Modeling of a negative feedback mechanism explains age-dependent genetic architecture in reproduction in domesticated C. elegans strains

ABSTRACTMost biological traits and common diseases have a strong but complex genetic basis, controlled by large numbers of genetic variants with small contributions to a trait or disease risk. The effect-size of most genetic variants is not absolute, but can depend on a number of factors including the age and genetic background of an organism. In order to understand the mechanisms that cause these changes, we are studying heritable trait differences between two domesticated strains of C. elegans. We previously identified a major effect locus, caused by a mutation in a component of the NURF chromatin remodeling complex, that regulated reproductive output in an age-dependent manner. The effect-size of this locus changes from positive to negative over the course of an animal’s reproductive lifespan. Using a previously published macroscale model of egg-laying rate in C. elegans, we show how time-dependent effect-size can be explained by an unequal use of sperm combined with negative feedback between sperm and ovulation rate. We validate a number of key predictions of this model using controlled mating experiments and quantification of oogenesis and sperm use. By incorporating this model into QTL mapping, we identify and partition new QTLs into specific aspects of the egg-laying process. Finally, we show how epistasis between two genetic variants is predicted by this modeling as a consequence of unequal use of sperm. This work demonstrates how modeling of multicellular communication systems can improve our ability to predict and understand the role of genetic variation on a complex phenotype. Negative autoregulatory feedback loops, common in transcriptional regulation, could play an important role in modifying genetic architecture in other traits.AUTHOR SUMMARYComplex traits are influenced not only by the individual effects of genetic variants, but also how these variants interact with the environment, age, and each other. While complex genetic architectures seem to be ubiquitous in natural traits, little is known about the mechanisms that cause them. Here we identify an example of age-dependent genetic architecture controlling the rate and timing of reproduction in the hermaphroditic nematode C. elegans. Using computational modeling, we demonstrate how this age-dependent genetic architecture can arise as a consequence of two factors: hormonal feedback on oocytes mediated by major sperm protein (MSP) released by sperm stored in the spermatheca and life history differences in sperm use caused by genetic variants. Our work also suggests how age-dependent epistasis can emerge from multicellular feedback systems.

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Corrigendum to: IQ motif containing D (IQCD), a new acrosomal protein involved in the acrosome reaction and fertilisation

Reproduction Fertility and Development ◽

10.1071/rd18416_co ◽

2019 ◽

Vol 31 (5) ◽

pp. 1033

Author(s):

Peng Zhang ◽

Wanjun Jiang ◽

Na Luo ◽

Wenbing Zhu ◽

Liqing Fan

Keyword(s):

Acrosome Reaction ◽

Development Stage ◽

Seminiferous Tubules ◽

Testicular Development ◽

Dependent Manner ◽

Iq Motif ◽

C Elegans ◽

Fertilisation Rate ◽

Age Dependent ◽

Mammalian Spermatozoa

The acrosome is single, large, dense-core secretory granule overlying the nucleus of most mammalian spermatozoa. Its exocytosis, the acrosome reaction, is a crucial event during fertilisation. In this study we identified a new acrosome-associated gene, namely IQ motif containing D (IQCD), expressed nearly in multiple tissues with highest expression levels in the testis. In mouse testis, Iqcd transcript accumulated from Postnatal Day (PND) 1 to adulthood. However, expression of IQCD protein at the testicular development stage started primarily from PND 18 and increased in an age-dependent manner until plateauing in adulthood. IQCD was primarily accumulated in the acrosome area of round and elongating spermatids within seminiferous tubules of the testes during the late stage of spermiogenesis; this immunolocalisation pattern is similar in mice and humans. IQCD levels in spermatozoa were significantly lower in IVF patients with total fertilisation failure or a low fertilisation rate than in healthy men. Anti-IQCD antibody significantly inhibited the acrosome reaction and slightly reduced protein tyrosine phosphorylation levels in human spermatozoa, but specifically blocked murine IVF. IQCD interacted with mammalian homolog of C. elegans uncoordinated gene 13 (Munc13) in spermatozoa and may participate in acrosome exocytosis. In conclusion, this study identified a new acrosomal protein, namely IQCD, which is involved in fertilisation and the acrosome reaction.

