Hormone Signaling and Phenotypic Plasticity in Nematode Development and Evolution

Phenotypic plasticity refers to the ability of an organism to adopt different phenotypes depending on environmental conditions. In animals and plants, the progression of juvenile development and the formation of dormant stages are often associated with phenotypic plasticity, indicating the importance of phenotypic plasticity for life-history theory. Phenotypic plasticity has long been emphasized as a crucial principle in ecology and as facilitator of phenotypic evolution. In nematodes, several examples of phenotypic plasticity have been studied at the genetic and developmental level. In addition, the influence of different environmental factors has been investigated under laboratory conditions. These studies have provided detailed insight into the molecular basis of phenotypic plasticity and its ecological and evolutionary implications. Here, we review recent studies on the formation of dauer larvae in Caenorhabditis elegans, the evolution of nematode parasitism and the generation of a novel feeding trait in Pristionchus pacificus. These examples reveal a conserved and co-opted role of an endocrine signaling module involving the steroid hormone dafachronic acid. We will discuss how hormone signaling might facilitate life-history and morphological evolution

A Comparative Genomics Exploration of Inter-partner Metabolic Signaling in the Coral-algal Symbiosis

At the foundation of coral reef ecosystems is the symbiosis between the coral host and its microbial community, particularly its photoautotrophic algae from the family Symbiodiniaceae. As a symbiosis centered around nutritional exchange, determining the mechanisms involved in the maintenance of this cooperative exchange is central to understanding how it breaks down. As the nutritional transfer primarily consists of sugars, this work first focuses on the cnidarian insulin signaling pathway, an evolutionarily important metazoan pathway involved in diverse functions, most notably metabolism. This dissertation unveiled 360 putative cnidarian insulin-like peptides (cnILPs) from existing transcriptomic datasets, where they were previously missed due to the bioinformatic methods employed. Significantly, symbiotic corals and anemones possessed the greatest diversity in insulin-like peptides compared to other cnidarian taxa. Conserved transcriptional responses of the cnILPs were also detected, particularly cnILP-B down-regulation in response to symbiosis along with a non-specific cnILP up-regulation in response to thermal stress. These trends coincide well with known transcriptional responses of ILPs in diverse organisms ranging from the nematode C. elegans to humans, implicating for the first time that insulin signaling similarly functions in symbiosis and stress response in non-bilaterians. This dissertation also focused on the genome of the thermotolerant Durusdinium trenchii, which is well-known to confer thermotolerance on diverse coral species. We identified considerable duplication of gene blocks, more than 10-100x that of other Symbiodinaceae species, in support of previous hypotheses regarding a near or whole genome duplication event. Importantly, within these duplicated gene regions we detected extensive positive selection on genes central to the maintenance and repair of chloroplast structures like thylakoid membranes and photosystem II, a primary site of damage during photoinhibition. Widespread genome duplication and adaptive selection on photosynthetic functions is significant as it aligns with previous physiological studies identifying this as a factor in the thermotolerance of D. trenchii. This dissertation for the first time not only substantiates previous hypotheses of genome duplication in D. trenchii, but connects this duplication to the acquisition of thermotolerance in D. trenchii. Altogether, this dissertation highlights the importance for further investigations into the functions of the insulin signaling pathway in coral-algal symbioses and stress response, as well as confirms genomic duplication and selection as contributing to the evolutionary acquisition of thermotolerance in the symbiont D. trenchii

Intermediary metabolism

Caenorhabditis elegans has orthologs for most of the key enzymes involved in eukaryotic intermediary metabolism, suggesting that the major metabolic pathways are probably present in this species. We discuss how metabolic patterns and activity change as the worm traverses development and ages, or responds to unfavorable external factors, such as temperature extremes or shortages in food or oxygen. Dauer diapause is marked by an enhanced resistance to oxidative stress and a shift toward microaerobic and anaplerotic metabolic pathways and hypometabolism, as indicated by the increased importance of the malate dismutation and glyoxylate pathways and the repression of citric acid cycle activity. These alterations promote prolonged survival of the dauer larva; some of these changes also accompany the extended lifespan of insulin/IGF-1 and several mitochondrial mutants. We also present a brief overview of the nutritional requirements, energy storage and waste products generated by C. elegans

