Faculty Opinions recommendation of RNA-Seq Reveals Acute Manganese Exposure Increases Endoplasmic Reticulum Related and Lipocalin mRNAs in Caenorhabditis elegans.

Caenorhabditis eleganssenses gentle touch via a mechanotransduction channel formed from the DEG/ENaC proteins MEC-4 and MEC-10. An additional protein, the paraoxonase-like protein MEC-6, is essential for transduction, and previous work suggested that MEC-6 was part of the transduction complex. We found that MEC-6 and a similar protein, POML-1, reside primarily in the endoplasmic reticulum and do not colocalize with MEC-4 on the plasma membrane in vivo. As with MEC-6, POML-1 is needed for touch sensitivity, for the neurodegeneration caused by themec-4(d)mutation, and for the expression and distribution of MEC-4 in vivo. Both proteins are likely needed for the proper folding or assembly of MEC-4 channels in vivo as measured by FRET. MEC-6 detectably increases the rate of MEC-4 accumulation on theXenopusoocyte plasma membrane. These results suggest that MEC-6 and POML-1 interact with MEC-4 to facilitate expression and localization of MEC-4 on the cell surface. Thus, MEC-6 and POML-1 act more like chaperones for MEC-4 than channel components.

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Comparative Transcriptomic Signature of the Simulated Microgravity Response in Caenorhabditis elegans

10.1101/531335 ◽

2019 ◽

Author(s):

İrem Çelen ◽

Aroshan Jayasinghe ◽

Jung H. Doh ◽

Chandran R. Sabanayagam

Keyword(s):

Caenorhabditis Elegans ◽

Simulated Microgravity ◽

Space Station ◽

Integrative Approach ◽

Biological Processes ◽

Rna Seq ◽

Transcriptomic Response ◽

Transcriptomic Signature ◽

Ground Conditions ◽

The Impact

AbstractBackgroundGiven the growing interest in human exploration of space, it is crucial to identify the effect of space conditions on biological processes. The International Space Station (ISS) greatly helps researchers determine these effects. However, the impact of the ISS-introduced potential confounders (e.g., the combination of radiation and microgravity exposures) on the biological processes are often neglected, and separate investigations are needed to uncover the impact of individual conditions.ResultsHere, we analyze the transcriptomic response of Caenorhabditis elegans to simulated microgravity and observe the maintained transcriptomic response after return to ground conditions for four, eight, and twelve days. Through the integration of our data with those in NASA GeneLab, we identify the gravitome, which we define as microgravity-responsive transcriptomic signatures. We show that 75% of the simulated microgravity-induced changes on gene expression persist after return to ground conditions for four days while most of these changes are reverted after twelve days return to ground conditions. Our results from integrative RNA-seq and mass spectrometry analyses suggest that simulated microgravity affects longevity regulating insulin/IGF-1 and sphingolipid signaling pathways.ConclusionsOur results address the sole impact of simulated microgravity on transcriptome by controlling for the other space-introduced conditions and utilizing RNA-seq. Using an integrative approach, we identify a conserved transcriptomic signature to microgravity and its sustained impact after return to the ground. Moreover, we present the effect of simulated microgravity on distinct ceramide profiles. Overall, this work can provide insights into the sole effect of microgravity on biological systems.

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A conserved family of proteins facilitates nascent lipid droplet budding from the ER

The Journal of Cell Biology ◽

10.1083/jcb.201505067 ◽

2015 ◽

Vol 211 (2) ◽

pp. 261-271 ◽

Cited By ~ 137

Author(s):

Vineet Choudhary ◽

Namrata Ojha ◽

Andy Golden ◽

William A. Prinz

Keyword(s):

Electron Microscopy ◽

Endoplasmic Reticulum ◽

Lipid Metabolism ◽

Caenorhabditis Elegans ◽

Lipid Droplet ◽

Lipid Droplets ◽

De Novo ◽

Fat Storage ◽

Higher Eukaryotes ◽

Er Membrane

Lipid droplets (LDs) are found in all cells and play critical roles in lipid metabolism. De novo LD biogenesis occurs in the endoplasmic reticulum (ER) but is not well understood. We imaged early stages of LD biogenesis using electron microscopy and found that nascent LDs form lens-like structures that are in the ER membrane, raising the question of how these nascent LDs bud from the ER as they grow. We found that a conserved family of proteins, fat storage-inducing transmembrane (FIT) proteins, is required for proper budding of LDs from the ER. Elimination or reduction of FIT proteins in yeast and higher eukaryotes causes LDs to remain in the ER membrane. Deletion of the single FIT protein in Caenorhabditis elegans is lethal, suggesting that LD budding is an essential process in this organism. Our findings indicated that FIT proteins are necessary to promote budding of nascent LDs from the ER.

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The inositol 5-phosphatase INPP5K participates in the fine control of ER organization

The Journal of Cell Biology ◽

10.1083/jcb.201802125 ◽

2018 ◽

Vol 217 (10) ◽

pp. 3577-3592 ◽

Cited By ~ 11

Author(s):

Rui Dong ◽

Ting Zhu ◽

Lorena Benedetti ◽

Swetha Gowrishankar ◽

Huichao Deng ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Caenorhabditis Elegans ◽

Independent Study ◽

Mutant Phenotype ◽

Network Organization ◽

Wild Type ◽

Fine Control

INPP5K (SKIP) is an inositol 5-phosphatase that localizes in part to the endoplasmic reticulum (ER). We show that recruitment of INPP5K to the ER is mediated by ARL6IP1, which shares features of ER-shaping proteins. Like ARL6IP1, INPP5K is preferentially localized in ER tubules and enriched, relative to other ER resident proteins (Sec61β, VAPB, and Sac1), in newly formed tubules that grow along microtubule tracks. Depletion of either INPP5K or ARL6IP1 results in the increase of ER sheets. In a convergent but independent study, a screen for mutations affecting the distribution of the ER network in dendrites of the PVD neurons of Caenorhabditis elegans led to the isolation of mutants in CIL-1, which encodes the INPP5K worm orthologue. The mutant phenotype was rescued by expression of wild type, but not of catalytically inactive CIL-1. Our results reveal an unexpected role of an ER localized polyphosphoinositide phosphatase in the fine control of ER network organization.

