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State-of-the-Art Molecular Biology in Chile

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 23136

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Special Issue Editors

Dr. Mauricio Retamal

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Guest Editor

Universidad del Desarrollo
Interests: Cancer; connexins; gap junctions; cancer stem cells; cell communication
Special Issues, Collections and Topics in MDPI journals

Dr. Rodrigo Del Rio

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Guest Editor

1. Laboratory of Cardiorespiratory Control, Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
2. Center for Aging and Regeneration CARE-UC, Santiago, Chile
3. Centro de Excelencia en Biomedicina de Magallanes (CEBIMA), Punta Arenas, Chile
Interests: brainstem cardiorespiratory networks; chemoreceptors; blood pressure; ventilation; heart failure
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular biology has been fundamental to the study of different processes that occur in cell, tissue, and animal physiology. Indeed, this discipline has helped us to understand how the interaction between proteins, nucleic acids, lipids, etc. account for numerous celullar processes. Furthermore, molecular biology has served to unveil several pathways that became dysfunctional during pathological settings, helping to develop several tools to improve cell and tissue function.

Chilean scientists have a long tradition of continous contribution to the understanding of how cells/organisms works, and have used molecular biology as one valuable tool for this purpose. For this reason, the main aim of this Special Issue is to highlight recent advances in molecular and cell physiology performed by Chilean scientists where the use of molecular biology has been instrumental. This call for articles will include genetics, cell biology/physiology, and molecular biology experimental approaches. Potential topics include, but are not limited to, the following:

Molecular biology in neurophsiology
Molecular biology in physioloy and cellular physiology
Molecular biology in genetics
Molecular biology in immunology
Molecular biology in pharcacology

Dr. Mauricio A. Retamal
Dr. Rodrigo Del Rio
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

molecular biology
chilean scientists
neurophsiology
physioloy and cellular physiology
genetics
ecology
immunology
pharmacology

Published Papers (10 papers)

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Research

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13 pages, 2489 KiB

Open AccessArticle

Exploring the Genetic Diversity of Epstein–Barr Virus among Patients with Gastric Cancer in Southern Chile

by María Elena Reyes, Louise Zanella, Ismael Riquelme, Kurt Buchegger, Bárbara Mora-Lagos, Pablo Guzmán, Patricia García, Juan C. Roa, Carmen Gloria Ili and Priscilla Brebi

Int. J. Mol. Sci. 2023, 24(14), 11276; https://doi.org/10.3390/ijms241411276 - 10 Jul 2023

Viewed by 1232

Abstract

The Epstein–Barr virus (EBV) has been associated with gastric cancer (GC), one of the deadliest malignancies in Chile and the world. Little is known about Chilean EBV strains. This study aims to investigate the frequency and genetic diversity of EBV in GC in patients in southern Chile. To evaluate the prevalence of EBV in GC patients from the Chilean population, we studied 54 GC samples using the gold standard detection method of EBV-encoded small RNA (EBER). The EBV-positive samples were subjected to amplification and sequencing of the Epstein–Barr virus nuclear protein 3A (EBNA3A) gene to evaluate the genetic diversity of EBV strains circulating in southern Chile. In total, 22.2% of the GC samples were EBV-positive and significantly associated with diffuse-type histology (p = 0.003). Phylogenetic analyses identified EBV-1 and EBV-2 in the GC samples, showing genetic diversity among Chilean isolates. This work provides important information for an epidemiological follow-up of the different EBV subtypes that may cause GC in southern Chile. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Chile)

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15 pages, 3174 KiB

Open AccessArticle

OPTO-BLUE: An Integrated Bidirectional Optogenetic Lentiviral Platform for Controlled Light-Induced Gene Expression

by Duxan Arancibia, Iracy Pol, Martín Vargas-Fernández, Rafaella V. Zárate, Janetti R. Signorelli and Pedro Zamorano