Regulation of Growth by Drosophila FoxO Transcription Factor

Forkhead box class O (FoxO) transcription factors are members of the forkhead box transcription factor superfamily, with orthologues in various species such as human, worm and fly. FoxO proteins are key regulators of growth, metabolism, stress resistance and, consequently, life span. FoxOs integrate signals from different pathways, e.g. the growth controlling Insulin-TOR signaling pathway and the stress induced JNK and Hippo signaling pathways. FoxO proteins have evolved to guide the cellular response to varying energy and stress conditions by inducing the expression of genes involved in the regulation of growth and metabolism. This work has aimed to deepen the understanding of how FoxO executes its biological functions. A particular emphasis has been laid to its role in growth control. Specifically, evidence is presented indicating that FoxO restricts tissue growth in a situation when TOR signaling is high. This finding can have implications in a human condition called Tuberous sclerosis, manifested by multiple benign tumors. Further, it is shown that FoxO directly binds to the promoter and regulates the expression of a Drosophila Adenylate cyclase gene, ac76e, which in turn modulates the fly s development and growth systemically. These results strengthen FoxOs position among central size regulators as it is able to operate at the level of individual cells as well as in the whole organism. Finally, an attempt to reveal the regulatory network upstream of FoxO has been carried out. Several putative FoxO activity regulators were identified in an RNAi screen of Drosophila kinases and phosphatases. The results underscore that FoxO is regulated through an elaborate network, ensuring the correct execution of key cellular processes in metabolism and response to stress. Overall, the evidence provided in this study strengthens our view of FoxO as a key integrator of growth and stress signals.Forkhead box class O (FoxO) geenienluennan säätelijä on konservoitunut proteiini, jonka toiminta liittyy mm. energia-aineenvaihduntaan, kasvun säätelyyn sekä solun suojeluun stressin aiheuttamilta vaurioilta. FoxO-proteiinit muodostavat perheen, jonka jäseniä esiintyy lähes kaikissa monisoluisissa. Näihin kuuluvat mm. ihminen, sukkulamato ja banaanikärpänen. FoxO-proteiinin tärkeimpänä tunnettuna tehtävänä voidaan pitää sen osallistumista aineenvaihdunnan ja kasvun mukauttamiseen ravinnon saatavuuteen. Sen säätelijöinä toimivat mm. ravinnetasoon reagoiva insuliini/TOR signalointiverkosto sekä solustressin aktivoimat JNK- ja Hippo-signaalinvälitysreitit. Kasvulle suotuisissa olosuhteissa FoxO-proteiinin aktiivisuus estetään insuliinisignaloinnin välityksellä. Kun ravinteita on vähän tai kun solun stressitaso kasvaa, esim. lisääntyneiden happiradikaalien seurauksena, FoxO siirtyy solulimasta tumaan, jossa se säätelee useiden eri geenien luentaa. Tällaisiin lukeutuvat mm. glukoosin uudismuodostuksessa oleellisten entsyymien pepck- ja g6pase-geenit, sekä solun jakautumisen negatiivisina säätelijöinä toimivat p27kip1- ja p21cip1-geenit. FoxO toimii sekä koko elimistön, että yksittäisen solun tasolla. Esimerkiksi maksassa FoxO-proteiinin tehtävänä on säädellä veren sokeritasoa, glukoosin uudismuodostuksen kautta. Energiaa kuluttavissa ja varastoivissa kudoksissa, kuten lihaksissa ja rasvakudoksessa, FoxO hidastaa kasvua ja aktivoi energiavaraston käyttöönottoa. Näiden prosessien säätely on elimistön aineenvaihdunnan tasapainon kannalta oleellista. Häiriöt FoxO-proteiinin säätelyssä onkin yhdistetty aineenvaihdunnan sairauksiin kuten insuliiniresistenssiin ja syövän syntyyn. Tässä työssä on tutkittu FoxO-proteiinin aktiivisuuden säätelyä sekä toimintaa, erityisesti kasvun säätelyn mekanismeja joissa FoxO on osallisena. Tutkimus on jaettu osajulkaisuihin, joiden tuloksena (1) on identifioitu uusia FoxO-proteiinin aktiivisuuden säätelijöitä (mm. PKC-, GSK-3β- ja POLO-kinaasit), (2) selvitetty FoxO-proteiinin roolia kudoksen kasvun säätelyssä tilanteessa, jossa TOR signalointireitti on yliaktiivinen, mm. perinnöllisessä sairaudessa nimeltään tuberoosiskleroosi, sekä (3) karakterisoitu uusi FoxO-proteiinin säätelemä geeni, ac76e, sekä selvitetty sen toimintaa banaanikärpäsen kasvun säätelyssä. Tämän tutkimuksen tulokset auttavat ymmärtämään kasvun säätelyn biologiaa sekä syventävät tietämystämme FoxO-proteiinin merkityksestä solun energiatasapainolle. Tulokset ovat askel kudosten kasvun ja aineenvaihdunnan säätelyn parempaan ymmärtämiseen

