Regulation of extracellular vesicles for protein secretion in Aspergillus nidulans
This study reveals that Aspergillus nidulans boosts extracellular vesicle production when ER-trafficked enzymes are induced, uncovering how fungi remodel their secretome through vesicle-mediated secretion to adapt to changing environments and biofilm formation.
Transcriptomic response to different heme sources in Trypanosoma cruzi epimastigotes
This study uncovers how the Chagas disease parasite adapts to changes in heme, an essential molecule for its survival, providing transcriptional clues to heme metabolism and identifying a previously unreported heme-binding protein in T. cruzi.
Luminal acetylation of microtubules is not essential for Plasmodium berghei and Toxoplasma gondii survival
Acetylation of α-tubulin at lysine 40 is not essential for cytoskeletal stability in Plasmodium berghei or Toxoplasma gondii, suggesting redundancy and plasticity in microtubule regulation in these parasites.
The dual-site agonist for human M2 muscarinic receptors Iper-8-naphtalimide induces mitochondrial dysfunction in Saccharomyces cerevisiae
S. cerevisiae is a model to study human GPCRs. N-8-Iper, active against glioblastoma via M2 receptor, causes mitochondrial damage in yeast by binding Ste2, highlighting evolutionary conservation of GPCRs.
Integrative Omics reveals changes in the cellular landscape of peroxisome-deficient pex3 yeast cells
To uncover the consequences of peroxisome deficiency, we compared Saccharomyces cerevisiae wild-type with pex3 cells, which lack peroxisomes, employing quantitative proteomics and transcriptomics technologies.
Regulation of extracellular vesicles for protein secretion in Aspergillus nidulans
Rebekkah E. Pope1, Patrick Ballmann2, Lisa Whitworth3 and Rolf A. Prade1,*
This study reveals that Aspergillus nidulans boosts extracellular vesicle production when ER-trafficked enzymes are induced, uncovering how fungi remodel their secretome through vesicle-mediated secretion to adapt to changing environments and biofilm formation.
Transcriptomic response to different heme sources in Trypanosoma cruzi epimastigotes
Evelyn Tevere1,a, María G. Mediavilla1,a, Cecilia B. Di Capua1, Marcelo L. Merli1, Carlos Robello2,3, Luisa Berná2,4 and Julia A. Cricco
This study uncovers how the Chagas disease parasite adapts to changes in heme, an essential molecule for its survival, providing transcriptional clues to heme metabolism and identifying a previously unreported heme-binding protein in T. cruzi.
Sir2 regulates selective autophagy in stationary-phase yeast cells
Ji-In Ryua, Juhye Junga, and Jeong-Yoon Kim
This study establishes Sir2 as a previously unrecognized regulator of selective autophagy during the stationary phase and highlight how cells dynamically control organelle degradation.
Filamentation protects Candida albicans from amphotericin B-induced programmed cell death via a mechanism involving the yeast metacaspase, MCA1
David J. Laprade, Melissa S. Brown#, Morgan L. McCarthy#, James J. Ritch, and Nicanor Austriaco
Candida albicans proliferates in two distinct cell types: blastopores and filaments. Programmed cell death is a controlled form of cell suicide that occurs when C. albicans cells are exposed to fungicidal drugs like amphotericin B and caspofungin, and to other stressful conditions. We provide evidence that programmed cell death is cell-type specific in yeast: Filamentous C. albicans cells are more resistant to amphotericin B- and caspofungin-induced programmed cell death than their blastospore counterparts. Our genetic data suggest that this phenomenon is mediated by a protective mechanism involving the yeast metacaspase, MCA1.
Formaldehyde fixation is detrimental to actin cables in glucose-depleted S. cerevisiae cells
Pavla Vasicova1,#, Mark Rinnerthaler2, Danusa Haskova1, Lenka Novakova1, Ivana Malcova1, Michael Breitenbach2, Jiri Hasek1
Actin filaments form cortical patches and emanating cables in fermenting cells of Saccharomyces cerevisiae. We assume that stability of actin cables reflects the metabolic status of the cell. Based on comparison of live and formaldehyde-fixed cells, our data suggest that formaldehyde affects respiration before fixation and this uneven signaling results in destabilization of actin cables in glucose-deprived cells.
