scholarly journals Evolution of herbivory remodels a Drosophila genome

2019 ◽  
Author(s):  
Andrew D. Gloss ◽  
Anna C. Nelson Dittrich ◽  
Richard T. Lapoint ◽  
Benjamin Goldman-Huertas ◽  
Kirsten I. Verster ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Model ◽  
Model Systems ◽  
Model Organisms ◽  
Close Relative ◽  
Herbivorous Insects ◽  
Drosophila Genome ◽  
Gene Repertoire ◽  
Living Plant ◽  
Mustard Oils

ABSTRACTOne-quarter of extant Eukaryotic species are herbivorous insects, yet the genomic basis of this extraordinary adaptive radiation is unclear. Recently-derived herbivorous species hold promise for understanding how colonization of living plant tissues shaped the evolution of herbivore genomes. Here, we characterized exceptional patterns of evolution coupled with a recent (<15 mya) transition to herbivory of mustard plants (Brassicaceae, including Arabidopsis thaliana) in the fly genus Scaptomyza, nested within the paraphyletic genus Drosophila. We discovered a radiation of mustard-specialized Scaptomyza species, comparable in diversity to the Drosophila melanogaster species subgroup. Stable isotope, behavioral, and viability assays revealed these flies are obligate herbivores. Genome sequencing of one species, S. flava, revealed that the evolution of herbivory drove a contraction in gene families involved in chemosensation and xenobiotic metabolism. Against this backdrop of losses, highly targeted gains (“blooms”) were found in Phase I and Phase II detoxification gene sub-families, including glutathione S-transferase (Gst) and cytochrome P450 (Cyp450) genes. S. flava has more validated paralogs of a single Cyp450 (N=6 for Cyp6g1) and Gst (N=5 for GstE5-8) than any other drosophilid. Functional studies of the Gst repertoire in S. flava showed that transcription of S. flava GstE5-8 paralogs was differentially regulated by dietary mustard oils, and of 22 heterologously expressed cytosolic S. flava GST enzymes, GSTE5-8 enzymes were exceptionally well-adapted to mustard oil detoxification in vitro. One, GSTE5-8a, was an order of magnitude more efficient at metabolizing mustard oils than GSTs from any other metazoan. The serendipitous intersection of two genetic model organisms, Drosophila and Arabidopsis, helped illuminate how an insect genome was remodeled during the evolutionary transformation to herbivory, identifying mechanisms that facilitated the evolution of the most diverse guild of animal life.SIGNIFICANCE STATEMENTThe origin of land plants >400 million years ago (mya) spurred the diversification of plant-feeding (herbivorous) insects and triggered an ongoing chemical co-evolutionary arms race. Because ancestors of most herbivorous insects first colonized plants >200 mya, the sands of time have buried evidence of how their genomes changed with their diet. We leveraged the serendipitous intersection of two genetic model systems: a close relative of yeast-feeding fruit fly (Drosophila melanogaster), the “wasabi fly” (Scaptomyza flava), that evolved to consume mustard plants including Arabidopsis thaliana. The yeast-to-mustard dietary transition remodeled the fly’s gene repertoire for sensing and detoxifying chemicals. Although many genes were lost, some underwent duplications that encode the most efficient detoxifying enzymes against mustard oils known from animals.

scholarly journals A circadian clock in Saccharomyces cerevisiae

2010 ◽  
Vol 107 (5) ◽  
pp. 2043-2047 ◽  
Author(s):  
Zheng Eelderink-Chen ◽  
Gabriella Mazzotta ◽  
Marcel Sturre ◽  
Jasper Bosman ◽  
Till Roenneberg ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Model ◽  
Circadian Clocks ◽  
Model Systems ◽  
Model Organisms ◽  
Biological Clocks ◽  
Experimental Systems ◽  
Fundamental Biological Process ◽  
Free Running ◽  
And Behavior

Circadian timing is a fundamental biological process, underlying cellular physiology in animals, plants, fungi, and cyanobacteria. Circadian clocks organize gene expression, metabolism, and behavior such that they occur at specific times of day. The biological clocks that orchestrate these daily changes confer a survival advantage and dominate daily behavior, for example, waking us in the morning and helping us to sleep at night. The molecular mechanism of circadian clocks has been sketched out in genetic model systems from prokaryotes to humans, revealing a combination of transcriptional and posttranscriptional pathways, but the clock mechanism is far from solved. Although Saccharomyces cerevisiae is among the most powerful genetic experimental systems and, as such, could greatly contribute to our understanding of cellular timing, it still remains absent from the repertoire of circadian model organisms. Here, we use continuous cultures of yeast, establishing conditions that reveal characteristic clock properties similar to those described in other species. Our results show that metabolism in yeast shows systematic circadian entrainment, responding to cycle length and zeitgeber (stimulus) strength, and a (heavily damped) free running rhythm. Furthermore, the clock is obvious in a standard, haploid, auxotrophic strain, opening the door for rapid progress into cellular clock mechanisms.

