1
|
Lee YT, Savini M, Chen T, Yang J, Zhao Q, Ding L, Gao SM, Senturk M, Sowa JN, Wang JD, Wang MC. Mitochondrial GTP metabolism controls reproductive aging in C. elegans. Dev Cell 2023; 58:2718-2731.e7. [PMID: 37708895 PMCID: PMC10842941 DOI: 10.1016/j.devcel.2023.08.019] [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: 05/26/2022] [Revised: 07/17/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP (mtGTP) metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP- but not ATP-specific succinyl-CoA synthetase (SCS) promotes reproductive longevity in Caenorhabditis elegans. We further identified an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion and reproductive longevity. Moreover, we discovered that bacterial inputs affect mtGTP levels and dynamics factors to modulate reproductive aging. These results demonstrate the significance of mtGTP metabolism in regulating oocyte mitochondrial homeostasis and reproductive longevity and identify mitochondrial fission induction as an effective strategy to improve reproductive health.
Collapse
Affiliation(s)
- Yi-Tang Lee
- Integrative Program of Molecular and Biochemical Sciences, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marzia Savini
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tao Chen
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Jin Yang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qian Zhao
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Lang Ding
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA; Graduate Program in Chemical, Physical & Structural Biology, Graduate School of Biomedical Science, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shihong Max Gao
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Mumine Senturk
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jessica N Sowa
- Department of Biology, West Chester University, West Chester, PA 19383, USA
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Meng C Wang
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
2
|
Lee YT, Savini M, Chen T, Yang J, Zhao Q, Ding L, Gao SM, Senturk M, Sowa J, Wang JD, Wang MC. Mitochondrial GTP Metabolism Regulates Reproductive Aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.02.535296. [PMID: 37066227 PMCID: PMC10103970 DOI: 10.1101/2023.04.02.535296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP- but not ATP-specific succinyl-CoA synthetase (SCS), promotes reproductive longevity in Caenorhabditis elegans. We further revealed an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by the GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion and reproductive longevity. Moreover, we discovered that bacterial inputs affect mitochondrial GTP and dynamics factors to modulate reproductive aging. These results demonstrate the significance of mitochondrial GTP metabolism in regulating oocyte mitochondrial homeostasis and reproductive longevity and reveal mitochondrial fission induction as an effective strategy to improve reproductive health.
Collapse
|
3
|
Benton D, Jaeger EC, Kilner A, Kimble A, Lowry J, Schleicher EM, Power KM, Uibel D, Eisele C, Bowerman B, Lyczak R. Interactions between the WEE-1.3 kinase and the PAM-1 aminopeptidase in oocyte maturation and the early C. elegans embryo. G3-GENES GENOMES GENETICS 2021; 11:6157833. [PMID: 33681968 PMCID: PMC8049411 DOI: 10.1093/g3journal/jkab063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/23/2021] [Indexed: 11/25/2022]
Abstract
Puromycin-sensitive aminopeptidases are found across phyla and are known to regulate the cell-cycle and play a protective role in neurodegenerative disease. PAM-1 is a puromycin-sensitive aminopeptidase important for meiotic exit and polarity establishment in the one-cell Caenorhabditis elegans embryo. Despite conservation of this aminopeptidase, little is known about its targets during development. In order to identify novel interactors, we conducted a suppressor screen and isolated four suppressing mutations in three genes that partially rescued the maternal-effect lethality of pam-1 mutants. Suppressed strains show improved embryonic viability and polarization of the anterior–posterior axis. We identified a missense mutation in wee-1.3 in one of these suppressed strains. WEE-1.3 is an inhibitory kinase that regulates maturation promoting factor. Although the missense mutation suppressed polarity phenotypes in pam-1, it does so without restoring centrosome–cortical contact or altering the cortical actomyosin cytoskeleton. To see if PAM-1 and WEE-1.3 interact in other processes, we examined oocyte maturation. Although depletion of wee-1.3 causes sterility due to precocious oocyte maturation, this effect was lessened in pam-1 worms, suggesting that PAM-1 and WEE-1.3 interact in this process. Levels of WEE-1.3 were comparable between wild-type and pam-1 strains, suggesting that WEE-1.3 is not a direct target of the aminopeptidase. Thus, we have established an interaction between PAM-1 and WEE-1.3 in multiple developmental processes and have identified suppressors that are likely to further our understanding of the role of puromycin-sensitive aminopeptidases during development.