Int. J. Mol. Sci. 2023, 24(11), 9537; https://doi.org/10.3390/ijms24119537 - 31 May 2023

Viewed by 1467

Abstract

Regulated systems for transgene expression are useful tools in basic research and a promising platform in biomedicine due to their regulated transgene expression by an inducer. The emergence of optogenetics expression systems enabled the construction of light-switchable systems, enhancing the spatial and temporal resolution of a transgene. The LightOn system is an optogenetic tool that regulates the expression of a gene of interest using blue light as an inducer. This system is based on a photosensitive protein (GAVPO), which dimerizes and binds to the UASG sequence in response to blue light, triggering the expression of a downstream transgene. Previously, we adapted the LightOn system to a dual lentiviral vector system for neurons. Here, we continue the optimization and assemble all components of the LightOn system into a single lentiviral plasmid, the OPTO-BLUE system. For functional validation, we used enhanced green fluorescent protein (EGFP) as an expression reporter (OPTO-BLUE-EGFP) and evaluated the efficiency of EGFP expression by transfection and transduction in HEK293-T cells exposed to continuous blue-light illumination. Altogether, these results prove that the optimized OPTO-BLUE system allows the light-controlled expression of a reporter protein according to a specific time and light intensity. Likewise, this system should provide an important molecular tool to modulate gene expression of any protein by blue light. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Chile)

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19 pages, 3542 KiB

Open AccessArticle

Unraveling the Molecular Basis of Mycosporine Biosynthesis in Fungi

by Dionisia Sepúlveda, Sebastián Campusano, Martín Moliné, Salvador Barahona, Marcelo Baeza, Jennifer Alcaíno, Fernando Colabella, Blanca Urzúa, Diego Libkind and Víctor Cifuentes

Int. J. Mol. Sci. 2023, 24(6), 5930; https://doi.org/10.3390/ijms24065930 - 21 Mar 2023

Cited by 4 | Viewed by 1768

Abstract

The Phaffia rhodozyma UCD 67-385 genome harbors a 7873 bp cluster containing DDGS, OMT, and ATPG, encoding 2-desmethy-4-deoxygadusol synthase, O-methyl transferase, and ATP-grasp ligase, respectively, of the mycosporine glutaminol (MG) biosynthesis pathway. Homozygous deletion mutants of the entire cluster, single-gene mutants, and the Δddgs^−/−;Δomt^−/− and Δomt^−/−;Δatpg^−/− double-gene mutants did not produce mycosporines. However, Δatpg^−/− accumulated the intermediate 4-deoxygadusol. Heterologous expression of the DDGS and OMT or DDGS, OMT, and ATPG cDNAs in Saccharomyces cerevisiae led to 4-deoxygadusol or MG production, respectively. Genetic integration of the complete cluster into the genome of the non-mycosporine-producing CBS 6938 wild-type strain resulted in a transgenic strain (CBS 6938_MYC) that produced MG and mycosporine glutaminol glucoside. These results indicate the function of DDGS, OMT, and ATPG in the mycosporine biosynthesis pathway. The transcription factor gene mutants Δmig1^−/−, Δcyc8^−/−, and Δopi1^−/− showed upregulation, Δrox1^−/− and Δskn7^−/− showed downregulation, and Δtup6^−/− and Δyap6^−/− showed no effect on mycosporinogenesis in glucose-containing medium. Finally, comparative analysis of the cluster sequences in several P. rhodozyma strains and the four newly described species of the genus showed the phylogenetic relationship of the P. rhodozyma strains and their differentiation from the other species of the genus Phaffia. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Chile)

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24 pages, 4076 KiB

Open AccessArticle

A Mouse Systems Genetics Approach Reveals Common and Uncommon Genetic Modifiers of Hepatic Lysosomal Enzyme Activities and Glycosphingolipids

by Anyelo Durán, David A. Priestman, Macarena Las Heras, Boris Rebolledo-Jaramillo, Valeria Olguín, Juan F. Calderón, Silvana Zanlungo, Jaime Gutiérrez, Frances M. Platt and Andrés D. Klein

