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Rosani U, De Felice S, Frizzo R, Kawato S, Wegner KM. FicD genes in invertebrates: A tale of transposons, pathogenic and integrated viruses. Gene 2024; 893:147895. [PMID: 37832807 DOI: 10.1016/j.gene.2023.147895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Many gene families are shared across the tree of life between distantly related species because of horizontal gene transfers (HGTs). However, the frequency of HGTs varies strongly between gene families and biotic realms suggesting differential selection pressures and functional bias. One gene family with a wide distribution are FIC-domain containing enzymes (FicDs). FicDs catalyze AMPylation, a post-translational protein modification consisting in the addition of adenosine monophosphate to accessible residues of target proteins. Beside the well-known conservation of FicDs in deuterostomes, we report the presence of a conserved FicD gene ortholog in a large number of protostomes and microbial eukaryotes. We also reported additional FicD gene copies in the genomes of some rotifers, parasitic worms and bivalves. A few dsDNA viruses of these invertebrates, including White spot syndrome virus, Cherax quadricarinatus iridovirus, Ostreid herpesvirus-1 and the beetle nudivirus, carry copies of FicDs, with phylogenetic analysis suggesting a common origin of these FicD copies and the duplicated FicDs of their invertebrate hosts. HGTs and gene duplications possibly mediated by endogenous viruses or genetic mobile elements seem to have contributed to the transfer of AMPylation ability from bacteria and eukaryotes to pathogenic viruses, where this pathway could have been hijacked to promote viral infection.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 35121 Padova, Italy.
| | - Sofia De Felice
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Riccardo Frizzo
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, 108-8477 Tokyo, Japan
| | - K Mathias Wegner
- Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research, Waddensea Station Sylt, 25992 List, Germany
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Gulen B, Kinch LN, Servage KA, Blevins A, Stewart NM, Gray HF, Casey AK, Orth K. FicD Sensitizes Cellular Response to Glucose Fluctuations in Mouse Embryonic Fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576705. [PMID: 38328056 PMCID: PMC10849547 DOI: 10.1101/2024.01.22.576705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
During homeostasis, the endoplasmic reticulum (ER) maintains productive transmembrane and secretory protein folding that is vital for proper cellular function. The ER-resident HSP70 chaperone, BiP, plays a pivotal role in sensing ER stress to activate the unfolded protein response (UPR). BiP function is regulated by the bifunctional enzyme FicD that mediates AMPylation and deAMPylation of BiP in response to changes in ER stress. AMPylated BiP acts as a molecular rheostat to regulate UPR signaling, yet little is known about the molecular consequences of FicD loss. In this study, we investigate the role of FicD in mouse embryonic fibroblast (MEF) response to pharmacologically and metabolically induced ER stress. We find differential BiP AMPylation signatures when comparing robust chemical ER stress inducers to physiological glucose starvation stress and recovery. Wildtype MEFs respond to pharmacological ER stress by downregulating BiP AMPylation. Conversely, BiP AMPylation in wildtype MEFs increases upon metabolic stress induced by glucose starvation. Deletion of FicD results in widespread gene expression changes under baseline growth conditions. In addition, FicD null MEFs exhibit dampened UPR signaling, altered cell stress recovery response, and unconstrained protein secretion. Taken together, our findings indicate that FicD is important for tampering UPR signaling, stress recovery, and the maintenance of secretory protein homeostasis. Significance Statement The chaperone BiP plays a key quality control role in the endoplasmic reticulum, the cellular location for the production, folding, and transport of secreted proteins. The enzyme FicD regulates BiP's activity through AMPylation and deAMPylation. Our study unveils the importance of FicD in regulating BiP and the unfolded protein response (UPR) during stress. We identify distinct BiP AMPylation signatures for different stressors, highlighting FicD's nuanced control. Deletion of FicD causes widespread gene expression changes, disrupts UPR signaling, alters stress recovery, and perturbs protein secretion in cells. These observations underscore the pivotal contribution of FicD for preserving secretory protein homeostasis. Our findings deepen the understanding of FicD's role in maintaining cellular resilience and open avenues for therapeutic strategies targeting UPR-associated diseases.