Collapse
Affiliation(s)
- Dorothy Benton
- Biology Department, Ursinus College, 601 E Main Street, Collegeville, PA 19426, USA
| | - Eva C Jaeger
- Biology Department, Ursinus College, 601 E Main Street, Collegeville, PA 19426, USA
| | - Arielle Kilner
- Biology Department, Ursinus College, 601 E Main Street, Collegeville, PA 19426, USA.,Biomedical Studies Department, Graduate School of Biomedical Sciences and Professional Studies, Drexel University College of Medicine, 2900 W. Queen Lane Philadelphia, PA 19129, US A
| | - Ashley Kimble
- Biology Department, Ursinus College, 601 E Main Street, Collegeville, PA 19426, USA
| | - Josh Lowry
- Institute of Molecular Biology, 1229 University of Oregon, 1318 Franklin Blvd., Eugene, OR 97403, USA
| | - Emily M Schleicher
- Biology Department, Ursinus College, 601 E Main Street, Collegeville, PA 19426, USA
| | - Kaiden M Power
- Biology Department, Ursinus College, 601 E Main Street, Collegeville, PA 19426, USA
| | - Danielle Uibel
- Biology Department, Ursinus College, 601 E Main Street, Collegeville, PA 19426, USA
| | - Caprice Eisele
- Biology Department, Ursinus College, 601 E Main Street, Collegeville, PA 19426, USA
| | - Bruce Bowerman
- Institute of Molecular Biology, 1229 University of Oregon, 1318 Franklin Blvd., Eugene, OR 97403, USA
| | - Rebecca Lyczak
- Biology Department, Ursinus College, 601 E Main Street, Collegeville, PA 19426, USA
| |
Collapse
|
4
|
Jud MC, Lowry J, Padilla T, Clifford E, Yang Y, Fennell F, Miller AK, Hamill D, Harvey AM, Avila-Zavala M, Shao H, Nguyen Tran N, Bao Z, Bowerman B. A genetic screen for temperature-sensitive morphogenesis-defective Caenorhabditis elegans mutants. G3-GENES GENOMES GENETICS 2021; 11:6169531. [PMID: 33713117 PMCID: PMC8133775 DOI: 10.1093/g3journal/jkab026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 11/21/2022]
Abstract
Morphogenesis involves coordinated cell migrations and cell shape changes that generate tissues and organs, and organize the body plan. Cell adhesion and the cytoskeleton are important for executing morphogenesis, but their regulation remains poorly understood. As genes required for embryonic morphogenesis may have earlier roles in development, temperature-sensitive embryonic-lethal mutations are useful tools for investigating this process. From a collection of ∼200 such Caenorhabditis elegans mutants, we have identified 17 that have highly penetrant embryonic morphogenesis defects after upshifts from the permissive to the restrictive temperature, just prior to the cell shape changes that mediate elongation of the ovoid embryo into a vermiform larva. Using whole genome sequencing, we identified the causal mutations in seven affected genes. These include three genes that have roles in producing the extracellular matrix, which is known to affect the morphogenesis of epithelial tissues in multicellular organisms: the rib-1 and rib-2 genes encode glycosyltransferases, and the emb-9 gene encodes a collagen subunit. We also used live imaging to characterize epidermal cell shape dynamics in one mutant, or1219ts, and observed cell elongation defects during dorsal intercalation and ventral enclosure that may be responsible for the body elongation defects. These results indicate that our screen has identified factors that influence morphogenesis and provides a platform for advancing our understanding of this fundamental biological process.
