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State-of-the-Art Molecular Microbiology in Spain

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

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 17233

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Collection Editor
Department of Biochemistry & Molecular Biology and Institute of Biotechnology & Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
Interests: yeast molecular biology; protein phosphorylation; protein phosphatases; signal transduction; cation homeostasis; cell cycle; gene expression; transcriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Topical Collection aims to provide a comprehensive overview of recent advances in both prokaryotic and eukaryotic molecular microbiology in Spain by inviting contributions from Spanish research institutes/laboratories that consolidate our understanding of this area. Topics include, but are not limited to, the following:

  • Antibiotic-resistance mechanisms;
  • Biosynthesis of macromolecules;
  • Cell division and cell-wall structure;
  • Gene expression and its regulation;
  • Gene transfer mechanisms;
  • Host–pathogen interactions, including host responses;
  • Induction of cell death by microorganisms;
  • Membrane biogenesis and function;
  • Pathogenicity mechanisms;
  • Posttranslational modifications;
  • Protein delivery (secretion and trafficking);
  • Signaling pathways and networks;
  • Systems biology;
  • Vaccines;
  • Virulence factors;
  • Antimicrobial peptides;
  • Therapeutic strategies.

Prof. Dr. Joaquin Arino
Collection Editor

Manuscript Submission Information

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Keywords

  • microbiology
  • gene expression regulation
  • biochemical processes
  • pathogenicity mechanisms
  • host–microbe interactions
  • bacteriophages
  • therapeutic strategies
  • molecular biology of Fungi
  • industrial application of microorganisms

Published Papers (10 papers)