Int. J. Mol. Sci. 2023, 24(5), 4915; https://doi.org/10.3390/ijms24054915 - 3 Mar 2023

Cited by 1 | Viewed by 1639

Abstract

Identification of genetic modulators of lysosomal enzyme activities and glycosphingolipids (GSLs) may facilitate the development of therapeutics for diseases in which they participate, including Lysosomal Storage Disorders (LSDs). To this end, we used a systems genetics approach: we measured 11 hepatic lysosomal enzymes and many of their natural substrates (GSLs), followed by modifier gene mapping by GWAS and transcriptomics associations in a panel of inbred strains. Unexpectedly, most GSLs showed no association between their levels and the enzyme activity that catabolizes them. Genomic mapping identified 30 shared predicted modifier genes between the enzymes and GSLs, which are clustered in three pathways and are associated with other diseases. Surprisingly, they are regulated by ten common transcription factors, and their majority by miRNA-340p. In conclusion, we have identified novel regulators of GSL metabolism, which may serve as therapeutic targets for LSDs and may suggest the involvement of GSL metabolism in other pathologies. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Chile)

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18 pages, 1163 KiB

Open AccessArticle

Carrot DcALFIN4 and DcALFIN7 Transcription Factors Boost Carotenoid Levels and Participate Differentially in Salt Stress Tolerance When Expressed in Arabidopsis thaliana and Actinidia deliciosa

by Luis Felipe Quiroz-Iturra, Kevin Simpson, Daniela Arias, Cristóbal Silva, Christian González-Calquin, Leticia Amaza, Michael Handford and Claudia Stange

Int. J. Mol. Sci. 2022, 23(20), 12157; https://doi.org/10.3390/ijms232012157 - 12 Oct 2022

Cited by 4 | Viewed by 1860

Abstract

ALFIN-like transcription factors (ALs) are involved in several physiological processes such as seed germination, root development and abiotic stress responses in plants. In carrot (Daucus carota), the expression of DcPSY2, a gene encoding phytoene synthase required for carotenoid biosynthesis, is induced after salt and abscisic acid (ABA) treatment. Interestingly, the DcPSY2 promoter contains multiple ALFIN response elements. By in silico analysis, we identified two putative genes with the molecular characteristics of ALs, DcAL4 and DcAL7, in the carrot transcriptome. These genes encode nuclear proteins that transactivate reporter genes and bind to the carrot DcPSY2 promoter in yeast. The expression of both genes is induced in carrot under salt stress, especially DcAL4 which also responds to ABA treatment. Transgenic homozygous T3 Arabidopsis thaliana lines that stably express DcAL4 and DcAL7 show a higher survival rate with respect to control plants after chronic salt stress. Of note is that DcAL4 lines present a better performance in salt treatments, correlating with the expression level of DcAL4, AtPSY and AtDXR and an increase in carotenoid and chlorophyll contents. Likewise, DcAL4 transgenic kiwi (Actinidia deliciosa) lines show increased carotenoid and chlorophyll content and higher survival rate compared to control plants after chronic salt treatment. Therefore, DcAL4 and DcAL7 encode functional transcription factors, while ectopic expression of DcAL4 provides increased tolerance to salinity in Arabidopsis and Kiwi plants. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Chile)

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19 pages, 6126 KiB

Open AccessArticle

Role of ROX1, SKN7, and YAP6 Stress Transcription Factors in the Production of Secondary Metabolites in Xanthophyllomyces dendrorhous

by Pilar Martínez-Moya, Sebastián Campusano, Dionisia Sepúlveda, Alberto Paradela, Jennifer Alcaíno, Marcelo Baeza and Víctor Cifuentes

Int. J. Mol. Sci. 2022, 23(16), 9282; https://doi.org/10.3390/ijms23169282 - 18 Aug 2022