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Whole-organism behavioral profiling reveals a role for dopamine in state-dependent motor program coupling in C. elegans

10.1101/2020.03.27.011015 ◽

2020 ◽

Author(s):

Nathan Cermak ◽

Stephanie K. Yu ◽

Rebekah Clark ◽

Yung-Chi Huang ◽

Steven W. Flavell

Keyword(s):

Motor Program ◽

Egg Laying ◽

Neural Mechanisms ◽

Dependent Manner ◽

Motor Programs ◽

C Elegans ◽

Motor Circuits ◽

State Dependent ◽

Behavioral States ◽

Behavioral Profiling

AbstractAnimal behaviors are commonly organized into long-lasting states that coordinately impact the generation of diverse motor outputs such as feeding, locomotion, and grooming. However, the neural mechanisms that coordinate these diverse motor programs remain poorly understood. Here, we examine how the distinct motor programs of the nematode C. elegans are coupled together across behavioral states. We describe a new imaging platform that permits automated, simultaneous quantification of each of the main C. elegans motor programs over hours or days. Analysis of these whole-organism behavioral profiles shows that the motor programs coordinately change as animals switch behavioral states. Utilizing genetics, optogenetics, and calcium imaging, we identify a new role for dopamine in coupling locomotion and egg-laying together across states. These results provide new insights into how the diverse motor programs throughout an organism are coordinated and suggest that neuromodulators like dopamine can couple motor circuits together in a state-dependent manner.

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IQ motif containing D (IQCD), a new acrosomal protein involved in the acrosome reaction and fertilisation

Reproduction Fertility and Development ◽

10.1071/rd18416 ◽

2019 ◽

Vol 31 (5) ◽

pp. 898 ◽

Cited By ~ 1

Author(s):

Peng Zhang ◽

Wanjun Jiang ◽

Na Luo ◽

Wenbing Zhu ◽

Liqing Fan

Keyword(s):

Acrosome Reaction ◽

Development Stage ◽

Seminiferous Tubules ◽

Testicular Development ◽

Dependent Manner ◽

Iq Motif ◽

C Elegans ◽

Fertilisation Rate ◽

Age Dependent ◽

Mammalian Spermatozoa

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Whole-organism behavioral profiling reveals a role for dopamine in state-dependent motor program coupling in C. elegans

eLife ◽

10.7554/elife.57093 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 4

Author(s):

Nathan Cermak ◽

Stephanie K Yu ◽

Rebekah Clark ◽

Yung-Chi Huang ◽

Saba N Baskoylu ◽

...

Keyword(s):

Motor Program ◽

Egg Laying ◽

Neural Mechanisms ◽

Dependent Manner ◽

Motor Programs ◽

C Elegans ◽

Motor Circuits ◽

State Dependent ◽

Behavioral States ◽

Behavioral Profiling

Animal behaviors are commonly organized into long-lasting states that coordinately impact the generation of diverse motor outputs such as feeding, locomotion, and grooming. However, the neural mechanisms that coordinate these distinct motor programs remain poorly understood. Here, we examine how the distinct motor programs of the nematode C. elegans are coupled together across behavioral states. We describe a new imaging platform that permits automated, simultaneous quantification of each of the main C. elegans motor programs over hours or days. Analysis of these whole-organism behavioral profiles shows that the motor programs coordinately change as animals switch behavioral states. Utilizing genetics, optogenetics, and calcium imaging, we identify a new role for dopamine in coupling locomotion and egg-laying together across states. These results provide new insights into how the diverse motor programs throughout an organism are coordinated and suggest that neuromodulators like dopamine can couple motor circuits together in a state-dependent manner.

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Age and diet shape the genetic architecture of body weight in Diversity Outbred mice

10.1101/2020.11.04.364398 ◽

2020 ◽

Author(s):

Kevin M. Wright ◽

Andrew Deighan ◽

Andrea Di Francesco ◽

Adam Freund ◽

Vladimir Jojic ◽

...