Identification of miRNAs involved in pear fruit development and quality

BACKGROUND: MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA identification in various plants ranging from model plants to perennial fruit trees. However, the role of miRNAs in pear (Pyrus bretschneideri) fruit development is not clear. Here, we investigated the miRNA profiles of pear fruits from different time stages during development with Illumina HiSeq 2000 platform and bioinformatics analysis. Quantitative real-time PCR was used to validate the expression levels of miRNAs. RESULTS: Both conserved and species-specific miRNAs in pear have been identified in this study. Total reads, ranging from 19,030,925 to 25,576,773, were obtained from six small RNA libraries constructed for different stages of fruit development after flowering. Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages. KEGG pathway analysis on 2,216 target genes of 188 known miRNAs and 1,127 target genes of 184 novel miRNAs showed that miRNAs are widely involved in the regulation of fruit development. Among these, a total of eleven miRNAs putatively participate in the pathway of lignin biosynthesis, nine miRNAs were identified to take part in sugar and acid metabolism, and MiR160 was identified to regulate auxin response factor. CONCLUSION: Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling. Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-953) contains supplementary material, which is available to authorized users

Longevity: Lesson from model organisms

Research on longevity and healthy aging promises to increase our lifespan and decrease the burden of degenerative diseases with important social and economic effects. Many aging theories have been proposed, and important aging pathways have been discovered. Model organisms have had a crucial role in this process because of their short lifespan, cheap maintenance, and manipulation possibilities. Yeasts, worms, fruit flies, or mammalian models such as mice, monkeys, and recently, dogs, have helped shed light on aging processes. Genes and molecular mechanisms that were found to be critical in simple eukaryotic cells and species have been confirmed in humans mainly by the functional analysis of mammalian orthologues. Here, we review conserved aging mechanisms discovered in different model systems that are implicated in human longevity as well and that could be the target of anti-aging interventions in human

Role of the Bifunctional Aminoacyl-tRNA Synthetase EPRS in Human Disease

Aminoacyl-tRNA synthetases (AARS) are a class of enzymes that catalyze the charging of tRNAs with cognate amino acids, a critical step that contributes to the fidelity of protein synthesis. Many AARSs also possess noncanonical functions such as regulation of apoptosis, mRNA translation, and RNA splicing. Some AARSs have evolved new domains with no apparent connection to their charging functions. For example, WHEP domains were originally identified in tryptophanyl-tRNA synthetase (WRS), histidyl-tRNA synthetase (HRS), and glutamyl-prolyl-tRNA synthetase (EPRS). EPRS is a unique bifunctional AARS, found only in higher eukaryotes, and consists of glutamyl-tRNA synthetase (ERS) and prolyl-tRNA synthetase (PRS) joined by a non-catalytic linker containing three WHEP domains in humans. Two compound heterozygous point mutations within human ERS (P14R and E205G) have been identified in the genomes of two patients with type 1 diabetes and bone disease. However, the mechanism by which these mutations contribute to disease is unknown. Our goal is to determine whether the point mutations affect the canonical catalytic activity of EPRS responsible for tRNA charging or noncanonical functions. Both P14 and E205 are highly conserved residues located in the GST and catalytic domain, respectively. An ERS variant appended to 2.5 WHEP domains (ERS 2.5W) has been purified and shown to display robust tRNA binding and aminoacylation activity in vitro. The P14R and E205G single mutants display the same binding affinity for tRNAGlu as WT ERS 2.5W, suggesting that the observed defect is at the catalytic step. Whereas the ERS 2.5W P14R mutant has near wild-type (WT) aminoacylation activity, the ERS 2.5W E205G variant has a severe aminoacylation defect. Both mutations, however, lead to reduced amino acid activation. Together with a collaborator, we are currently characterizing the effect of these two mutations on cell proliferation and the integrated stress response. Taken together, this work has important implications for the understanding of AARS-related human disease mechanisms and development of new therapeutics.College of Arts & SciencesOffice of Undergraduate Research & Creative InquiryNo embargoAcademic Major: Biochemistr

