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Essential Molecules in Life: Regulation, Defense, and Longevity

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: 25 June 2024 | Viewed by 7588

Special Issue Editors


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Guest Editor
Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Avenida Fuentenueva 1, 18071 Granada, Spain
Interests: study of the anticancer potential of natural and derivatives products derived from the olive grove; molecular pathways involved in anticancer processes; glucose metabolism and its regulation; enzimology and kinetics; biochemical characterization of anti-inflammatory and anti-oxidant properties; proteomics and metabolomics associated with cancer; cell growth processes: protein synthesis and degradation
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Zoology, University of Granada, 18012 Granada, Spain
Interests: animal welfare; aquatic toxicology; functional molecules; natural compounds; oxidative stress and immunology
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, 18012 Granada, Spain
Interests: anticancer bioactivities of natural products; functional proteomics; gene regulation by microRNAs; molecular characterization during inflammation and oxidative stress
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

During the reproduction, development, longevity and evolution of the different living beings that make up the extraordinary biodiversity of animal and plant species in their environment, there have been, are and will be chemical molecules that have played a crucial role in assisting these biological processes.

Many are the examples we can give, such as amino acids, monosaccharides, disaccharides and polysaccharides, nucleotides, essential fatty acids, significant lipids, primary metabolites, secondary metabolites, peptides, low molecular weight proteins, high molecular weight proteins, different types of nucleic acids.

Different amino acids, such as aromatic, branched, sulfur-containing and simple ones like glycine, have been authentic precursors of molecules indispensable for life, among them we must mention regulators of enzymatic and metabolic activity, hormones, neurotransmitters, coenzymes, proteins like collagen, etc.

Among the nucleotides that, in addition to being the constituents of the different nucleic acids, such as DNA and RNA, single-, di- and triphosphorylated nucleosides, are presented as true regulators of metabolic activity, as a store of chemical energy or as biosynthetic precursors; cyclic nucleotides, such as cyclic AMP and cyclic GMP as cellular and physiological regulators. In this section, we should also include the different types of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) because of their relevant role in most cellular, physiological and pathological processes, which have been highlighted in recent years.

Essential fatty acids (n3 and n6 series), simple lipids such as cholesterol and its derivatives, or complex lipids such as cephalins, lecithins, inositols, cardiolipins, etc., which also behave as authentic and indispensable in the regulation and development of numerous cellular processes.

Primary metabolites such as pyruvate, acetyl-CoA, etc. that behave as metabolic crossroads; or secondary metabolites such as the different classes of phytochemicals that are key to understanding not only the defense of the organisms that generate them, but also behave as authentic regulators of immune, inflammatory, anticancer, antioxidant, etc. activity, all of these bioactivities being key to understanding the role in biological longevity.

The rest of the key molecules, peptides, low molecular weight proteins, high molecular weight proteins, different types of nucleic acids, are equally essential to understand the behavior, development and evolution of living beings.

Therefore, this special issue aims to publish the most recent and innovative advances of all the molecules and macromolecules defined above, as well as others not mentioned, both the original ones and different chemical derivatives of them, to help us understand their role in the prevention, defense, development, longevity and evolution of all living beings.

Prof. Dr. José Antonio Lupiáñez
Dr. Amalia Pérez-Jiménez
Dr. Eva E. Rufino Palomares
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

  • glucose metabolism and its regulation
  • enzimology and kinetics
  • metabolism and evolution
  • cell growth
  • protein synthesis and degradation
  • cell proliferation and apoptosis
  • cancer
  • metastasis and angiogenesis
  • oxidative stress
  • genomic
  • proteomic and metab

Published Papers (5 papers)