Collapse
Affiliation(s)
- Molly C Jud
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Josh Lowry
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Thalia Padilla
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Erin Clifford
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Yuqi Yang
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Francesca Fennell
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Alexander K Miller
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Danielle Hamill
- Department of Zoology, Ohio Wesleyan University, Delaware, OH, 43015, USA
| | - Austin M Harvey
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Martha Avila-Zavala
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Hong Shao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Nhan Nguyen Tran
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Bruce Bowerman
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| |
Collapse
|
5
|
Chen Y, Leboutet R, Largeau C, Zentout S, Lefebvre C, Delahodde A, Culetto E, Legouis R. Autophagy facilitates mitochondrial rebuilding after acute heat stress via a DRP-1-dependent process. J Cell Biol 2021; 220:e201909139. [PMID: 33734301 PMCID: PMC7980257 DOI: 10.1083/jcb.201909139] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/21/2020] [Accepted: 01/21/2021] [Indexed: 02/06/2023] Open
Abstract
Acute heat stress (aHS) can induce strong developmental defects in Caenorhabditis elegans larva but not lethality or sterility. This stress results in transitory fragmentation of mitochondria, formation of aggregates in the matrix, and decrease of mitochondrial respiration. Moreover, active autophagic flux associated with mitophagy events enables the rebuilding of the mitochondrial network and developmental recovery, showing that the autophagic response is protective. This adaptation to aHS does not require Pink1/Parkin or the mitophagy receptors DCT-1/NIX and FUNDC1. We also find that mitochondria are a major site for autophagosome biogenesis in the epidermis in both standard and heat stress conditions. In addition, we report that the depletion of the dynamin-related protein 1 (DRP-1) affects autophagic processes and the adaptation to aHS. In drp-1 animals, the abnormal mitochondria tend to modify their shape upon aHS but are unable to achieve fragmentation. Autophagy is induced, but autophagosomes are abnormally elongated and clustered on mitochondria. Our data support a role for DRP-1 in coordinating mitochondrial fission and autophagosome biogenesis in stress conditions.
Collapse
Affiliation(s)
- Yanfang Chen
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Romane Leboutet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
- INSERM U1280, Gif‐sur‐Yvette, France
| | - Céline Largeau
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
- INSERM U1280, Gif‐sur‐Yvette, France
| | - Siham Zentout
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Christophe Lefebvre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
- INSERM U1280, Gif‐sur‐Yvette, France
| | - Agnès Delahodde
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Emmanuel Culetto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
- INSERM U1280, Gif‐sur‐Yvette, France
| | - Renaud Legouis
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
- INSERM U1280, Gif‐sur‐Yvette, France
| |
Collapse
|
6
|
Molecular Basis of Neuronal Autophagy in Ageing: Insights from Caenorhabditis elegans. Cells 2021; 10:cells10030694. [PMID: 33800981 PMCID: PMC8004021 DOI: 10.3390/cells10030694] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/19/2023] Open
Abstract
Autophagy is an evolutionarily conserved degradation process maintaining cell homeostasis. Induction of autophagy is triggered as a response to a broad range of cellular stress conditions, such as nutrient deprivation, protein aggregation, organelle damage and pathogen invasion. Macroautophagy involves the sequestration of cytoplasmic contents in a double-membrane organelle referred to as the autophagosome with subsequent degradation of its contents upon delivery to lysosomes. Autophagy plays critical roles in development, maintenance and survival of distinct cell populations including neurons. Consequently, age-dependent decline in autophagy predisposes animals for age-related diseases including neurodegeneration and compromises healthspan and longevity. In this review, we summarize recent advances in our understanding of the role of neuronal autophagy in ageing, focusing on studies in the nematode Caenorhabditis elegans.