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Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles

BMC Biology ◽

10.1186/s12915-015-0116-6 ◽

2015 ◽

Vol 13 (1) ◽

Cited By ~ 46

Author(s):

Stephen M Blazie ◽

Cody Babb ◽

Henry Wilky ◽

Alan Rawls ◽

Jin G Park ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Alternative Polyadenylation ◽

Rna Seq ◽

Tissue Specific ◽

Specific Alternative

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A role for Rab5 in structuring the endoplasmic reticulum

The Journal of Cell Biology ◽

10.1083/jcb.200701139 ◽

2007 ◽

Vol 178 (1) ◽

pp. 43-56 ◽

Cited By ~ 128

Author(s):

Anjon Audhya ◽

Arshad Desai ◽

Karen Oegema

Keyword(s):

Endoplasmic Reticulum ◽

Caenorhabditis Elegans ◽

Nuclear Envelope ◽

Rab Gtpases ◽

C Elegans ◽

Rab Family ◽

Kinetics Of

The endoplasmic reticulum (ER) is a contiguous network of interconnected membrane sheets and tubules. The ER is differentiated into distinct domains, including the peripheral ER and nuclear envelope. Inhibition of two ER proteins, Rtn4a and DP1/NogoA, was previously shown to inhibit the formation of ER tubules in vitro. We show that the formation of ER tubules in vitro also requires a Rab family GTPase. Characterization of the 29 Caenorhabditis elegans Rab GTPases reveals that depletion of RAB-5 phenocopies the defects in peripheral ER structure that result from depletion of RET-1 and YOP-1, the C. elegans homologues of Rtn4a and DP1/NogoA. Perturbation of endocytosis by other means did not affect ER structure; the role of RAB-5 in ER morphology is thus independent of its well-studied requirement for endocytosis. RAB-5 and YOP-1/RET-1 also control the kinetics of nuclear envelope disassembly, which suggests an important role for the morphology of the peripheral ER in this process.

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Endoplasmic Reticulum Homeostasis Is Modulated by the Forkhead Transcription Factor FKH-9 During Infection of Caenorhabditis elegans

Genetics ◽

10.1534/genetics.118.301450 ◽

2018 ◽

Vol 210 (4) ◽

pp. 1329-1337 ◽

Cited By ~ 7

Author(s):

Erik J. Tillman ◽

Claire E. Richardson ◽

Douglas J. Cattie ◽

Kirthi C. Reddy ◽

Nicolas J. Lehrbach ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Transcription Factor ◽

Caenorhabditis Elegans ◽

Forkhead Transcription Factor

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A novel endoplasmic stress mediator, Kelch domain containing 7B (KLHDC7B), increased Harakiri (HRK) in the SubAB-induced apoptosis signaling pathway

Cell Death Discovery ◽

10.1038/s41420-021-00753-0 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Kinnosuke Yahiro ◽

Kohei Ogura ◽

Hiroyasu Tsutsuki ◽

Sunao Iyoda ◽

Makoto Ohnishi ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Er Stress ◽

Signaling Pathway ◽

Gastrointestinal Symptoms ◽

Parp Cleavage ◽

Rna Seq ◽

Gene Encoding ◽

Apoptotic Pathway ◽

Kelch Domain ◽

Induced Apoptosis

AbstractLocus for Enterocyte Effacement (LEE)-positive Shiga-toxigenic Escherichia coli (STEC) contributes to many global foodborne diseases, with infection characterized by severe gastrointestinal symptoms, including bloody diarrhea. The incidence of LEE-negative STEC-mediated disease is also increasing globally. Subtilase cytotoxin (SubAB) is released by some LEE-negative STEC strains. It cleaves BiP, which is a chaperone protein located in the endoplasmic reticulum (ER), thereby causing apoptosis induced by ER stress. To date, the apoptotic signaling pathway mediated by SubAB has not been identified. In the current study, RNA-seq analysis showed that SubAB significantly induced the expression of Kelch domain containing 7B (KLHDC7B). We explored the role of KLHDC7B in the SubAB-induced apoptotic pathway. SubAB-induced KLHDC7B mRNA expression was increased after 12 h of incubation of toxin with HeLa cells. KLHDC7B expression was downregulated by knockdown of PKR-like endoplasmic reticulum kinase (PERK), CEBP homologous protein (CHOP), activating transcription factor 4 (ATF4), and CEBP β (CEBPB). KLHDC7B knockdown suppressed SubAB-stimulated CHOP expression, poly(ADP-ribose) polymerase (PARP) cleavage, and cytotoxicity. The over-expressed KLHDC7B was localized to the nucleus and cytosolic fractions. Next, we used RNA-seq to analyze the effect of KLHDC7B knockdown on apoptosis induced by SubAB, and found that the gene encoding for the pro-apoptotic Bcl-2 family protein, Harakiri (HRK), was upregulated in SubAB-treated control cells. However, this effect was not observed in SubAB-treated KLHDC7B-knockdown cells. Therefore, we identified the pathway through which SubAB-induced KLHDC7B regulates HRK expression, which is essential for apoptosis in toxin-mediated ER stress.

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