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Research

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17 pages, 7937 KiB  
Article
The ENA1 Na+-ATPase Gene Is Regulated by the SPS Sensing Pathway and the Stp1/Stp2 Transcription Factors
by Abdelghani Zekhnini, Marcel Albacar, Antonio Casamayor and Joaquín Ariño
Int. J. Mol. Sci. 2023, 24(6), 5548; https://doi.org/10.3390/ijms24065548 - 14 Mar 2023
Cited by 1 | Viewed by 1274
Abstract
The Saccharomyces cerevisiae ENA1 gene, encoding a Na+-ATPase, responds transcriptionally to the alkalinization of the medium by means of a network of signals that involves the Rim101, the Snf1 and PKA kinases, and the calcineurin/Crz1 pathways. We show here that the [...] Read more.
The Saccharomyces cerevisiae ENA1 gene, encoding a Na+-ATPase, responds transcriptionally to the alkalinization of the medium by means of a network of signals that involves the Rim101, the Snf1 and PKA kinases, and the calcineurin/Crz1 pathways. We show here that the ENA1 promoter also contains a consensus sequence, located at nt −553/−544, for the Stp1/2 transcription factors, the downstream components of the amino acid sensing SPS pathway. Mutation of this sequence or deletion of either STP1 or STP2 decreases the activity of a reporter containing this region in response to alkalinization as well as to changes in the amino acid composition in the medium. Expression driven from the entire ENA1 promoter was affected with similar potency by the deletion of PTR3, SSY5, or simultaneous deletion of STP1 and STP2 when cells were exposed to alkaline pH or moderate salt stress. However, it was not altered by the deletion of SSY1, encoding the amino acid sensor. In fact, functional mapping of the ENA1 promoter reveals a region spanning from nt −742 to −577 that enhances transcription, specifically in the absence of Ssy1. We also found that the basal and alkaline pH-induced expression from the HXT2, TRX2, and, particularly, SIT1 promoters was notably decreased in an stp1 stp2 deletion mutant, whereas the PHO84 and PHO89 gene reporters were unaffected. Our findings add a further layer of complexity to the regulation of ENA1 and suggest that the SPS pathway might participate in the regulation of a subset of alkali-inducible genes. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Microbiology in Spain)
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23 pages, 7750 KiB  
Article
Analysis of the Localization of Schizosaccharomyces pombe Glucan Synthases in the Presence of the Antifungal Agent Caspofungin
by Esther San-Quirico, M. Ángeles Curto, Laura Gómez-Delgado, M. Belén Moreno, Pilar Pérez, Juan Carlos Ribas and Juan Carlos G. Cortés
Int. J. Mol. Sci. 2023, 24(5), 4299; https://doi.org/10.3390/ijms24054299 - 21 Feb 2023
Viewed by 1197
Abstract
In recent years, invasive fungal infections have emerged as a common source of infections in immunosuppressed patients. All fungal cells are surrounded by a cell wall that is essential for cell integrity and survival. It prevents cell death and lysis resulting from high [...] Read more.
In recent years, invasive fungal infections have emerged as a common source of infections in immunosuppressed patients. All fungal cells are surrounded by a cell wall that is essential for cell integrity and survival. It prevents cell death and lysis resulting from high internal turgor pressure. Since the cell wall is not present in animal cells, it is an ideal target for selective invasive fungal infection treatments. The antifungal family known as echinocandins, which specifically inhibit the synthesis of the cell wall β(13)glucan, has been established as an alternative treatment for mycoses. To explore the mechanism of action of these antifungals, we analyzed the cell morphology and glucan synthases localization in Schizosaccharomyces pombe cells during the initial times of growth in the presence of the echinocandin drug caspofungin. S. pombe are rod-shaped cells that grow at the poles and divide by a central division septum. The cell wall and septum are formed by different glucans, which are synthesized by four essential glucan synthases: Bgs1, Bgs3, Bgs4, and Ags1. Thus, S. pombe is not only a perfect model for studying the synthesis of the fungal β(1-3)glucan, but also it is ideal for examining the mechanisms of action and resistance of cell wall antifungals. Herein, we examined the cells in a drug susceptibility test in the presence of either lethal or sublethal concentrations of caspofungin, finding that exposure to the drug for long periods at high concentrations (>10 µg/mL) induced cell growth arrest and the formation of rounded, swollen, and dead cells, whereas low concentrations (<10 µg/mL) permitted cell growth with a mild effect on cell morphology. Interestingly, short-term treatments