Collapse
|
7
|
Lysosomal activity regulates Caenorhabditis elegans mitochondrial dynamics through vitamin B12 metabolism. Proc Natl Acad Sci U S A 2020; 117:19970-19981. [PMID: 32737159 DOI: 10.1073/pnas.2008021117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial fission and fusion are highly regulated by energy demand and physiological conditions to control the production, activity, and movement of these organelles. Mitochondria are arrayed in a periodic pattern in Caenorhabditis elegans muscle, but this pattern is disrupted by mutations in the mitochondrial fission component dynamin DRP-1. Here we show that the dramatically disorganized mitochondria caused by a mitochondrial fission-defective dynamin mutation is strongly suppressed to a more periodic pattern by a second mutation in lysosomal biogenesis or acidification. Vitamin B12 is normally imported from the bacterial diet via lysosomal degradation of B12-binding proteins and transport of vitamin B12 to the mitochondrion and cytoplasm. We show that the lysosomal dysfunction induced by gene inactivations of lysosomal biogenesis or acidification factors causes vitamin B12 deficiency. Growth of the C. elegans dynamin mutant on an Escherichia coli strain with low vitamin B12 also strongly suppressed the mitochondrial fission defect. Of the two C. elegans enzymes that require B12, gene inactivation of methionine synthase suppressed the mitochondrial fission defect of a dynamin mutation. We show that lysosomal dysfunction induced mitochondrial biogenesis, which is mediated by vitamin B12 deficiency and methionine restriction. S-adenosylmethionine, the methyl donor of many methylation reactions, including histones, is synthesized from methionine by S-adenosylmethionine synthase; inactivation of the sams-1 S-adenosylmethionine synthase also suppresses the drp-1 fission defect, suggesting that vitamin B12 regulates mitochondrial biogenesis and then affects mitochondrial fission via chromatin pathways.
Collapse
|
8
|
Oh KH, Sheoran S, Richmond JE, Kim H. Alcohol induces mitochondrial fragmentation and stress responses to maintain normal muscle function in Caenorhabditis elegans. FASEB J 2020; 34:8204-8216. [PMID: 32294300 DOI: 10.1096/fj.201903166r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/30/2020] [Accepted: 04/06/2020] [Indexed: 12/17/2022]
Abstract
Chronic excessive ethanol consumption has distinct toxic and adverse effects on a variety of tissues. In skeletal muscle, ethanol causes alcoholic myopathy, which is characterized by myofiber atrophy and the loss of muscle strength. Alcoholic myopathy is more prevalent than all inherited muscle diseases combined. Current evidence indicates that ethanol directly impairs muscle organization and function. However, the underlying mechanism by which ethanol causes toxicity in muscle is poorly understood. Here, we show that the nematode Caenorhabditis elegans exhibits the key features of alcoholic myopathy when exposed to ethanol. As in mammals, ethanol exposure impairs muscle strength and induces the expression of protective genes, including oxidative stress response genes. In addition, ethanol exposure causes the fragmentation of mitochondrial networks aligned with myofibril lattices. This ethanol-induced mitochondrial fragmentation is dependent on the mitochondrial fission factor DRP-1 (dynamin-related protein 1) and its receptor proteins on the outer mitochondrial membrane. Our data indicate that this fragmentation contributes to the activation of the mitochondrial unfolded protein response (UPR). We also found that robust, perpetual mitochondrial UPR activation effectively reduces muscle weakness caused by ethanol exposure. Our results strongly suggest that the modulation of mitochondrial stress responses may provide a method to ameliorate alcohol toxicity and damage to muscle.
