scholarly journals “What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Biology ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 25 ◽  
Author(s):  
Roberta Moschetti ◽  
Antonio Palazzo ◽  
Patrizio Lorusso ◽  
Luigi Viggiano ◽  
René Massimiliano Marsano
Keyword(s):  
Transposable Elements ◽  
Transcriptional Control ◽  
Environmental Changes ◽  
Model Organism ◽  
Model Organisms ◽  
Regulatory Sequences ◽  
Transcriptional Pattern ◽  
Constitutive Components ◽  
Host Genes

Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome’s structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE–host interactions in any complex eukaryotic genome.

scholarly journals Mitochondrial Carriers and Substrates Transport Network: A Lesson from Saccharomyces cerevisiae

2021 ◽  
Vol 22 (16) ◽  
pp. 8496
Author(s):  
Alessandra Ferramosca ◽  
Vincenzo Zara
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Metabolic Pathways ◽  
Environmental Changes ◽  
Human Cells ◽  
Metabolic Reprogramming ◽  
Model Organisms ◽  
Mitochondrial Carrier ◽  
Mitochondrial Carriers ◽  
Functional Connections

The yeast Saccharomyces cerevisiae is one of the most widely used model organisms for investigating various aspects of basic cellular functions that are conserved in human cells. This organism, as well as human cells, can modulate its metabolism in response to specific growth conditions, different environmental changes, and nutrient depletion. This adaptation results in a metabolic reprogramming of specific metabolic pathways. Mitochondrial carriers play a fundamental role in cellular metabolism, connecting mitochondrial with cytosolic reactions. By transporting substrates across the inner membrane of mitochondria, they contribute to many processes that are central to cellular function. The genome of Saccharomyces cerevisiae encodes 35 members of the mitochondrial carrier family, most of which have been functionally characterized. The aim of this review is to describe the role of the so far identified yeast mitochondrial carriers in cell metabolism, attempting to show the functional connections between substrates transport and specific metabolic pathways, such as oxidative phosphorylation, lipid metabolism, gluconeogenesis, and amino acids synthesis. Analysis of the literature reveals that these proteins transport substrates involved in the same metabolic pathway with a high degree of flexibility and coordination. The understanding of the role of mitochondrial carriers in yeast biology and metabolism could be useful for clarifying unexplored aspects related to the mitochondrial carrier network. Such knowledge will hopefully help in obtaining more insight into the molecular basis of human diseases.

scholarly journals Sex and the TEs: transposable elements in sexual development and function in animals

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Corentin Dechaud ◽  
Jean-Nicolas Volff ◽  
Manfred Schartl ◽  
Magali Naville
Keyword(s):  
Transposable Elements ◽  
Sexual Reproduction ◽  
Dna Sequences ◽  
Sexual Development ◽  
Regulatory Sequences ◽  
New Host ◽  
Transpositional Activity ◽  
Evolutionary Success ◽  
And Function ◽  
Host Genes

Abstract Transposable elements are endogenous DNA sequences able to integrate into and multiply within genomes. They constitute a major source of genetic innovations, as they can not only rearrange genomes but also spread ready-to-use regulatory sequences able to modify host gene expression, and even can give birth to new host genes. As their evolutionary success depends on their vertical transmission, transposable elements are intrinsically linked to reproduction. In organisms with sexual reproduction, this implies that transposable elements have to manifest their transpositional activity in germ cells or their progenitors. The control of sexual development and function can be very versatile, and several studies have demonstrated the implication of transposable elements in the evolution of sex. In this review, we report the functional and evolutionary relationships between transposable elements and sexual reproduction in animals. In particular, we highlight how transposable elements can influence expression of sexual development genes, and how, reciprocally, they are tightly controlled in gonads. We also review how transposable elements contribute to the organization, expression and evolution of sexual development genes and sex chromosomes. This underscores the intricate co-evolution between host functions and transposable elements, which regularly shift from a parasitic to a domesticated status useful to the host.

scholarly journals Are Model Organisms Theoretical Models?

Disputatio ◽  
2017 ◽  
Vol 9 (47) ◽  
pp. 471-498
Author(s):  
Veli-Pekka Parkkinen
Keyword(s):  
Animal Models ◽  
Causal Structure ◽  
Model Organism ◽  
Theoretical Models ◽  
Theoretical Modelling ◽  
Model Organisms ◽  
Target System ◽  
Inductive Step ◽  
Epistemic Role