Amphioxus muscle transcriptomes reveal vertebrate-like myoblast fusion genes and a highly conserved role of insulin signalling in the metabolism of muscle

Madeleine E. Aase-Remedios and Clara Coll-Lladó were supported by funding from the University of St Andrews, School of Biology and additional support from St Leonards College (MEAR), the CORBEL grant European Research Infrastructure cluster project and European Assemble Plus (H2020-INFRAIA-1-2016-2017; grant no.730984). Transcriptome sequencing was done with an award under the BBSRC TGAC Capacity and Capability Challenge.Background:   The formation and functioning of muscles are fundamental aspects of animal biology, and the evolution of ‘muscle genes’ is central to our understanding of this tissue. Feeding-fasting-refeeding experiments have been widely used to assess muscle cellular and metabolic responses to nutrition. Though these studies have focused on vertebrate models and only a few invertebrate systems, they have found similar processes are involved in muscle degradation and maintenance. Motivation for these studies stems from interest in diseases whose pathologies involve muscle atrophy, a symptom also triggered by fasting, as well as commercial interest in the muscle mass of animals kept for consumption. Experimentally modelling atrophy by manipulating nutritional state causes muscle mass to be depleted during starvation and replenished with refeeding so that the genetic mechanisms controlling muscle growth and degradation can be understood. Results:  Using amphioxus, the earliest branching chordate lineage, we address the gap in previous work stemming from comparisons between distantly related vertebrate and invertebrate models. Our amphioxus feeding-fasting-refeeding muscle transcriptomes reveal a highly conserved myogenic program and that the pro-orthologues of many vertebrate myoblast fusion genes were present in the ancestral chordate, despite these invertebrate chordates having unfused mononucleate myocytes. We found that genes differentially expressed between fed and fasted amphioxus were orthologous to the genes that respond to nutritional state in vertebrates. This response is driven in a large part by the highly conserved IGF/Akt/FOXO pathway, where depleted nutrient levels result in activation of FOXO, a transcription factor with many autophagy-related gene targets. Conclusion:  Reconstruction of these gene networks and pathways in amphioxus muscle provides a key point of comparison between the distantly related groups assessed thus far, significantly refining the reconstruction of the ancestral state for chordate myoblast fusion genes and identifying the extensive role of duplicated genes in the IGF/Akt/FOXO pathway across animals. Our study elucidates the evolutionary trajectory of muscle genes as they relate to the increased complexity of vertebrate muscles and muscle development.Publisher PDFPeer reviewe

Rakkude paljunemist soodustav AKT signaalirada kui potentsiaalne kasvajavastase ravi sihtmärk