Collapse
Affiliation(s)
- Kelly H Oh
- Department of Cell Biology & Anatomy, Center for Cancer Cell Biology, Immunology, and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA.,School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Seema Sheoran
- Department of Biological Science, University of Illinois at Chicago, Chicago, IL, USA
| | - Janet E Richmond
- Department of Biological Science, University of Illinois at Chicago, Chicago, IL, USA
| | - Hongkyun Kim
- Department of Cell Biology & Anatomy, Center for Cancer Cell Biology, Immunology, and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA.,School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| |
Collapse
|
9
|
Testa ND, Kaul S, Le KN, Zhan M, Lu H, Paaby AB. A portable, low-cost device for precise control of specimen temperature under stereomicroscopes. PLoS One 2020; 15:e0230241. [PMID: 32160236 PMCID: PMC7065815 DOI: 10.1371/journal.pone.0230241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/25/2020] [Indexed: 11/27/2022] Open
Abstract
To facilitate precise and convenient control of biological sample temperature, we developed a low-cost device that can be used independently or with any stereomicroscope. The purpose of the device is to control the thermal environment during experimental intervals in which a specimen must be manipulated outside of an incubator, e.g. for dissection or slide-mounting in preparation for imaging. Sample temperatures can be both cooled to below and heated to above room temperatures, and stably maintained at a precision of +/- 0.1˚C. To demonstrate the utility of this device, we report improved characterization of the penetrance of a short-acting temperature-sensitive allele in C. elegans embryos, and identification of the upper temperature threshold for embryonic viability for six Caenorhabditis species. By controlling the temperature environment even as a specimen is manipulated, this device offers consistency and flexibility, reduces environmental noise, and enables precision timing in experiments requiring temperature shifts.
Collapse
Affiliation(s)
- Nicholas D. Testa
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Samiksha Kaul
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Kim N. Le
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Mei Zhan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Annalise B. Paaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
- * E-mail:
| |
Collapse
|
10
|
Evolutionary Dynamics of the SKN-1 → MED → END-1,3 Regulatory Gene Cascade in Caenorhabditis Endoderm Specification. G3-GENES GENOMES GENETICS 2020; 10:333-356. [PMID: 31740453 PMCID: PMC6945043 DOI: 10.1534/g3.119.400724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene regulatory networks and their evolution are important in the study of animal development. In the nematode, Caenorhabditis elegans, the endoderm (gut) is generated from a single embryonic precursor, E. Gut is specified by the maternal factor SKN-1, which activates the MED → END-1,3 → ELT-2,7 cascade of GATA transcription factors. In this work, genome sequences from over two dozen species within the Caenorhabditis genus are used to identify MED and END-1,3 orthologs. Predictions are validated by comparison of gene structure, protein conservation, and putative cis-regulatory sites. All three factors occur together, but only within the Elegans supergroup, suggesting they originated at its base. The MED factors are the most diverse and exhibit an unexpectedly extensive gene amplification. In contrast, the highly conserved END-1 orthologs are unique in nearly all species and share extended regions of conservation. The END-1,3 proteins share a region upstream of their zinc finger and an unusual amino-terminal poly-serine domain exhibiting high codon bias. Compared with END-1, the END-3 proteins are otherwise less conserved as a group and are typically found as paralogous duplicates. Hence, all three factors are under different evolutionary constraints. Promoter comparisons identify motifs that suggest the SKN-1, MED, and END factors function in a similar gut specification network across the Elegans supergroup that has been conserved for tens of millions of years. A model is proposed to account for the rapid origin of this essential kernel in the gut specification network, by the upstream intercalation of duplicate genes into a simpler ancestral network.
Collapse
|
11
|
Byrne JJ, Soh MS, Chandhok G, Vijayaraghavan T, Teoh JS, Crawford S, Cobham AE, Yapa NMB, Mirth CK, Neumann B. Disruption of mitochondrial dynamics affects behaviour and lifespan in Caenorhabditis elegans. Cell Mol Life Sci 2019; 76:1967-1985. [PMID: 30840087 PMCID: PMC6478650 DOI: 10.1007/s00018-019-03024-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 01/29/2023]
Abstract
Mitochondria are essential components of eukaryotic cells, carrying out critical physiological processes that include energy production and calcium buffering. Consequently, mitochondrial dysfunction is associated with a range of human diseases. Fundamental to their function is the ability to transition through fission and fusion states, which is regulated by several GTPases. Here, we have developed new methods for the non-subjective quantification of mitochondrial morphology in muscle and neuronal cells of Caenorhabditis elegans. Using these techniques, we uncover surprising tissue-specific differences in mitochondrial morphology when fusion or fission proteins are absent. From ultrastructural analysis, we reveal a novel role for the fusion protein FZO-1/mitofusin 2 in regulating the structure of the inner mitochondrial membrane. Moreover, we have determined the influence of the individual mitochondrial fission (DRP-1/DRP1) and fusion (FZO-1/mitofusin 1,2; EAT-3/OPA1) proteins on animal behaviour and lifespan. We show that loss of these mitochondrial fusion or fission regulators induced age-dependent and progressive deficits in animal movement, as well as in muscle and neuronal function. Our results reveal that disruption of fusion induces more profound defects than lack of fission on animal behaviour and tissue function, and imply that while fusion is required throughout life, fission is more important later in life likely to combat ageing-associated stressors. Furthermore, our data demonstrate that mitochondrial function is not strictly dependent on morphology, with no correlation found between morphological changes and behavioural defects. Surprisingly, we find that disruption of either mitochondrial fission or fusion significantly reduces median lifespan, but maximal lifespan is unchanged, demonstrating that mitochondrial dynamics play an important role in limiting variance in longevity across isogenic populations. Overall, our study provides important new insights into the central role of mitochondrial dynamics in maintaining organismal health.