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Research

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17 pages, 338 KiB  
Article
Effect of Nutraceutical Factors on Hepatic Intermediary Metabolism in Wistar Rats with Induced Tendinopathy
by Marta Ramos-Barbero, Eva E. Rufino-Palomares, Sergio Serrano-Carmona, Manuel Hernández-Yera, Leticia García-Salguero, José Antonio Lupiáñez and Amalia Pérez-Jiménez
Int. J. Mol. Sci. 2024, 25(1), 629; https://doi.org/10.3390/ijms25010629 - 03 Jan 2024
Viewed by 808
Abstract
Tendinopathy (TP) is a complex clinical syndrome characterized by local inflammation, pain in the affected area, and loss of performance, preceded by tendon injury. The disease develops in three phases: Inflammatory phase, proliferative phase, and remodeling phase. There are currently no proven treatments [...] Read more.
Tendinopathy (TP) is a complex clinical syndrome characterized by local inflammation, pain in the affected area, and loss of performance, preceded by tendon injury. The disease develops in three phases: Inflammatory phase, proliferative phase, and remodeling phase. There are currently no proven treatments for early reversal of this type of injury. However, the metabolic pathways of the transition metabolism, which are necessary for the proper functioning of the organism, are known. These metabolic pathways can be modified by a number of external factors, such as nutritional supplements. In this study, the modulatory effect of four dietary supplements, maslinic acid (MA), hydroxytyrosol (HT), glycine, and aspartate (AA), on hepatic intermediary metabolism was observed in Wistar rats with induced tendinopathy at different stages of the disease. Induced tendinopathy in rats produces alterations in the liver intermediary metabolism. Nutraceutical treatments modify the intermediary metabolism in the different phases of tendinopathy, so AA treatment produced a decrease in carbohydrate metabolism. In lipid metabolism, MA and AA caused a decrease in lipogenesis at the tendinopathy and increased fatty acid oxidation. In protein metabolism, MA treatment increased GDH and AST activity; HT decreased ALT activity; and the AA treatment does not cause any alteration. Use of nutritional supplements of diet could help to regulate the intermediary metabolism in the TP. Full article
(This article belongs to the Special Issue Essential Molecules in Life: Regulation, Defense, and Longevity)
18 pages, 5483 KiB  
Article
Multi-Omics Analysis Reveals the Pathogenesis of Growth-Disordered Raccoon Dog
by Danyang Chen, Xiaolan Guo, Kaiying Wang, Weigang Zhao, Zhongjuan Chang, Quankai Wang and Chao Xu
Int. J. Mol. Sci. 2023, 24(18), 14237; https://doi.org/10.3390/ijms241814237 - 18 Sep 2023
Viewed by 870
Abstract
Microorganisms of the genus Eperythrozoon are a zoonotic chronic infectious disease with wide distribution. We found that raccoons infected with Eperythrozoon showed obvious stunting, which seriously affected the economic benefits of raccoon dogs. To investigate the pathogenesis of the raccoon dog, we used [...] Read more.
Microorganisms of the genus Eperythrozoon are a zoonotic chronic infectious disease with wide distribution. We found that raccoons infected with Eperythrozoon showed obvious stunting, which seriously affected the economic benefits of raccoon dogs. To investigate the pathogenesis of the raccoon dog, we used transcriptome and proteome sequencing to analyze the changes in mRNA, miRNA, and protein expression in raccoon dogs infected with Eperythrozoon and normal raccoons. The results showed that the expression levels of genes related to immunity, metabolism, and enzyme activity were significantly changed. Among these, ERLIN1, IGF1R, CREB3L1, TNS1, TENC1, and mTOR play key roles. Additionally, the miR-1268, miR-125b, miR-10-5p, and miR-10 as central miRNAs regulate the expression of these genes. Integrated transcriptomic and proteomic analyses revealed consistent trends in mRNA and protein changes in MYH9, FKBP1A, PRKCA, and CYP11B2. These results suggest that Eperythrozoon may contribute to the slow development of raccoons by affecting the expression of mRNAs and miRNAs, reducing their immunity and causing metabolic abnormalities. Full article
(This article belongs to the Special Issue Essential Molecules in Life: Regulation, Defense, and Longevity)
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20 pages, 12763 KiB  
Article
In Silico Identification and Analysis of Proteins Containing the Phox Homology Phosphoinositide-Binding Domain in Kinetoplastea Protists: Evolutionary Conservation and Uniqueness of Phox-Homology-Domain-Containing Protein Architectures
by Marina Petsana, Ahmed F. Roumia, Pantelis G. Bagos, Haralabia Boleti and Georgia G. Braliou
Int. J. Mol. Sci. 2023, 24(14), 11521; https://doi.org/10.3390/ijms241411521 - 15 Jul 2023
Cited by 1 | Viewed by 1248
Abstract
Kinetoplastea are free living and parasitic protists with unique features among Eukaryota. Pathogenic Kinetoplastea parasites (i.e., Trypanosoma and Leishmania spp.) undergo several developmental transitions essential for survival in their hosts. These transitions require membrane and cytoskeleton reorganizations that involve phosphoinositides (PIs). Phospholipids like [...] Read more.
Kinetoplastea are free living and parasitic protists with unique features among Eukaryota. Pathogenic Kinetoplastea parasites (i.e., Trypanosoma and Leishmania spp.) undergo several developmental transitions essential for survival in their hosts. These transitions require membrane and cytoskeleton reorganizations that involve phosphoinositides (PIs). Phospholipids like PIs are key regulators of vital functions in all eukaryotes including signal transduction, protein transport and sorting, membrane trafficking, and cytoskeleton and membrane remodeling. A large repertoire of PI-metabolizing enzymes and PI-binding proteins/effectors carrying distinct PI-binding modules like the PX (phox homology) module could play significant roles in the life and virulence of pathogenic Kinetoplastea. The aim of this study was to retrieve the entire spectrum of Kinetoplastea protein sequences containing the PX module (PX-proteins), predict their structures, and identify in them evolutionary conserved and unique traits. Using a large array of bioinformatics tools, protein IDs from two searches (based on PFam’s pHMM for PX domain (PF00787)) were combined, aligned, and utilized for the construction of a new Kinetoplastea_PX pHMM. This three-step search retrieved 170 PX-protein sequences. Structural domain configuration analysis identified PX, Pkinase, Lipocalin_5, and Vps5/BAR3-WASP domains and clustered them into five distinct subfamilies. Phylogenetic tree and domain architecture analysis showed that some domain architectures exist in proteomes of all Kinetoplastea spp., while others are genus-specific. Finally, amino acid conservation logos of the Kinetoplastea spp. and Homo sapiens PX domains revealed high evolutionary conservation in residues forming the critical structural motifs for PtdIns3P recognition. This study highlights the PX-Pkinase domain architecture as unique within Trypanosoma spp. and forms the basis for a targeted functional analysis of Kinetoplastea PX-proteins as putative targets for a rational design of anti-parasitic drugs. Full article
(This article belongs to the Special Issue Essential Molecules in Life: Regulation, Defense, and Longevity)
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17 pages, 3174 KiB  
Article
Transcriptome Profiling of Prostate Cancer, Considering Risk Groups and the TMPRSS2-ERG Molecular Subtype
by Anastasiya A. Kobelyatskaya, Elena A. Pudova, Irina V. Katunina, Anastasiya V. Snezhkina, Maria S. Fedorova, Vladislav S. Pavlov, Anastasiya O. Kotelnikova, Kirill M. Nyushko, Boris Y. Alekseev, George S. Krasnov and Anna V. Kudryavtseva
Int. J. Mol. Sci. 2023, 24(11), 9282; https://doi.org/10.3390/ijms24119282 - 25 May 2023
Cited by 2 | Viewed by 1297
Abstract
Molecular heterogeneity in prostate cancer (PCa) is one of the key reasons underlying the differing likelihoods of recurrence after surgical treatment in individual patients of the same clinical category. In this study, we performed RNA-Seq profiling of 58 localized PCa and 43 locally [...] Read more.
Molecular heterogeneity in prostate cancer (PCa) is one of the key reasons underlying the differing likelihoods of recurrence after surgical treatment in individual patients of the same clinical category. In this study, we performed RNA-Seq profiling of 58 localized PCa and 43 locally advanced PCa tissue samples obtained as a result of radical prostatectomy on a cohort of Russian patients. Based on bioinformatics analysis, we examined features of the transcriptome profiles within the high-risk group, including within the most commonly represented molecular subtype, TMPRSS2-ERG. The most significantly affected biological processes in the samples were also identified, so that they may be further studied in the search for new potential therapeutic targets for the categories of PCa under consideration. The highest predictive potential was found with the EEF1A1P5, RPLP0P6, ZNF483, CIBAR1, HECTD2, OGN, and CLIC4 genes. We also reviewed the main transcriptome changes in the groups at intermediate risk of PCa—Gleason Score 7 (groups 2 and 3 according to the ISUP classification)—on the basis of which the LPL, MYC, and TWIST1 genes were identified as promising additional prognostic markers, the statistical significance of which was confirmed using qPCR validation. Full article
(This article belongs to the Special Issue Essential Molecules in Life: Regulation, Defense, and Longevity)
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Review