with either high or low concentrations of the drug induced effects contrary to those observed in the susceptibility tests. Thus, low drug concentrations induced a cell death phenotype that was not observed at high drug concentrations, which caused transient fungistatic cell growth arrest. After 3 h, high concentrations of the drug caused the following: (i) a decrease in the GFP-Bgs1 fluorescence level; (ii) altered locations of Bgs3, Bgs4, and Ags1; and (iii) a simultaneous accumulation of cells with calcofluor-stained incomplete septa, which at longer times resulted in septation uncoupling from plasma membrane ingression. The incomplete septa revealed with calcofluor were found to be complete when observed via the membrane-associated GFP-Bgs or Ags1-GFP. Finally, we found that the accumulation of incomplete septa depended on Pmk1, the last kinase of the cell wall integrity pathway. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Microbiology in Spain)
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17 pages, 3554 KiB  
Article
Aft1 Nuclear Localization and Transcriptional Response to Iron Starvation Rely upon TORC2/Ypk1 Signaling and Sphingolipid Biosynthesis
by Sandra Montellà-Manuel, Nuria Pujol-Carrion and Maria Angeles de la Torre-Ruiz
Int. J. Mol. Sci. 2023, 24(3), 2438; https://doi.org/10.3390/ijms24032438 - 26 Jan 2023
Cited by 2 | Viewed by 1468
Abstract
Iron scarcity provokes a cellular response consisting of the strong expression of high-affinity systems to optimize iron uptake and mobilization. Aft1 is a primary transcription factor involved in iron homeostasis and controls the expression of high-affinity iron uptake genes in Saccharomyces cerevisiae. [...] Read more.
Iron scarcity provokes a cellular response consisting of the strong expression of high-affinity systems to optimize iron uptake and mobilization. Aft1 is a primary transcription factor involved in iron homeostasis and controls the expression of high-affinity iron uptake genes in Saccharomyces cerevisiae. Aft1 responds to iron deprivation by translocating from the cytoplasm to the nucleus. Here, we demonstrate that the AGC kinase Ypk1, as well as its upstream regulator TOR Complex 2 (TORC2), are required for proper Aft1 nuclear localization following iron deprivation. We exclude a role for TOR Complex 1 (TORC1) and its downstream effector Sch9, suggesting this response is specific for the TORC2 arm of the TOR pathway. Remarkably, we demonstrate that Aft1 nuclear localization and a robust transcriptional response to iron starvation also require biosynthesis of sphingolipids, including complex sphingolipids such as inositol phosphorylceramide (IPC) and upstream precursors, e.g., long-chain bases (LCBs) and ceramides. Furthermore, we observe the deficiency of Aft1 nuclear localization and impaired transcriptional response in the absence of iron when TORC2-Ypk1 is impaired is partially suppressed by exogenous addition of the LCB dihydrosphingosine (DHS). This latter result is consistent with prior studies linking sphingolipid biosynthesis to TORC2-Ypk1 signaling. Taken together, these results reveal a novel role for sphingolipids, controlled by TORC2-Ypk1, for proper localization and activity of Aft1 in response to iron scarcity. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Microbiology in Spain)
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16 pages, 1385 KiB  
Article
Phenotypic and Safety Assessment of the Cheese Strain Lactiplantibacillus plantarum LL441, and Sequence Analysis of its Complete Genome and Plasmidome
by Ana Belén Flórez, Lucía Vázquez, Javier Rodríguez and Baltasar Mayo
Int. J. Mol. Sci. 2023, 24(1), 605; https://doi.org/10.3390/ijms24010605 - 29 Dec 2022
Cited by 3 | Viewed by 1569
Abstract
This work describes the phenotypic typing and complete genome analysis of LL441, a dairy Lactiplantibacillus plantarum strain. LL441 utilized a large range of carbohydrates and showed strong activity of some carbohydrate-degrading enzymes. The strain grew slowly in milk and produced acids and ketones [...] Read more.
This work describes the phenotypic typing and complete genome analysis of LL441, a dairy Lactiplantibacillus plantarum strain. LL441 utilized a large range of carbohydrates and showed strong activity of some carbohydrate-degrading enzymes. The strain grew slowly in milk and produced acids and ketones along with other volatile compounds. The genome of LL441 included eight circular molecules, the bacterial chromosome, and seven plasmids (pLL441-1 through pLL441-7), ranging in size from 8.7 to 53.3 kbp. Genome analysis revealed vast arrays of genes involved in carbohydrate utilization and flavor formation in milk, as well as genes providing acid and bile resistance. No genes coding for virulence traits or pathogenicity factors were detected. Chromosome and plasmids were packed with insertion sequence (IS) elements. Plasmids were also abundant in genes encoding heavy metal resistance traits and plasmid maintenance functions. Technologically relevant phenotypes linked to plasmids, such as the production of plantaricin C (pLL441-1), lactose utilization (pLL441-2), and bacteriophage resistance (pLL441-4), were also identified. The absence of acquired antibiotic resistance and of phenotypes and genes of concern suggests L. plantarum LL441 be safe. The strain might therefore have a use as a starter or starter component in dairy and other food fermentations or as a probiotic. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Microbiology in Spain)
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15 pages, 2632 KiB  
Article
Manganese Stress Tolerance Depends on Yap1 and Stress-Activated MAP Kinases
by Inés G. de Oya, Elena Jiménez-Gutiérrez, Hélène Gaillard, María Molina, Humberto Martín and Ralf Erik Wellinger
Int. J. Mol. Sci. 2022, 23(24), 15706; https://doi.org/10.3390/ijms232415706 - 11 Dec 2022
Cited by 1 | Viewed by 1466
Abstract
Understanding which intracellular signaling pathways are activated by manganese stress is crucial to decipher how metal overload compromise cellular integrity. Here, we unveil a role for oxidative and cell wall stress signaling in the response to manganese stress in yeast. We find that [...] Read more.
Understanding which intracellular signaling pathways are activated by manganese stress is crucial to decipher how metal overload compromise cellular integrity. Here, we unveil a role for oxidative and cell wall stress signaling in the response to manganese stress in yeast. We find that the oxidative stress transcription factor Yap1 protects cells against manganese toxicity. Conversely, extracellular manganese addition causes a rapid decay in Yap1 protein levels. In addition, manganese stress activates the MAPKs Hog1 and Slt2 (Mpk1) and leads to an up-regulation of the Slt2 downstream transcription factor target Rlm1. Importantly, Yap1 and Slt2 are both required to protect cells from oxidative stress in mutants impaired in manganese detoxification. Under such circumstances, Slt2 activation is enhanced upon Yap1 depletion suggesting an interplay between different stress signaling nodes to optimize cellular stress responses and manganese tolerance. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Microbiology in Spain)
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20 pages, 3288 KiB  
Article
Adaptation of Saccharomyces Species to High-Iron Conditions
by Raquel Sorribes-Dauden, Tania Jordá, David Peris, María Teresa Martínez-Pastor and Sergi Puig
Int. J. Mol. Sci. 2022, 23(22), 13965; https://doi.org/10.3390/ijms232213965 - 12 Nov 2022
Cited by 1 | Viewed by 1210
Abstract
Iron is an indispensable element that participates as an essential cofactor in multiple biological processes. However, when present in excess, iron can engage in redox reactions that generate reactive oxygen species that damage cells at multiple levels. In this report, we characterized the [...] Read more.
Iron is an indispensable element that participates as an essential cofactor in multiple biological processes. However, when present in excess, iron can engage in redox reactions that generate reactive oxygen species that damage cells at multiple levels. In this report, we characterized the response of budding yeast species from the Saccharomyces genus to elevated environmental iron concentrations. We have observed that S. cerevisiae strains are more resistant to high-iron concentrations than Saccharomyces non-cerevisiae species. Liquid growth assays showed that species evolutionarily closer to S. cerevisiae, such as S. paradoxus, S. jurei, S. mikatae, and S. arboricola, were more resistant to high-iron levels than the more distant species S. eubayanus and S. uvarum. Remarkably, S. kudriavzevii strains were especially iron sensitive. Growth assays in solid media suggested that S. cerevisiae and S. paradoxus were more resistant to the oxidative stress caused by elevated iron concentrations. When comparing iron accumulation and sensitivity, different patterns were observed. As previously described for S. cerevisiae, S. uvarum and particular strains of S. kudriavzevii and S. paradoxus became more sensitive to iron while accumulating more intracellular iron levels. However, no remarkable changes in intracellular iron accumulation were observed for the remainder of species. These results indicate that different mechanisms of response to elevated iron concentrations exist in the different species of the genus Saccharomyces. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Microbiology in Spain)
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Review