Keyword(s):

Body Weight ◽

Genetic Architecture ◽

Mixed Model ◽

Linear Mixed Model ◽

Environment Interaction ◽

Dependent Manner ◽

Dietary Interventions ◽

Functional Variants ◽

Diversity Outbred ◽

Age Dependent

AbstractUnderstanding how genetic variation shapes an age-dependent complex trait relies on accurate quantification of both the additive genetic effects and genotype-environment interaction effects in an age-dependent manner. We used a generalization of the linear mixed model to quantify diet-dependent genetic contributions to body weight and growth rate measured from early development through adulthood of 960 Diversity Outbred female mice subjected to five dietary interventions. We observed that heritability of body weight remained substantially high (h2 ≈ 0.8) throughout adulthood under the 40% calorie restriction diet, while heritability, although still appreciably high, declined with age under all other dietary regimes. We identified 14 loci significantly associated with body weight in an age-dependent manner and 19 loci that contribute to body weight in an age- and diet-dependent manner. We found the effect of body weight alleles to be dynamic with respect to genomic background, age, and diet, identifying the scope of pleiotropy and several instances of allelic heterogeneity. In many cases, we fine-mapped these loci to narrow genomic intervals containing a few genes and impute putative functional variants from the genome sequence of the DO founders. Of the loci associated with body weight in a diet-dependent manner, many have been previously linked to neurological function and behavior in mice or humans. These results enable us to more fully understand the dynamics of the genetic architecture of body weight with age and in response to different dietary interventions, and to predict the effectiveness of dietary intervention on overall health in distinct genetic backgrounds.

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The PP2A/4/6 subfamily of phosphoprotein phosphatases regulates DAF-16 during aging and confers resistance to environmental stress in postreproductive adult C. elegans

10.1101/2020.02.18.953687 ◽

2020 ◽

Author(s):

Rebecca S. Rivard ◽

Julia M. Morris ◽

Matthew J. Youngman

Keyword(s):

Environmental Stress ◽

Transcriptional Activity ◽

Reverse Genetics ◽

Dependent Manner ◽

C Elegans ◽

Forkhead Box ◽

Phosphoprotein Phosphatases ◽

Complex Functions ◽

Age Dependent ◽

Foxo Transcription Factors

AbstractInsulin and insulin-like growth factors are longevity determinants that negatively regulate Forkhead box class O (FoxO) transcription factors. In C. elegans mutations that constitutively activate DAF-16, the ortholog of mammalian FoxO3a, extend lifespan by two-fold. While environmental insults induce DAF-16 activity in younger animals, it also becomes activated in an age-dependent manner in the absence of stress, modulating gene expression well into late adulthood. The mechanism by which DAF-16 activity is regulated during aging has not been defined. Since phosphorylation of DAF-16 generally leads to its inhibition, we asked whether phosphatases might be necessary for its increased transcriptional activity in adult C. elegans. We focused on the PP2A/4/6 subfamily of phosphoprotein phosphatases, members of which had been implicated to regulate DAF-16 under low insulin signaling conditions but had not been investigated during aging in wildtype animals. Using reverse genetics, we functionally characterized all C. elegans orthologs of human catalytic, regulatory, and scaffolding subunits of PP2A/4/6 holoenzymes in postreproductive adults. We found that PP2A complex constituents PAA-1 and PPTR-1 regulate DAF-16 during aging and that they cooperate with the catalytic subunit LET-92 to protect adult animals from ultraviolet radiation. PP4 complex members PPH-4.1/4.2, SMK-1, and PPFR-2 also appear to regulate DAF-16 in an age-dependent manner, and they contribute to innate immunity. Interestingly, SUR-6 but no other subunit of the PP2A complex was necessary for the survival of pathogen-infected animals, suggesting that a heterotypic PP4 complex functions during aging. Finally, we found that PP6 complex constituents PPH-6 and SAPS-1 contribute to host defense during aging, apparently without affecting DAF-16 transcriptional activity. Our studies indicate that a set of PP2A/4/6 complexes protect adult C. elegans from environmental stress, thus preserving healthspan. Therefore, along with their functions in cell division and development, the PP2A/4/6 phosphatases also appear to play critical roles later in life.

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Role of oxidation of excitation-contraction coupling machinery in age-dependent loss of muscle function in C. elegans

10.1101/2021.12.05.471286 ◽

2021 ◽

Author(s):

Haikel Dridi ◽

Frances Forrester ◽

Alisa Umanskaya ◽

Wenjun Xie ◽

Steven Reiken ◽

...

