Gtp Binding ◽

Ribosomal Rna Processing

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Essential role of NbNOG1 in ribosomal RNA processing

Journal of Integrative Plant Biology ◽

10.1111/jipb.12691 ◽

2018 ◽

Vol 60 (11) ◽

pp. 1018-1022 ◽

Cited By ~ 1

Author(s):

Jiangbo Guo ◽

Shaojie Han ◽

Jinping Zhao ◽

Cuihua Xin ◽

Xiyin Zheng ◽

...

Keyword(s):

Ribosomal Rna ◽

Rna Processing ◽

Essential Role ◽

Ribosomal Rna Processing

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Autophagy-dependent ribosomal RNA degradation is essential for maintaining nucleotide homeostasis during C. elegans development

eLife ◽

10.7554/elife.36588 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 17

Author(s):

Yubing Liu ◽

Wei Zou ◽

Peiguo Yang ◽

Li Wang ◽

Yan Ma ◽

...

Keyword(s):

Ribosomal Rna ◽

Ribosomal Proteins ◽

De Novo ◽

Normal Growth ◽

Growth Conditions ◽

Rna Degradation ◽

Pyrimidine Nucleotides ◽

C Elegans ◽

Key Enzyme ◽

Simultaneous Loss

Ribosome degradation through the autophagy-lysosome pathway is crucial for cell survival during nutrient starvation, but whether it occurs under normal growth conditions and contributes to animal physiology remains unaddressed. In this study, we identified RNST-2, a C. elegans T2 family endoribonuclease, as the key enzyme that degrades ribosomal RNA in lysosomes. We found that loss of rnst-2 causes accumulation of rRNA and ribosomal proteins in enlarged lysosomes and both phenotypes are suppressed by blocking autophagy, which indicates that RNST-2 mediates autophagic degradation of ribosomal RNA in lysosomes. rnst-2(lf) mutants are defective in embryonic and larval development and are short-lived. Remarkably, simultaneous loss of RNST-2 and de novo synthesis of pyrimidine nucleotides leads to complete embryonic lethality, which is suppressed by supplements of uridine or cytidine. Our study reveals an essential role of autophagy-dependent degradation of ribosomal RNA in maintaining nucleotide homeostasis during animal development.

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