Insights into dynamin-associated disorders through analysis of equivalent mutations in the yeast dynamin Vps1
Laila Moustaq, Iwona I. Smaczynska-de Rooij, Sarah E. Palmer, Christopher J. Marklew, Kathryn R. Ayscough
The dynamins represent a superfamily of proteins that have been shown to function in a wide range of membrane fusion and fission events. An increasing number of mutations in the human classical dynamins, Dyn-1 and Dyn-2 has been reported, with diseases caused by these changes ranging from Charcot-Marie-Tooth disorder to epileptic encephalopathies. This study aimed to use the dynamin-like protein Vps1 of Saccharomyces cerevisiae as a model to gain insights into the mechanistic defects caused by specific dynamin mutations considered to underlie a number of diseases.
Genomic saturation mutagenesis and polygenic analysis identify novel yeast genes affecting ethyl acetate production, a non-selectable polygenic trait
Tom Den Abt1,2, Ben Souffriau1,2, Maria R. Foulquié-Moreno1,2, Jorge Duitama3, and Johan M. Thevelein1,2
Isolation of mutants in populations of microorganisms has been a valuable tool in experimental genetics for decades. The main disadvantage, however, is the inability of isolating mutants in non-selectable polygenic traits. Our study shows that genomic saturation mutagenesis combined with complex trait polygenic analysis could be used successfully to identify causative alleles underlying many non-selectable, polygenic traits in small collections of haploid strains with multiple induced mutations.
Differentiated cytoplasmic granule formation in quiescent and non-quiescent cells upon chronological aging
Hsin-Yi Lee1,3,†, Kuo-Yu Cheng2,3,†, Jung-Chi Chao3 and Jun-Yi Leu3
Stationary phase cultures represent a complicated cell population comprising at least two different cell types, quiescent (Q) and non-quiescent (NQ) cells. The authors show that the cell fate of NQ cells is largely irreversible even if they are allowed to reenter mitosis. Their results reveal that the formation of different granule structures may represent the early stage of cell type differentiation in yeast stationary phase cultures.
Towards understanding the gliotoxin detoxification mechanism: in vivo thiomethylation protects yeast from gliotoxin cytotoxicity
Elizabeth B. Smith, Stephen K. Dolan, David A. Fitzpatrick, Sean Doyle and Gary W. Jones
Gliotoxin is a mycotoxin produced by some species of ascomycete fungi including the opportunistic human pathogen Aspergillus fumigatus. In order to produce gliotoxin the host organism needs to have evolved a self-protection mechanism. The authors demonstrate that the activity of a novel thiomethyltransferase is requiered for protection against exogenous gliotoxin and provide implications for understanding the evolution of gliotoxin self-protection mechanisms.
Mitochondrial proteomics of the acetic acid – induced programmed cell death response in a highly tolerant Zygosaccharomyces bailii – derived hybrid strain
Joana F Guerreiro1, Belém Sampaio-Marques2,3, Renata Soares4, Ana Varela Coelho4, Cecília Leão2,3, Paula Ludovico2,3, Isabel Sá-Correia1
Very high concentrations of acetic acid at low pH induce programmed cell death (PCD) in both the experimental model Saccharomyces cerevisiae and in Zygosaccharomyces bailii, the latter being considered the most problematic acidic food spoilage yeast due to its remarkable intrinsic resistance to this food preservative. This study offers insights into the mechanisms involved in acetic acid – induced PCD in the Z. bailii-derived hybrid strain ISA1307 by analyzing the yeast mitochondrial protein expression profile of cells challenged by acetic acid.
The transcriptional repressor Sum1p counteracts Sir2p in regulation of the actin cytoskeleton, mitochondrial quality control and replicative lifespan in Saccharomyces cerevisiae
Ryo Higuchi-Sanabria1, Jason D. Vevea1,3, Joseph K. Charalel1,4, Maria L. Sapar5, Liza A. Pon1,2
Increasing the stability or dynamics of the actin cytoskeleton can extend lifespan in C. elegans and S. cerevisiae. Actin cables of budding yeast, bundles of actin filaments that mediate cargo transport, affect lifespan control through effects on mitochondrial quality control. Here, we report that Sum1p and Sir2p inversely regulate actin and mitochondrial maintenance, as well as lifespan.
Inhibition of Aβ42 oligomerization in yeast by a PICALM ortholog and certain FDA approved drugs
Sei-Kyoung Park1, Kiira Ratia2, Mariam Ba1, Maria Valencik1 and Susan W. Liebman1,3
The formation of small Aβ42 oligomers has been implicated as a toxic species in Alzheimer disease (AD). Here, we show that the mechanism of the PICALM, human AD risk factor, is likely to reduce the level of Aβ42 oligomers in cells. We screened FDA-approved drugs to identify candidates that prevent the formation of Aβ42 small oligomers using the yeast Aβ42-RF reporter system. We also showed that each of the drug hits counteract yeast and mammalian cell toxicity associated with Aβ42 small aggregates.