Keyword(s):

Exercise Capacity ◽

Muscle Function ◽

Body Wall ◽

Body Wall Muscle ◽

Macromolecular Complex ◽

Mammalian Skeletal Muscle ◽

Dependent Manner ◽

C Elegans ◽

Reduced Body ◽

Age Dependent

ABSTRACTAge-dependent loss of body wall muscle function and impaired locomotion occur within 2 weeks in C. elegans; however, the underlying mechanism has not been fully elucidated. In humans, age-dependent loss of muscle function occurs at about 80 years of age and has been linked to dysfunction of ryanodine receptor (RyR)/intracellular calcium (Ca2+) release channels on the sarcoplasmic reticulum (SR). Mammalian skeletal muscle RyR1 channels undergo age-related remodeling due to oxidative overload, leading to loss of the stabilizing subunit calstabin1 (FKBP12) from the channel macromolecular complex. This destabilizes the closed state of the channel resulting in intracellular Ca2+ leak, reduced muscle function, and impaired exercise capacity. We now show that the C. elegans RyR homolog, UNC-68, exhibits a remarkable degree of evolutionary conservation with mammalian RyR channels and similar age-dependent dysfunction. Like RyR1 in mammals UNC-68 encodes a protein that comprises a macromolecular complex which includes the calstabin1 homolog FKB-2 and is immunoreactive with antibodies raised against the RyR1 complex. Further, as in aged mammals, UNC-68 is oxidized and depleted of FKB-2 in an age-dependent manner, resulting in “leaky” channels, depleted SR Ca2+ stores, reduced body wall muscle Ca2+ transients, and age-dependent muscle weakness. FKB-2 (ok3007)-deficient worms exhibit reduced exercise capacity. Pharmacologically induced oxidization of UNC-68 and depletion of FKB-2 from the channel independently caused reduced body wall muscle Ca2+ transients. Preventing FKB-2 depletion from the UNC-68 macromolecular complex using the Rycal drug S107 improved muscle Ca2+ transients and function. Taken together, these data suggest that UNC-68 oxidation plays a role in age-dependent loss of muscle function. Remarkably, this age-dependent loss of muscle function induced by oxidative overload, which takes ~2 years in mice and ~80 years in humans, occurs in less than 2-3 weeks in C. elegans, suggesting that reduced anti-oxidant capacity may contribute to the differences in life span amongst species.

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Axon Injury-Induced Autophagy Activation Is Impaired in a C. elegans Model of Tauopathy

International Journal of Molecular Sciences ◽

10.3390/ijms21228559 ◽

2020 ◽

Vol 21 (22) ◽

pp. 8559

Author(s):

Su-Hyuk Ko ◽

Gilberto Gonzalez ◽

Zhijie Liu ◽

Lizhen Chen

Keyword(s):

Axon Regeneration ◽

Dependent Manner ◽

Regeneration Capacity ◽

Transgenic Expression ◽

Axon Injury ◽

C Elegans ◽

Age Dependent ◽

Tau Aggregation ◽

Axonal Trafficking ◽

Neuronal Stress

Autophagy is a conserved pathway that plays a key role in cell homeostasis in normal settings, as well as abnormal and stress conditions. Autophagy dysfunction is found in various neurodegenerative diseases, although it remains unclear whether autophagy impairment is a contributor or consequence of neurodegeneration. Axonal injury is an acute neuronal stress that triggers autophagic responses in an age-dependent manner. In this study, we investigate the injury-triggered autophagy response in a C. elegans model of tauopathy. We found that transgenic expression of pro-aggregant Tau, but not the anti-aggregant Tau, abolished axon injury-induced autophagy activation, resulting in a reduced axon regeneration capacity. Furthermore, axonal trafficking of autophagic vesicles were significantly reduced in the animals expressing pro-aggregant F3ΔK280 Tau, indicating that Tau aggregation impairs autophagy regulation. Importantly, the reduced number of total or trafficking autophagic vesicles in the tauopathy model was not restored by the autophagy activator rapamycin. Loss of PTL-1, the sole Tau homologue in C. elegans, also led to impaired injury-induced autophagy activation, but with an increased basal level of autophagic vesicles. Therefore, we have demonstrated that Tau aggregation as well as Tau depletion both lead to disruption of injury-induced autophagy responses, suggesting that aberrant protein aggregation or microtubule dysfunction can modulate autophagy regulation in neurons after injury.