Väitekirja elektrooniline versioon ei sisalda publikatsioone.AKT kinaas on seriin/treoniinkinaas, mis kuulub AGC valkude perekonda. Sihtmärkvalke fosforüleerides reguleerib AKT rakkudes mitmeid olulisi füsioloogilisi protsesse nagu rakkude elulemus, rakutsükli edenemine, metabolism, transkriptsioon, valkude süntees, rakkude liikuvus jne. Kontrollimatult aktiivset PI3K/AKT signaalirada on kirjeldatud inimese maksa-, aju-, rinna-, soole- ja eesnäärmekasvajates ning seda loetakse mõnede kasvajate puhul halva prognoosi markeriks. Käesoleva töö raames leidsime, et aktiveeritud AKT signaalirada osaleb ka healoomulise hüperproliferatiivse patoloogia – Dupuytreni kontraktuuri - arengus. AKT kinaasi olulisuse ja sagedase seotuse tõttu kasvajate tekkimisega, peetakse teda heaks märklauaks kasvajavastaste terapeutikumide väljatöötamisel. Praeguseks on avastatud ja kliinilistesse katsetustesse võetud juba mitmeid AKT signaaliraja inhibiitoreid, kuid paraku on tugevad mittespetsiifilised kõrvaltoimed ja toksilisus takistanud nende edasise kasutamise raviskeemides. Käesoleva doktoritöö põhieesmärk oli leida ja iseloomustada AKT signaaliraja aktiivsust pärssivaid väikesemolekulaarseid aineid, mida võiks kasutada potentsiaalsete kasvajavastaste ravimitena. Otsitavate inhibiitorite täpsem sihtmärk oli AKT1 ja PDPK1 valkude omavaheline interaktsioon, mis on vajalik AKT1 esmaseks aktiveerimiseks. Väikesemolekulaarsete ainete skriinimine valgu komplementaarsusel põhinevat lähenemisviisi kasutades ning sellele järgnenud erinevatest meetoditest koosnenud valideerimisprotsess tuvastas ühe kemikaali – NSC156529 - mis pidurdas erinevat päritolu kasvajarakkude paljunemist nii koekultuuri tingimustes kui in vivo hiire kasvajamudelis. Tuumorirakkude töötlemine NSC156529 kemikaaliga mõjutas lisaks AKT kinaasi enda aktiivsusele ka AKT-i märklaudvalkude aktiivsust, viidates sellele, et antud kemikaal mõjutab AKT signaaliraja poolt reguleeritud raku biokeemilisi protsesse. Kuna in vivo kasvajamudelitest eraldatud tuumorite analüüsimisel leiti NSC156529 kemikaaliga töödeldud kasvajates rakkude diferentseerumisele viitavate markerite suurenenud ekspressioon, järeldati, et lisaks suudab NSC156529 tuumorirakkude paljunemist pärssida neid diferentseeruma suunates. Käesoleva töö kokkuvõtteks võib öelda, et AKT kinaasiga seotud signaalirada on sobiv märklaud kasvajavastaste terapeutikumide väljatöötamiseks ning testitud ühend NSC156529 võiks olla potentsiaalne kandidaat AKT signaaliraja aktiivsuse pärssimiseks kasvajarakkudes.AKT protein is a serine/threonine kinase, which belongs to AGC group of protein kinases. By substrate phosphorylation AKT regulates several physiological processes in the cells, such as cell survival, cell cycle promotion, metabolism, transcription, translation, cell migration etc. Aberrantly activated PI3K/AKT signaling has been frequently found in several human tumors, like liver, brain, breast, colorectal and prostate cancers, and it is a poor prognostic marker for a number of cancer types. In this work we found that the activated AKT signaling might play a role in the progression of benign hyperproliferative pathology – the Dupuytren’s contracture. Due to AKT involvement in critical steps of human tumor pathogenesis, targeting AKT pathway has become a promising strategy in anti-cancer therapy. Although a number of small molecule AKT kinase inhibitors have been developed and tested in clinical trials, severe side effects have prevented their use in current treatment schemes. The main purpose of the present thesis was to identify and characterize the inhibitors of AKT signaling pathway that could be used as potential anti-cancer drugs. The exact target of the inhibitors was the AKT1-PDPK1 interaction, which is the first step in AKT activation cascade. Protein complementation-based screening and the following experiments revealed one chemical – NSC156529 – which inhibited the growth of tumor cells from different origin in cell culture as well as in a mouse tumor xenograft model. In addition to AKT activity inhibition, cancer cell incubation with NSC156529 chemical also reduced the phosphorylation of AKT downstream target proteins, which confirmed that NSC156529 treatment inhibited the key biochemical activities of the AKT signaling pathway. The analysis of NSC156529-treated xenografts revealed increased expression level of differentiation markers, suggesting that NSC156529 could limit tumor growth at least in part by directing cancer cells to differentiate. Conclusively, inhibiting activated AKT-regulated signaling pathway in tumor cells is a promising anti-cancer drug target and the small molecular compound NSC156529 could be a potent suppressor of AKT1 pathway in tumor cells harboring active AKT signaling