Cited by 2 | Viewed by 1729

Abstract

Xanthophyllomyces dendrorhous is a natural source of astaxanthin and mycosporines. This yeast has been isolated from high and cold mountainous regions around the world, and the production of these secondary metabolites may be a survival strategy against the stress conditions present in its environment. Biosynthesis of astaxanthin is regulated by catabolic repression through the interaction between MIG1 and corepressor CYC8–TUP1. To evaluate the role of the stress-associated transcription factors SKN7, ROX1, and YAP6, we employed an omic and phenotypic approach. Null mutants were constructed and grown in two fermentable carbon sources. The yeast proteome and transcriptome were quantified by iTRAQ and RNA-seq, respectively. The total carotenoid, sterol, and mycosporine contents were determined and compared to the wild-type strain. Each mutant strain showed significant metabolic changes compared to the wild type that were correlated to its phenotype. In a metabolic context, the principal pathways affected were glycolysis/gluconeogenesis, the pentose phosphate (PP) pathway, and the citrate (TCA) cycle. Additionally, fatty acid synthesis was affected. The absence of ROX1 generated a significant decline in carotenoid production. In contrast, a rise in mycosporine and sterol synthesis was shown in the absence of the transcription factors SKN7 and YAP6, respectively. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Chile)

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16 pages, 4160 KiB

Open AccessArticle

Extracellular Cysteines Are Critical to Form Functional Cx46 Hemichannels

by Ainoa Fernández-Olivares, Eduardo Durán-Jara, Daniel A. Verdugo, Mariana C. Fiori, Guillermo A. Altenberg, Jimmy Stehberg, Iván Alfaro, Juan Francisco Calderón and Mauricio A. Retamal

Int. J. Mol. Sci. 2022, 23(13), 7252; https://doi.org/10.3390/ijms23137252 - 29 Jun 2022

Cited by 6 | Viewed by 1852

Abstract

Connexin (Cxs) hemichannels participate in several physiological and pathological processes, but the molecular mechanisms that control their gating remain elusive. We aimed at determining the role of extracellular cysteines (Cys) in the gating and function of Cx46 hemichannels. We studied Cx46 and mutated all of its extracellular Cys to alanine (Ala) (one at a time) and studied the effects of the Cys mutations on Cx46 expression, localization, and hemichannel activity. Wild-type Cx46 and Cys mutants were expressed at comparable levels, with similar cellular localization. However, functional experiments showed that hemichannels formed by the Cys mutants did not open either in response to membrane depolarization or removal of extracellular divalent cations. Molecular-dynamics simulations showed that Cys mutants may show a possible alteration in the electrostatic potential of the hemichannel pore and an altered disposition of important residues that could contribute to the selectivity and voltage dependency in the hemichannels. Replacement of extracellular Cys resulted in “permanently closed hemichannels”, which is congruent with the inhibition of the Cx46 hemichannel by lipid peroxides, through the oxidation of extracellular Cys. These results point to the modification of extracellular Cys as potential targets for the treatment of Cx46-hemichannel associated pathologies, such as cataracts and cancer, and may shed light into the gating mechanisms of other Cx hemichannels. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Chile)

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Review

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18 pages, 2296 KiB

Open AccessReview

Hypertensive Nephropathy: Unveiling the Possible Involvement of Hemichannels and Pannexons

by Claudia M. Lucero, Juan Prieto-Villalobos, Lucas Marambio-Ruiz, Javiera Balmazabal, Tanhia F. Alvear, Matías Vega, Paola Barra, Mauricio A. Retamal, Juan A. Orellana and Gonzalo I. Gómez

Int. J. Mol. Sci. 2022, 23(24), 15936; https://doi.org/10.3390/ijms232415936 - 14 Dec 2022