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The Use of Dietary Antifungal Agent Terbinafine in Artificial Diet and Its Effects on Some Biological and Biochemical Parameters of the Model Organism Galleria mellonella (Lepidoptera: Pyralidae)

Journal of Economic Entomology ◽

10.1093/jee/toaa039 ◽

2020 ◽

Vol 113 (3) ◽

pp. 1110-1117 ◽

Cited By ~ 2

Author(s):

Suzan Kastamonuluoğlu ◽

Kemal Büyükgüzel ◽

Ender Büyükgüzel

Keyword(s):

Antifungal Agent ◽

Artificial Diet ◽

Galleria Mellonella ◽

Control Diet ◽

Protein Carbonyl ◽

Egg Laying ◽

Biological Traits ◽

Dependent Manner ◽

Greater Wax Moth ◽

Wax Moth

Abstract Diet quality widely affects the survival, development, fecundity, longevity, and hatchability of insects. We used the greater wax moth Galleria mellonella (Linnaeus) to determine the effects of the antifungal, antibiotic terbinafine on some of its’ biological parameters. The effects of terbinafine on malondialdehyde (MDA) and protein carbonyl (PCO) contents and the activity of the detoxification enzyme, glutathione S-transferase (GST), in the midgut of seventh-instar larvae of G. mellonella were also investigated. The insects were reared on an artificial diet containing terbinafine at concentrations of 0.001, 0.01, 0.1, and 1 g. The survival rates at all development stages of G. mellonella were significantly decreased at all terbinafine concentrations. The females from a control diet produced 82.9 ± 18.1 eggs; however, this number was significantly reduced to 51.4 ± 9.6 in females given a 0.1 g terbinafine diet. The highest concentration of terbinafine (1 g) completely inhibited egg laying. Terbinafine significantly increased MDA content and GST activity in the midgut tissue of seventh-instar larvae in a dose-dependent manner. Relative to controls, these low dietary concentrations of terbinafine significantly increased midgut PCO content; a 0.1 g terbinafine concentration raised PCO content from 155.19 ± 21.8 to 737.17 ± 36.4 nmol/mg protein. This study shows concentration-dependent effects on the biological traits of the greater wax moth G. mellonella, including the oxidative status and detoxification capacity of the midgut. Low terbinafine concentrations may be possible for use as an antifungal agent in insect-rearing diets.

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The PP2A/4/6 subfamily of phosphoprotein phosphatases regulates DAF-16 and confers resistance to environmental stress in postreproductive adult C. elegans

PLoS ONE ◽

10.1371/journal.pone.0229812 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0229812

Author(s):

Rebecca S. Rivard ◽

Julia M. Morris ◽

Matthew J. Youngman

Keyword(s):

Environmental Stress ◽

Transcriptional Activity ◽

Reverse Genetics ◽

Dependent Manner ◽

C Elegans ◽

Forkhead Box ◽

Phosphoprotein Phosphatases ◽

Age Dependent ◽

Foxo Transcription Factors ◽

Insulin Like Growth Factors

Insulin and insulin-like growth factors are longevity determinants that negatively regulate Forkhead box class O (FoxO) transcription factors. In C. elegans mutations that constitutively activate DAF-16, the ortholog of mammalian FoxO3a, extend lifespan by two-fold. While environmental insults induce DAF-16 activity in younger animals, it also becomes activated in an age-dependent manner in the absence of stress, modulating gene expression well into late adulthood. The mechanism by which DAF-16 activity is regulated during aging has not been defined. Since phosphorylation of DAF-16 generally leads to its inhibition, we asked whether phosphatases might be necessary for its increased transcriptional activity in adult C. elegans. We focused on the PP2A/4/6 subfamily of phosphoprotein phosphatases, members of which had been implicated to regulate DAF-16 under low insulin signaling conditions but had not been investigated during aging in wildtype animals. Using reverse genetics, we functionally characterized all C. elegans orthologs of human catalytic, regulatory, and scaffolding subunits of PP2A/4/6 holoenzymes in postreproductive adults. We found that PP2A complex constituents PAA-1 and PPTR-1 regulate DAF-16 transcriptional activity during aging and that they cooperate with the catalytic subunit LET-92 to protect adult animals from ultraviolet radiation. PP4 complex members PPH-4.1/4.2, and SMK-1 also appear to regulate DAF-16 in an age-dependent manner, and together with PPFR-2 they contribute to innate immunity. Interestingly, SUR-6 but no other subunit of the PP2A complex was necessary for the survival of pathogen-infected animals. Finally, we found that PP6 complex constituents PPH-6 and SAPS-1 contribute to host defense during aging, apparently without affecting DAF-16 transcriptional activity. Our studies indicate that a set of PP2A/4/6 complexes protect adult C. elegans from environmental stress, thus preserving healthspan. Therefore, along with their functions in cell division and development, the PP2A/4/6 phosphatases also appear to play critical roles later in life.

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