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22 pages, 4046 KiB  
Review
TOR Complex 1: Orchestrating Nutrient Signaling and Cell Cycle Progression
by Magdalena Foltman and Alberto Sanchez-Diaz
Int. J. Mol. Sci. 2023, 24(21), 15745; https://doi.org/10.3390/ijms242115745 - 30 Oct 2023
Viewed by 1278
Abstract
The highly conserved TOR signaling pathway is crucial for coordinating cellular growth with the cell cycle machinery in eukaryotes. One of the two TOR complexes in budding yeast, TORC1, integrates environmental cues and promotes cell growth. While cells grow, they need to copy [...] Read more.
The highly conserved TOR signaling pathway is crucial for coordinating cellular growth with the cell cycle machinery in eukaryotes. One of the two TOR complexes in budding yeast, TORC1, integrates environmental cues and promotes cell growth. While cells grow, they need to copy their chromosomes, segregate them in mitosis, divide all their components during cytokinesis, and finally physically separate mother and daughter cells to start a new cell cycle apart from each other. To maintain cell size homeostasis and chromosome stability, it is crucial that mechanisms that control growth are connected and coordinated with the cell cycle. Successive periods of high and low TORC1 activity would participate in the adequate cell cycle progression. Here, we review the known molecular mechanisms through which TORC1 regulates the cell cycle in the budding yeast Saccharomyces cerevisiae that have been extensively used as a model organism to understand the role of its mammalian ortholog, mTORC1. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Microbiology in Spain)
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19 pages, 3164 KiB  
Review
Fission Yeast Rho1p-GEFs: From Polarity and Cell Wall Synthesis to Genome Stability
by Patricia García, Rubén Celador, Jorge Pérez-Parrilla and Yolanda Sánchez
Int. J. Mol. Sci. 2022, 23(22), 13888; https://doi.org/10.3390/ijms232213888 - 11 Nov 2022
Cited by 2 | Viewed by 1815
Abstract
Rho1p is a membrane-associated protein that belongs to the Rho family of small GTPases. These proteins coordinate processes such as actin remodelling and polarised secretion to maintain the shape and homeostasis of yeast cells. In response to extracellular stimuli, Rho1p undergoes conformational switching [...] Read more.
Rho1p is a membrane-associated protein that belongs to the Rho family of small GTPases. These proteins coordinate processes such as actin remodelling and polarised secretion to maintain the shape and homeostasis of yeast cells. In response to extracellular stimuli, Rho1p undergoes conformational switching between a guanosine triphosphate (GTP)-bound active state and a guanosine diphosphate (GDP)-bound inactive state. Cycling is improved with guanine nucleotide exchange factor (GEF) activity necessary to activate signalling and GTPase activating protein (GAP) activity required for subsequent signal depletion. This review focuses on fission yeast Rho1p GEFs, Rgf1p, Rgf2p, and Rgf3p that belong to the family of DH-PH domain-containing Dbl-related GEFs. They are multi-domain proteins that detect biological signals that induce or inhibit their catalytic activity over Rho1p. Each of them activates Rho1p in different places and times. Rgf1p acts preferentially during polarised growth. Rgf2p is required for sporulation, and Rgf3p plays an essential function in septum synthesis. In addition, we outline the noncanonical roles of Rho1p-GEFs in genomic instability. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Microbiology in Spain)
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15 pages, 1380 KiB  
Review
Chitin Synthesis in Yeast: A Matter of Trafficking
by Noelia Sánchez and César Roncero
Int. J. Mol. Sci. 2022, 23(20), 12251; https://doi.org/10.3390/ijms232012251 - 14 Oct 2022
Cited by 5 | Viewed by 2199
Abstract
Chitin synthesis has attracted scientific interest for decades as an essential part of fungal biology and for its potential as a target for antifungal therapies. While this interest remains, three decades ago, pioneering molecular studies on chitin synthesis regulation identified the major chitin [...] Read more.
Chitin synthesis has attracted scientific interest for decades as an essential part of fungal biology and for its potential as a target for antifungal therapies. While this interest remains, three decades ago, pioneering molecular studies on chitin synthesis regulation identified the major chitin synthase in yeast, Chs3, as an authentic paradigm in the field of the intracellular trafficking of integral membrane proteins. Over the years, researchers have shown how the intracellular trafficking of Chs3 recapitulates all the steps in the intracellular trafficking of integral membrane proteins, from their synthesis in the endoplasmic reticulum to their degradation in the vacuole. This trafficking includes specific mechanisms for sorting in the trans-Golgi network, regulated endocytosis, and endosomal recycling at different levels. This review summarizes the work carried out on chitin synthesis regulation, mostly focusing on Chs3 as a molecular model to study the mechanisms involved in the control of the intracellular trafficking of proteins. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Microbiology in Spain)
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15 pages, 717 KiB  
Review
Candida albicans Potassium Transporters
by Francisco J. Ruiz-Castilla, Francisco S. Ruiz Pérez, Laura Ramos-Moreno and José Ramos
Int. J. Mol. Sci. 2022, 23(9), 4884; https://doi.org/10.3390/ijms23094884 - 28 Apr 2022
Cited by 1 | Viewed by 2709
Abstract
Potassium is basic for life. All living organisms require high amounts of intracellular potassium, which fulfils multiple functions. To reach efficient potassium homeostasis, eukaryotic cells have developed a complex and tightly regulated system of transporters present both in the plasma membrane and in [...] Read more.
Potassium is basic for life. All living organisms require high amounts of intracellular potassium, which fulfils multiple functions. To reach efficient potassium homeostasis, eukaryotic cells have developed a complex and tightly regulated system of transporters present both in the plasma membrane and in the membranes of internal organelles that allow correct intracellular potassium content and distribution. We review the information available on the pathogenic yeast Candida albicans. While some of the plasma membrane potassium transporters are relatively well known and experimental data about their nature, function or regulation have been published, in the case of most of the transporters present in intracellular membranes, their existence and even function have just been deduced because of their homology with those present in other yeasts, such as Saccharomyces cerevisiae. Finally, we analyse the possible links between pathogenicity and potassium homeostasis. We comment on the possibility of using some of these transporters as tentative targets in the search for new antifungal drugs. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Microbiology in Spain)
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