Cited by 8 | Viewed by 4187

Abstract

Hypertension is one of the most common risk factors for developing chronic cardiovascular diseases, including hypertensive nephropathy. Within the glomerulus, hypertension causes damage and activation of mesangial cells (MCs), eliciting the production of large amounts of vasoactive and proinflammatory agents. Accordingly, the activation of AT1 receptors by the vasoactive molecule angiotensin II (AngII) contributes to the pathogenesis of renal damage, which is mediated mostly by the dysfunction of intracellular Ca²⁺ ([Ca²⁺]_i) signaling. Similarly, inflammation entails complex processes, where [Ca²⁺]_i also play crucial roles. Deregulation of this second messenger increases cell damage and promotes fibrosis, reduces renal blood flow, and impairs the glomerular filtration barrier. In vertebrates, [Ca²⁺]_i signaling depends, in part, on the activity of two families of large-pore channels: hemichannels and pannexons. Interestingly, the opening of these channels depends on [Ca²⁺]_i signaling. In this review, we propose that the opening of channels formed by connexins and/or pannexins mediated by AngII induces the ATP release to the extracellular media, with the subsequent activation of purinergic receptors. This process could elicit Ca²⁺ overload and constitute a feed-forward mechanism, leading to kidney damage. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Chile)

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29 pages, 3346 KiB

Open AccessReview

Aquaporin Gating: A New Twist to Unravel Permeation through Water Channels

by Marcelo Ozu, Juan José Alvear-Arias, Miguel Fernandez, Agustín Caviglia, Antonio Peña-Pichicoi, Christian Carrillo, Emerson Carmona, Anselmo Otero-Gonzalez, José Antonio Garate, Gabriela Amodeo and Carlos Gonzalez

Int. J. Mol. Sci. 2022, 23(20), 12317; https://doi.org/10.3390/ijms232012317 - 14 Oct 2022

Cited by 4 | Viewed by 3161

Abstract

Aquaporins (AQPs) are small transmembrane tetrameric proteins that facilitate water, solute and gas exchange. Their presence has been extensively reported in the biological membranes of almost all living organisms. Although their discovery is much more recent than ion transport systems, different biophysical approaches have contributed to confirm that permeation through each monomer is consistent with closed and open states, introducing the term gating mechanism into the field. The study of AQPs in their native membrane or overexpressed in heterologous systems have experimentally demonstrated that water membrane permeability can be reversibly modified in response to specific modulators. For some regulation mechanisms, such as pH changes, evidence for gating is also supported by high-resolution structures of the water channel in different configurations as well as molecular dynamics simulation. Both experimental and simulation approaches sustain that the rearrangement of conserved residues contributes to occlude the cavity of the channel restricting water permeation. Interestingly, specific charged and conserved residues are present in the environment of the pore and, thus, the tetrameric structure can be subjected to alter the positions of these charges to sustain gating. Thus, is it possible to explore whether the displacement of these charges (gating current) leads to conformational changes? To our knowledge, this question has not yet been addressed at all. In this review, we intend to analyze the suitability of this proposal for the first time. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Chile)

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14 pages, 1162 KiB

Open AccessReview

Genetic Background Matters: Population-Based Studies in Model Organisms for Translational Research

by Valeria Olguín, Anyelo Durán, Macarena Las Heras, Juan Carlos Rubilar, Francisco A. Cubillos, Patricio Olguín and Andrés D. Klein

Int. J. Mol. Sci. 2022, 23(14), 7570; https://doi.org/10.3390/ijms23147570 - 8 Jul 2022

Cited by 4 | Viewed by 2703

Abstract

We are all similar but a bit different. These differences are partially due to variations in our genomes and are related to the heterogeneity of symptoms and responses to treatments that patients exhibit. Most animal studies are performed in one single strain with one manipulation. However, due to the lack of variability, therapies are not always reproducible when treatments are translated to humans. Panels of already sequenced organisms are valuable tools for mimicking human phenotypic heterogeneities and gene mapping. This review summarizes the current knowledge of mouse, fly, and yeast panels with insightful applications for translational research. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Chile)

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