Collapse
Affiliation(s)
- Joseph J Byrne
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Ming S Soh
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Gursimran Chandhok
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Tarika Vijayaraghavan
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Jean-Sébastien Teoh
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Simon Crawford
- Monash Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Melbourne, VIC, 3800, Australia
| | - Ansa E Cobham
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Nethmi M B Yapa
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Christen K Mirth
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Brent Neumann
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia.
| |
Collapse
|
12
|
Palmisano NJ, Meléndez A. Autophagy in C. elegans development. Dev Biol 2019; 447:103-125. [PMID: 29709599 PMCID: PMC6204124 DOI: 10.1016/j.ydbio.2018.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 03/19/2018] [Accepted: 04/12/2018] [Indexed: 12/11/2022]
Abstract
Autophagy involves the sequestration of cytoplasmic contents in a double-membrane structure referred to as the autophagosome and the degradation of its contents upon delivery to lysosomes. Autophagy activity has a role in multiple biological processes during the development of the nematode Caenorhabditis elegans. Basal levels of autophagy are required to remove aggregate prone proteins, paternal mitochondria, and spermatid-specific membranous organelles. During larval development, autophagy is required for the remodeling that occurs during dauer development, and autophagy can selectively degrade components of the miRNA-induced silencing complex, and modulate miRNA-mediated silencing. Basal levels of autophagy are important in synapse formation and in the germ line, to promote the proliferation of proliferating stem cells. Autophagy activity is also required for the efficient removal of apoptotic cell corpses by promoting phagosome maturation. Finally, autophagy is also involved in lipid homeostasis and in the aging process. In this review, we first describe the molecular complexes involved in the process of autophagy, its regulation, and mechanisms for cargo recognition. In the second section, we discuss the developmental contexts where autophagy has been shown to be important. Studies in C. elegans provide valuable insights into the physiological relevance of this process during metazoan development.
Collapse
Affiliation(s)
- Nicholas J Palmisano
- Biology Department, Queens College, CUNY, Flushing, NY, USA; Biology Ph.D. Program, The Graduate Center of the City University of New York, NK, USA
| | - Alicia Meléndez
- Biology Department, Queens College, CUNY, Flushing, NY, USA; Biology Ph.D. Program, The Graduate Center of the City University of New York, NK, USA; Biochemistry Ph.D. Program, The Graduate Center of the City University of New York, NY, USA.
| |
Collapse
|
13
|
Henis-Korenblit S, Meléndez A. Methods to Determine the Role of Autophagy Proteins in C. elegans Aging. Methods Mol Biol 2019; 1880:561-586. [PMID: 30610723 DOI: 10.1007/978-1-4939-8873-0_37] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
This chapter describes methods for the analysis of autophagy proteins in C. elegans aging. We discuss the strains to be considered, the methods for the delivery of double-stranded RNA, and the methods to measure autophagy levels, autophagic flux, and degradation by autophagy.
Collapse
Affiliation(s)
- Sivan Henis-Korenblit
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
| | - Alicia Meléndez
- Department of Biology, Queens College, The City University of New York, Flushing, NY, USA.