scholarly journals Domesticated gag Gene of Drosophila LTR Retrotransposons Is Involved in Response to Oxidative Stress

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 396 ◽  
Author(s):  
Pavel Makhnovskii ◽  
Yevheniia Balakireva ◽  
Lidia Nefedova ◽  
Anton Lavrenov ◽  
Ilya Kuzmin ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Signaling Pathway ◽  
Genetic Model ◽  
Gene Promoter ◽  
Ammonium Persulfate ◽  
Model Organisms ◽  
Binding Motif ◽  
Drosophila Genome ◽  
Ltr Retrotransposons ◽  
Protective Function

Drosophila melanogaster is one of the most extensively used genetic model organisms for studying LTR retrotransposons that are represented by various groups in its genome. However, the phenomenon of molecular domestication of LTR retrotransposons has been insufficiently studied in Drosophila, as well as in other invertebrates. The present work is devoted to studying the role of the domesticated gag gene, Gagr, in the Drosophila genome. The Gagr gene has been shown to be involved in the response to stress caused by exposure to ammonium persulfate, but not in the stress response to oligomycin A, zeomycin, and cadmium chloride. Ammonium persulfate tissue specifically activates the expression of Gagr in the tissues of the carcass, but not in the gut. We found that the Gagr gene promoter contains one binding motif for the transcription factor kayak, a component of the JNK signaling pathway, and two binding motifs for the transcription factor Stat92E, a component of the Jak-STAT signaling pathway. Remarkably, Gagr orthologs contain the second binding motif for Stat92E only in D. melanogaster, D. simulans and D. sechellia, whereas in D. yakuba and D. erecta, Gagr orthologs contain a single motif, and there are no binding sites for Stat92E in the promoters of Gagr orthologs in D. ananassae and in species outside the melanogaster group. The data obtained indicate the formation of the protective function of the Gagr gene during evolution.

scholarly journals Sept8/SEPTIN8 involvement in cellular structure and kidney damage is identified by genetic mapping and a novel human tubule hypoxic model

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gregory R. Keele ◽  
Jeremy W. Prokop ◽  
Hong He ◽  
Katie Holl ◽  
John Littrell ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Model ◽  
Association Studies ◽  
Model Systems ◽  
Linear Mixed Effect Model ◽  
Genome Wide Association Studies ◽  
Tubulointerstitial Injury ◽  
Heritable Variation ◽  
Mixed Effect

AbstractChronic kidney disease (CKD), which can ultimately progress to kidney failure, is influenced by genetics and the environment. Genes identified in human genome wide association studies (GWAS) explain only a small proportion of the heritable variation and lack functional validation, indicating the need for additional model systems. Outbred heterogeneous stock (HS) rats have been used for genetic fine-mapping of complex traits, but have not previously been used for CKD traits. We performed GWAS for urinary protein excretion (UPE) and CKD related serum biochemistries in 245 male HS rats. Quantitative trait loci (QTL) were identified using a linear mixed effect model that tested for association with imputed genotypes. Candidate genes were identified using bioinformatics tools and targeted RNAseq followed by testing in a novel in vitro model of human tubule, hypoxia-induced damage. We identified two QTL for UPE and five for serum biochemistries. Protein modeling identified a missense variant within Septin 8 (Sept8) as a candidate for UPE. Sept8/SEPTIN8 expression increased in HS rats with elevated UPE and tubulointerstitial injury and in the in vitro hypoxia model. SEPTIN8 is detected within proximal tubule cells in human kidney samples and localizes with acetyl-alpha tubulin in the culture system. After hypoxia, SEPTIN8 staining becomes diffuse and appears to relocalize with actin. These data suggest a role of SEPTIN8 in cellular organization and structure in response to environmental stress. This study demonstrates that integration of a rat genetic model with an environmentally induced tubule damage system identifies Sept8/SEPTIN8 and informs novel aspects of the complex gene by environmental interactions contributing to CKD risk.

scholarly journals The ATXN2 Orthologs CID3 and CID4, Act Redundantly to In-Fluence Developmental Pathways throughout the Life Cycle of Arabidopsis thaliana

2021 ◽  
Vol 22 (6) ◽  
pp. 3068
Author(s):  
Zaira M. López-Juárez ◽  
Laura Aguilar-Henonin ◽  
Plinio Guzmán
Keyword(s):  
Arabidopsis Thaliana ◽  
Life Cycle ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Leaf Growth ◽  
Transcriptome Profiling ◽  
Developmental Pathways ◽  
Model Organisms ◽  
Key Factors