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25 pages, 6919 KiB  
Review
Aestivation in Nature: Physiological Strategies and Evolutionary Adaptations in Hypometabolic States
by Chunxi Jiang, Kenneth B. Storey, Hongsheng Yang and Lina Sun
Int. J. Mol. Sci. 2023, 24(18), 14093; https://doi.org/10.3390/ijms241814093 - 14 Sep 2023
Cited by 2 | Viewed by 2660
Abstract
Aestivation is considered to be one of the “purest” hypometabolic states in nature, as it involves aerobic dormancy that can be induced and sustained without complex factors. Animals that undergo aestivation to protect themselves from environmental stressors such as high temperatures, droughts, and [...] Read more.
Aestivation is considered to be one of the “purest” hypometabolic states in nature, as it involves aerobic dormancy that can be induced and sustained without complex factors. Animals that undergo aestivation to protect themselves from environmental stressors such as high temperatures, droughts, and food shortages. However, this shift in body metabolism presents new challenges for survival, including oxidative stress upon awakening from aestivation, accumulation of toxic metabolites, changes in energy sources, adjustments to immune status, muscle atrophy due to prolonged immobility, and degeneration of internal organs due to prolonged food deprivation. In this review, we summarize the physiological and metabolic strategies, key regulatory factors, and networks utilized by aestivating animals to address the aforementioned components of aestivation. Furthermore, we present a comprehensive overview of the advancements made in aestivation research across major species, including amphibians, fish, reptiles, annelids, mollusks, and echinoderms, categorized according to their respective evolutionary positions. This approach offers a distinct perspective for comparative analysis, facilitating an understanding of the shared traits and unique features of aestivation across different groups of organisms. Full article
(This article belongs to the Special Issue Essential Molecules in Life: Regulation, Defense, and Longevity)
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