AbstractThis article compares the epistemic roles of theoretical models and model organisms in science, and specifically the role of non-human animal models in biomedicine. Much of the previous literature on this topic shares an assumption that animal models and theoretical models have a broadly similar epistemic role—that of indirect representation of a target through the study of a surrogate system. Recently, Levy and Currie (2015) have argued that model organism research and theoretical modelling differ in the justification of model-to-target inferences, such that a unified account based on the widely accepted idea of modelling as indirect representation does not similarly apply to both. I defend a similar conclusion, but argue that the distinction between animal models and theoretical models does not always track a difference in the justification of model-to-target inferences. Case studies of the use of animal models in biomedicine are presented to illustrate this. However, Levy and Currie’s point can be argued for in a different way. I argue for the following distinction. Model organisms (and other concrete models) function as surrogate sources of evidence, from which results are transferred to their targets by empirical extrapolation. By contrast, theoretical modelling does not involve such an inductive step. Rather, theoretical models are used for drawing conclusions from what is already known or assumed about the target system. Codifying assumptions about the causal structure of the target in external representational media (e.g. equations, graphs) allows one to apply explicit inferential rules to reach conclusions that could not be reached with unaided cognition alone (cf. Kuorikoski and Ylikoski 2015).

scholarly journals Homeostasis in the Central Dogma of Molecular Biology: the importance of mRNA instability

2019 ◽  
Author(s):  
José E. Pérez-Ortín ◽  
Vicente Tordera ◽  
Sebastián Chávez
Keyword(s):  
Molecular Biology ◽  
Model Organism ◽  
Model Organisms ◽  
Published Data ◽  
Central Dogma ◽  
E Coli ◽  
Response Capacity ◽  
Cultured Human Cells ◽  
The Cost

AbstractCell survival requires the control of biomolecule concentration, i.e. biomolecules should approach homeostasis. With information-carrying macromolecules, the particular concentration variation ranges depend on each type: DNA is not buffered, but mRNA and protein concentrations are homeostatically controlled, which leads to the ribostasis and proteostasis concepts. In recent years, we have studied the particular features of mRNA ribostasis and proteostasis in the model organismS. cerevisiae. Here we extend this study by comparing published data from three other model organisms:E. coli, S. pombeand cultured human cells. We describe how mRNA ribostasis is less strict than proteostasis. A constant ratio appears between the average decay and dilution rates during cell growth for mRNA, but not for proteins. We postulate that this is due to a trade-off between the cost of synthesis and the response capacity. This compromise takes place at the transcription level, but is not possible at the translation level as the high stability of proteins,versusthat of mRNAs, precludes it. We hypothesize that the middle-place role of mRNA in theCentral Dogmaof Molecular Biology and its chemical instability make it more suitable than proteins for the fast changes needed for gene regulation.Graphical Abstract

scholarly journals The past, present and future of Dictyostelium as a model system

2019 ◽  
Vol 63 (8-9-10) ◽  
pp. 321-331 ◽  
Author(s):  
Salvatore Bozzaro
Keyword(s):  
Dictyostelium Discoideum ◽  
Social Evolution ◽  
Model Organism ◽  
Model Organisms ◽  
Human Genes ◽  
The Social ◽  
Microbial Infections ◽  
Technological Developments ◽  
Soil Amoeba

The social amoeba Dictyostelium discoideum has been a preferred model organism during the last 50 years, particularly for the study of cell motility and chemotaxis, phagocytosis and macropinocytosis, intercellular adhesion, pattern formation, caspase-independent cell death and more recently autophagy and social evolution. Being a soil amoeba and professional phagocyte, thus exposed to a variety of potential pathogens, D. discoideum has also proven to be a powerful genetic and cellular model for investigating host-pathogen interactions and microbial infections. The finding that the Dictyostelium genome harbours several homologs of human genes responsible for a variety of diseases has stimulated their analysis, providing new insights into the mechanism of action of the encoded proteins and in some cases into the defect underlying the disease. Recent technological developments have covered the genetic gap between mammals and non-mammalian model organisms, challenging the modelling role of the latter. Is there a future for Dictyostelium discoideum as a model organism?

scholarly journals Model Organisms and Model Environments: A Rodent Laboratory in Science, Medicine and Society

2011 ◽  
Vol 55 (3) ◽  
pp. 365-368 ◽  
Author(s):  
Edmund Ramsden
Keyword(s):  
Model Organism ◽  
Model Organisms ◽  
Experimental Systems ◽  
Scientific Objects

In recent years there has been increasing interest in the role of animals in science and medicine. While historians have tended to focus on the processes of standardisation, increasing attention is being given to the surprising and unexpected elements of the model organism. Experimental organisms are, simultaneously, both artefacts and samples of nature. Rachel Ankeny and Sabina Leonelli put it clearly and succinctly: ‘they are systems that have been engineered and modified to enable the controlled investigation of specific phenomena, yet at the same time they remain largely mysterious products of millennia of evolution, whose behaviours, structures, and physiology are for the most part still relatively ill-understood by scientists.’ In continuously generating new questions, organisms provide novelty so essential to successful experimental systems. They are, as Hans-Jörg Rheinberger would argue, scientific objects or ‘epistemic things’, not merely predictable ‘technical objects’.

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