RNA-binding proteins (RBPs) are key elements involved in post-transcriptional regulation. Ataxin-2 (ATXN2) is an evolutionarily conserved RBP protein, whose function has been studied in several model organisms, from Saccharomyces cerevisiae to the Homo sapiens. ATXN2 interacts with poly(A) binding proteins (PABP) and binds to specific sequences at the 3′UTR of target mRNAs to stabilize them. CTC-Interacting Domain3 (CID3) and CID4 are two ATXN2 orthologs present in plant genomes whose function is unknown. In the present study, phenotypical and transcriptome profiling were used to examine the role of CID3 and CID4 in Arabidopsis thaliana. We found that they act redundantly to influence pathways throughout the life cycle. cid3cid4 double mutant showed a delay in flowering time and a reduced rosette size. Transcriptome profiling revealed that key factors that promote floral transition and floral meristem identity were downregulated in cid3cid4 whereas the flowering repressor FLOWERING LOCUS C (FLC) was upregulated. Expression of key factors in the photoperiodic regulation of flowering and circadian clock pathways, were also altered in cid3cid4, as well as the expression of several transcription factors and miRNAs encoding genes involved in leaf growth dynamics. These findings reveal that ATXN2 orthologs may have a role in developmental pathways throughout the life cycle of plants.

scholarly journals Extended JAZ degron sequence for plant hormone binding in jasmonate co-receptor of tomato SlCOI1-SlJAZ

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rina Saito ◽  
Kengo Hayashi ◽  
Haruna Nomoto ◽  
Misuzu Nakayama ◽  
Yousuke Takaoka ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Development ◽  
Genetic Modification ◽  
Tomato Plant ◽  
Plant Hormone ◽  
Herbivorous Insects ◽  
Hormone Binding ◽  
Plant Body

Abstract(+)-7-iso-Jasmonoyl-l-isoleucine (JA-Ile) is a lipid-derived phytohormone implicated in plant development, reproduction, and defense in response to pathogens and herbivorous insects. All these effects are instigated by the perception of JA-Ile by the COI1-JAZ co-receptor in the plant body, which in Arabidopsis thaliana is profoundly influenced by the short JAZ degron sequence (V/L)P(Q/I)AR(R/K) of the JAZ protein. Here, we report that SlJAZ-SlCOI1, the COI1-JAZ co-receptor found in the tomato plant, relies on the extended JAZ degron sequence (V/L)P(Q/I)AR(R/K)XSLX instead of the canonical JAZ degron. This finding illuminates our understanding of the mechanism of ligand perception by JA-Ile in this plant, and will inform both efforts to improve it by genetic modification of the SlCOI1-SlJAZ co-receptor, and the development of the synthetic agonists/antagonists.

scholarly journals Insights into mammalian biology from the wild house mouse Mus musculus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Megan Phifer-Rixey ◽  
Michael W Nachman
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Genetic Model ◽  
Inbred Strains ◽  
Mendelian Inheritance ◽  
Model Organisms ◽  
House Mice ◽  
Small Subset ◽  
Wild Mice ◽  
Wide Range

The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system.

Abstract 426: Laminin Downregulation Facilitates Cardiomyocyte Coupling in situ to Increase Contractile Function

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Ayla Sessions ◽  
Gaurav Kaushik ◽  
Adam Engler
Keyword(s):  
Basement Membrane ◽  
Contractile Function ◽  
Current Model ◽  
Model Systems ◽  
Model Organisms ◽  
Muscle Physiology ◽  
Heart Tube ◽  
Age Related ◽  
New Evidence

Aging is associated with extensive remodeling of the heart, including basement membrane extracellular matrix (ECM) components that surround cardiomyocytes. Remodeling is thought to contribute to impaired cardiac mechanotransduction, but the contribution of specific basement membrane ECM components to age-related cardiac remodeling is unclear, owing to current model systems being complex and slow to age. To investigate the effect of basement membrane remodeling on mechanical function in genetically tractable, rapidly aging, and simple model organisms, we employed Drosophila melanogaster, which has a simple trilayered heart tube composed of only basement membrane ECM. We observed differential regulation of collagens between laboratory Drosophila strains , i.e. yellow-white ( yw ) and white-1118 ( w 1118 ), leading to changes in muscle physiology, which were linked to severity of dysfunction with age. Therefore, we sought to understand the extent to which basement membrane ECM modulates lateral cardiomyocyte coupling and contractile function during aging. Cardiac-restricted knockdown of ECM genes Pericardin , Laminin A , and Viking in Drosophila prevented age-associated heart tube restriction and increased contractility, even under viscous load. Most notably, reduction of Laminin A expression decreased levels of other genes that co-assemble in ECM, leading to overall preservation of contractile velocity and extension of median organismal lifespan by 3 weeks or 39%. These data provide new evidence of a direct link between basement membrane ECM homeostasis, contractility, and maintenance of lifespan.