- Biology and Biochemistry PhD Programs, The Graduate Center of the City University of New York, New York, NY, USA.
| |
Collapse
|
14
|
Hernando-Rodríguez B, Erinjeri AP, Rodríguez-Palero MJ, Millar V, González-Hernández S, Olmedo M, Schulze B, Baumeister R, Muñoz MJ, Askjaer P, Artal-Sanz M. Combined flow cytometry and high-throughput image analysis for the study of essential genes in Caenorhabditis elegans. BMC Biol 2018; 16:36. [PMID: 29598825 PMCID: PMC5875015 DOI: 10.1186/s12915-018-0496-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/06/2018] [Indexed: 12/28/2022] Open
Abstract
Background Advances in automated image-based microscopy platforms coupled with high-throughput liquid workflows have facilitated the design of large-scale screens utilising multicellular model organisms such as Caenorhabditis elegans to identify genetic interactions, therapeutic drugs or disease modifiers. However, the analysis of essential genes has lagged behind because lethal or sterile mutations pose a bottleneck for high-throughput approaches, and a systematic way to analyse genetic interactions of essential genes in multicellular organisms has been lacking. Results In C. elegans, non-conditional lethal mutations can be maintained in heterozygosity using chromosome balancers, commonly expressing green fluorescent protein (GFP) in the pharynx. However, gene expression or function is typically monitored by the use of fluorescent reporters marked with the same fluorophore, presenting a challenge to sort worm populations of interest, particularly at early larval stages. Here, we develop a sorting strategy capable of selecting homozygous mutants carrying a GFP stress reporter from GFP-balanced animals at the second larval stage. Because sorting is not completely error-free, we develop an automated high-throughput image analysis protocol that identifies and discards animals carrying the chromosome balancer. We demonstrate the experimental usefulness of combining sorting of homozygous lethal mutants and automated image analysis in a functional genomic RNA interference (RNAi) screen for genes that genetically interact with mitochondrial prohibitin (PHB). Lack of PHB results in embryonic lethality, while homozygous PHB deletion mutants develop into sterile adults due to maternal contribution and strongly induce the mitochondrial unfolded protein response (UPRmt). In a chromosome-wide RNAi screen for C. elegans genes having human orthologues, we uncover both known and new PHB genetic interactors affecting the UPRmt and growth. Conclusions The method presented here allows the study of balanced lethal mutations in a high-throughput manner. It can be easily adapted depending on the user’s requirements and should serve as a useful resource for the C. elegans community for probing new biological aspects of essential nematode genes as well as the generation of more comprehensive genetic networks. Electronic supplementary material The online version of this article (10.1186/s12915-018-0496-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Blanca Hernando-Rodríguez
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Annmary Paul Erinjeri
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - María Jesús Rodríguez-Palero
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Val Millar
- GE Healthcare Life Sciences, Maynard Centre, Forest Farm, Whitchurch, Cardiff, UK.,Present address: Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sara González-Hernández
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain.,Present address: Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - María Olmedo
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain.,Present address: Department of Genetics, University of Seville, Seville, Spain
| | - Bettina Schulze
- Centre for Biological Signalling Studies (BIOSS), Laboratory for Bioinformatics and Molecular Genetics, Faculty of Biology, and ZBMZ Center for Biochemistry and Molecular Cell Biology (Faculty of Medicine), Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Ralf Baumeister
- Centre for Biological Signalling Studies (BIOSS), Laboratory for Bioinformatics and Molecular Genetics, Faculty of Biology, and ZBMZ Center for Biochemistry and Molecular Cell Biology (Faculty of Medicine), Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Manuel J Muñoz
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain
| | - Marta Artal-Sanz
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain. .,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain.
| |
Collapse
|
15
|
MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes. Genetics 2017; 207:447-463. [PMID: 28827289 PMCID: PMC5629315 DOI: 10.1534/genetics.117.300179] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/30/2017] [Indexed: 11/18/2022] Open
Abstract
Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans. Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2. We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures.
Collapse
|