Peering into the ‘black box’ of pathogen recognition by cellular autophagy systems
Shu-chin Lai# and Rodney J Devenish
Autophagy is an intracellular process that plays an important role in protecting eukaryotic cells and maintaining intracellular homeostasis. This review summarises the available evidence regarding the specific recognition of invading pathogens by which they are targeted into host autophagy pathways.
Per aspera ad astra: When harmful chromosomal translocations become a plus value in genetic evolution. Lessons from Saccharomyces cerevisiae
Valentina Tosato and Carlo V. Bruschi
This review will focus on chromosomal translocations (either spontaneous or induced) in budding yeast. Indeed, very few organisms tolerate so well aneuploidy like Saccharomyces, allowing in depth studies on chromosomal numerical aberrations. The phenomenon of post-translocational adaptation (PTA) is discussed, providing some new unpublished data and proposing the hypothesis that translocations may drive evolution through adaptive genetic selection.
Intracellular phase for an extracellular bacterial pathogen: MgtC shows the way
Audrey Bernut1,#, Claudine Belon1, Chantal Soscia2, Sophie Bleves2, Anne-Béatrice Blanc-Potard1
This article discusses the article “A macrophage subversion factor is shared by intracellular and extracellular pathogens” by Belon et al. (PLoS Pathogens 11(6): e1004969, 2015).
The role of transcriptional ‘futile cycles’ in autophagy and microbial pathogenesis
Guowu Hu1, Travis McQuiston1, Amélie Bernard2, Yoon-Dong Park1, Jin Qiu1, Ali Vural3, Nannan Zhang1, Scott R. Waterman1, Nathan H. Blewett4, Timothy G. Myers5, John H. Kehrl3, Gulbu Uzel1, Daniel J. Klionsky2 and Peter R. Williamson1
Eukaryotic cells utilize macroautophagy (hereafter autophagy) to recycle cellular materials during nutrient stress. Target of rapamycin (Tor) is a central regulator of this process, acting by post-translational mechanisms, phosphorylating preformed autophagy-related (Atg) proteins to repress autophagy during log-phase growth. A role for this regulatory process in fungal virulence was further demonstrated by showing that overexpression of the Dcp2-associated mRNA-binding protein Vad1 in the AIDS-associated pathogen Cryptococcus neoformans results in constitutive repression of autophagy even under starvation conditions as well as attenuated virulence in a mouse model. In summary, Tor-dependent post-transcriptional regulation of autophagy plays a key role in the facilitation of microbial pathogenesis.
The many facets of homologous recombination at telomeres
Clémence Claussin and Michael Chang
The ends of linear chromosomes are capped by nucleoprotein structures called telomeres. A dysfunctional telomere may resemble a DNA double-strand break (DSB), which is a severe form of DNA damage. The presence of one DSB is sufficient to drive cell cycle arrest and cell death. Therefore cells have evolved mechanisms to repair DSBs such as homologous recombination (HR). HR-mediated repair of telomeres can lead to genome instability, a hallmark of cancer cells, which is why such repair is normally inhibited. However, some HR-mediated processes are required for proper telomere function. The need for some recombination activities at telomeres but not others necessitates careful and complex regulation, defects in which can lead to catastrophic consequences. Furthermore, some cell types can maintain telomeres via telomerase-independent, recombination-mediated mechanisms. In humans, these mechanisms…
From the baker to the bedside: yeast models of Parkinson’s disease
Regina Menezes1,2, Sandra Tenreiro3,5, Diana Macedo2, Cláudia N. Santos1,2, Tiago Fleming Outeiro4,5,6
The baker’s yeast Saccharomyces cerevisiae has been extensively explored for our understanding of fundamental cell biology processes highly conserved in the eukaryotic kingdom. This review provides a brief historical perspective on the emergence of yeast as an experimental model and on how the field evolved to exploit the potential of the model for tackling the intricacies of various human diseases. In particular, the authors focus on existing yeast models of the molecular underpinnings of Parkinson’s disease (PD), focusing primarily on the central role of protein quality control systems.
Why are essential genes essential? – The essentiality of Saccharomyces genes
Zhaojie Zhang and Qun Ren
Essential genes are defined as required for the survival of an organism or a cell. This article reviews and analyzes the levels of essentiality of the Saccharomyces cerevisiae genes and groups the genes into four categories: (1) Conditional essential: essential only under certain circumstances or growth conditions; (2) Essential: required for survival under optimal growth conditions; (3) Redundant essential: synthetic lethal due to redundant pathways or gene duplication; and (4) Absolute essential: the minimal genes required for maintaining a cellular life under a stress-free environment. The essential and non-essential functions of the essential genes are further analyzed.