Abstract 371: Down Regulation of ECM Genes Laminin and Collagen IV Lead to Preserved Cardiac Function With Age and Increased Lifespan in Drosophila

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Ayla O Sessions
Keyword(s):  
Diastolic Dysfunction ◽  
High Speed ◽  
Current Model ◽  
Collagen Iv ◽  
Model Systems ◽  
Model Organisms ◽  
Heart Tube ◽  
Ecm Remodeling ◽  
Intercalated Discs ◽  
And Performance

Increased deposition of extracellular matrix (ECM) is observed in all advanced age heart failure patients, but current model systems are complex and slow to age. To investigate the effect of extracellular remodeling on mechanical function in genetically tractable, rapidly aging, and simple model organisms, we employed Drosophila melanogaster, which has a simple trilayered heart tube. We found that two common wildtype strains of Drosophila, i.e. yellow-white (yw) and white-1118 (w1118), exhibit different cytoskeletal and ECM remodeling with age. Using a recently developed nanoindentation method to measure cardiomyocyte stiffness and high speed optical imaging to assess contractility of intact Drosophila hearts, we found that yw flies had stiffer intercalated discs (ICD) and exhibited diastolic dysfunction with age. On the other hand, w1118 flies had a shorter lifespan compared to yw, did not exhibit ICD stiffening, had a less severe diastolic dysfunction, and showed an increase in ECM layer thickness between ventral muscle (VM) and cardiomyocyte (CM) layers of the heart tube. To modulate ECM and assess its effect in the aged w1118 flies, we knocked-down ECM genes LamininA and Viking (homologous to Collagen IV). Both ECM KD genotypes exhibited diastolic dilation with increased fractional shortening at adult (1wk) and aged (5wk) time points. The LamininA KD resulted in decreased cardiomyocyte stiffness correlating with increased relaxation velocities in adult flies and preservation of shortening and relaxation velocities in aged flies over controls. However, both the LamininA and Collagen IV KD flies experienced a basal increase in the decoupling of their cardiomyocytes as determined by heart period variance and % fibrillar heart-beats. These conductance issues were not enough to counteract the increased cardiac output and performance with age, and the Collagen IV KD outlived controls by 1.5 weeks median survival and the LamininA KD by 3 weeks. This suggests that the cell-ECM contacts in the basement membrane are intimately tied not only to the coupling of the cardiomyocytes of the Drosophila heart tube but also to cytoskeletal remodeling, but perhaps different ECM proteins have different mechanisms for interacting with the cardiomyocyte cytoskeleton.

scholarly journals Halophytism: What Have We Learnt From Arabidopsis thaliana Relative Model Systems?

2018 ◽  
Vol 178 (3) ◽  
pp. 972-988 ◽  
Author(s):  
Yana Kazachkova ◽  
Gil Eshel ◽  
Pramod Pantha ◽  
John M. Cheeseman ◽  
Maheshi Dassanayake ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Model Systems

scholarly journals Antifungal Activities of Antineoplastic Agents:Saccharomyces cerevisiae as a Model System To Study Drug Action

1999 ◽  
Vol 12 (4) ◽  
pp. 583-611 ◽  
Author(s):  
Maria E. Cardenas ◽  
M. Cristina Cruz ◽  
Maurizio Del Poeta ◽  
Namjin Chung ◽  
John R. Perfect ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Kinase Inhibitor ◽  
Genetic Model ◽  
Fungal Infections ◽  
Study Drug ◽  
Drug Action ◽  
Mechanisms Of Action ◽  
Model Systems ◽  
Screening Tools ◽  
Sphingolipid Metabolism

SUMMARY Recent evolutionary studies reveal that microorganisms including yeasts and fungi are more closely related to mammals than was previously appreciated. Possibly as a consequence, many natural-product toxins that have antimicrobial activity are also toxic to mammalian cells. While this makes it difficult to discover antifungal agents without toxic side effects, it also has enabled detailed studies of drug action in simple genetic model systems. We review here studies on the antifungal actions of antineoplasmic agents. Topics covered include the mechanisms of action of inhibitors of topoisomerases I and II; the immunosuppressants rapamycin, cyclosporin A, and FK506; the phosphatidylinositol 3-kinase inhibitor wortmannin; the angiogenesis inhibitors fumagillin and ovalicin; the HSP90 inhibitor geldanamycin; and agents that inhibit sphingolipid metabolism. In general, these natural products inhibit target proteins conserved from microorganisms to humans. These studies highlight the potential of microorganisms as screening tools to elucidate the mechanisms of action of novel pharmacological agents with unique effects against specific mammalian cell types, including neoplastic cells. In addition, this analysis suggests that antineoplastic agents and derivatives might find novel indications in the treatment of fungal infections, for which few agents are presently available, toxicity remains a serious concern, and drug resistance is emerging.

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