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Gulen B, Casey A, Orth K. AMPylation of small GTPases by Fic enzymes. FEBS Lett 2023; 597:883-891. [PMID: 36239538 PMCID: PMC10050140 DOI: 10.1002/1873-3468.14516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/17/2022] [Accepted: 10/06/2022] [Indexed: 12/14/2022]
Abstract
Small GTPases orchestrate numerous cellular pathways, acting as molecular switches and regulatory hubs to transmit molecular signals and because of this, they are often the target of pathogens. During infection, pathogens manipulate host cellular networks using post-translational modifications (PTMs). AMPylation, the modification of proteins with AMP, has been identified as a common PTM utilized by pathogens to hijack GTPase signalling during infection. AMPylation is primarily carried out by enzymes with a filamentation induced by cyclic-AMP (Fic) domain. Modification of small GTPases by AMP renders GTPases impervious to upstream regulatory inputs, resulting in unregulated downstream effector outputs for host cellular processes. Here, we overview Fic-mediated AMPylation of small GTPases by pathogens and other related PTMs catalysed by Fic enzymes on GTPases.
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Affiliation(s)
- Burak Gulen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amanda Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX and Howard Hughes Medical Institute, Dallas, TX, USA
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Abstract
RNA ligases are present across all forms of life. While enzymatic RNA ligation between 5'-PO4 and 3'-OH termini is prevalent in viruses, fungi, and plants, such RNA ligases are yet to be identified in vertebrates. Here, using a nucleotide-based chemical probe targeting human AMPylated proteome, we have enriched and identified the hitherto uncharacterised human protein chromosome 12 open reading frame 29 (C12orf29) as a human enzyme promoting RNA ligation between 5'-PO4 and 3'-OH termini. C12orf29 catalyses ATP-dependent RNA ligation via a three-step mechanism, involving tandem auto- and RNA AMPylation. Knock-out of C12ORF29 gene impedes the cellular resilience to oxidative stress featuring concurrent RNA degradation, which suggests a role of C12orf29 in maintaining RNA integrity. These data provide the groundwork for establishing a human RNA repair pathway.
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Casey AK, Gray HF, Chimalapati S, Hernandez G, Moehlman AT, Stewart N, Fields HA, Gulen B, Servage KA, Stefanius K, Blevins A, Evers BM, Krämer H, Orth K. Fic-mediated AMPylation tempers the unfolded protein response during physiological stress. Proc Natl Acad Sci U S A 2022; 119:e2208317119. [PMID: 35914137 PMCID: PMC9371680 DOI: 10.1073/pnas.2208317119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/09/2022] [Indexed: 12/14/2022] Open
Abstract
The proper balance of synthesis, folding, modification, and degradation of proteins, also known as protein homeostasis, is vital to cellular health and function. The unfolded protein response (UPR) is activated when the mechanisms maintaining protein homeostasis in the endoplasmic reticulum become overwhelmed. However, prolonged or strong UPR responses can result in elevated inflammation and cellular damage. Previously, we discovered that the enzyme filamentation induced by cyclic-AMP (Fic) can modulate the UPR response via posttranslational modification of binding immunoglobulin protein (BiP) by AMPylation during homeostasis and deAMPylation during stress. Loss of fic in Drosophila leads to vision defects and altered UPR activation in the fly eye. To investigate the importance of Fic-mediated AMPylation in a mammalian system, we generated a conditional null allele of Fic in mice and characterized the effect of Fic loss on the exocrine pancreas. Compared to controls, Fic-/- mice exhibit elevated serum markers for pancreatic dysfunction and display enhanced UPR signaling in the exocrine pancreas in response to physiological and pharmacological stress. In addition, both fic-/- flies and Fic-/- mice show reduced capacity to recover from damage by stress that triggers the UPR. These findings show that Fic-mediated AMPylation acts as a molecular rheostat that is required to temper the UPR response in the mammalian pancreas during physiological stress. Based on these findings, we propose that repeated physiological stress in differentiated tissues requires this rheostat for tissue resilience and continued function over the lifetime of an animal.
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Affiliation(s)
- Amanda K. Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hillery F. Gray
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Suneeta Chimalapati
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Genaro Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Andrew T. Moehlman
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Nathan Stewart
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hazel A. Fields
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Burak Gulen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kelly A. Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Karoliina Stefanius
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Aubrie Blevins
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Bret M. Evers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Helmut Krämer
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
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