Membrane depolarization-triggered responsive diversification leads to antibiotic tolerance
Natalie Verstraeten, Wouter Joris Knapen, Maarten Fauvart, Jan Michiels
In this article, the authors discuss the article “Obg and membrane depolarization are part of a microbial bet-hedging strategy that leads to antibiotic tolerance”, Verstraeten et al., Mol. Cell 2015 Jul 2; 59 (1): 9-21.
Evolutionary rewiring of bacterial regulatory networks
Tiffany B. Taylor1,*, Geraldine Mulley1, Liam J. McGuffin1, Louise J. Johnson1, Michael A. Brockhurst2, Tanya Arseneault1,3, Mark W. Silby4 and Robert W. Jackson1,5
Bacteria have evolved complex regulatory networks that enable integration of multiple intracellular and extracellular signals to coordinate responses to environmental changes. However, our knowledge of how regulatory systems function and evolve is still relatively limited. There is often extensive homology between components of different networks, due to past cycles of gene duplication, divergence, and horizontal gene transfer, raising the possibility of cross-talk or redundancy. Consequently, evolutionary resilience is built into gene networks – homology between regulators can potentially allow rapid rescue of lost regulatory function across distant regions of the genome. This article discusses Taylor, et al. Science (2015), 347(6225), reporting mutations that facilitate cross-talk between pathways can contribute to gene network evolution, but which come with severe pleiotropic costs. Arising from this work are a number of questions surrounding how this phenomenon occurs.
Patterns of protein synthesis in the budding yeast cell cycle: variable or constant?
Eun-Gyu No, Heidi M Blank and Michael Polymenis
Proteins are the principal macromolecular constituent of proliferating cells, and protein synthesis is viewed as a primary metric of cell growth. While there are celebrated examples of proteins whose levels are periodic in the cell cycle (e.g., cyclins), the concentration of most proteins was not thought to change in the cell cycle, but some recent results challenge this notion. The ‘bulk’ protein is the focus of this article, specifically the rate of its synthesis, in the budding yeast Saccharomyces cerevisiae.
Ribose 5-phosphate: the key metabolite bridging the metabolisms of nucleotides and amino acids during stringent response in Escherichia coli?
Paulina Katarzyna Grucela1, Tobias Fuhrer2, Uwe Sauer2, Yanjie Chao3 and Yong Everett Zhang1
Here we propose the metabolite ribose 5’-phosphate as the key link between nucleotide and amino acid metabolisms and a working model integrating both the transcriptional and metabolic effects of (p)ppGpp on E. coli physiological adaptation during the stringent response.
Flagellated bacterial porter for in situ tumor vaccine
Haiheng Xu1, Yiqiao Hu1, 2 and Jinhui Wu1, 2, 3
Cancer immunotherapy, which use the own immune system to attack tumors, are increasingly popular treatments. But, due to the tumor immunosuppressive microenvironment, the antigen presentation in the tumor is limited. Recently, a growing number of people use bacteria to stimulate the body’s immunity for tumor treatment due to bacteria themselves have a variety of elements that activate Toll-like receptors. Here, we discuss the use of motility of flagellate bacteria to transport antigens to the tumor periphery to activate peritumoral dendritic cells to enhance the effect of in situ tumor vaccines.
The rise of Candida auris: from unique traits to co-infection potential
Nadine B. Egger1,§, Katharina Kainz1,§, Adina Schulze1, Maria A. Bauer1, Frank Madeo1-3 and Didac Carmona-Gutierrez1
Candida auris is a multidrug resistant (MDR) fungal pathogen with a crude mortality rate of 30-60%. First identified in 2009, C. auris has been rapidly rising to become a global risk in clinical settings and was declared an urgent health threat by the Centers for Disease Control and Prevention (CDC). A concerted global action is thus needed to successfully tackle the challenges created by this emerging fungal pathogen. In this brief article, we underline the importance of unique virulence traits, including its easy transformation, its persistence outside the host and its resilience against multiple cellular stresses, as well as of environmental factors that have mainly contributed to the rise of this superbug.
A hundred spotlights on microbiology: how microorganisms shape our lives
Didac Carmona-Gutierrez1, Katharina Kainz1, Andreas Zimmermann1, Sebastian J. Hofer1, Maria A. Bauer1, Christoph Ruckenstuhl1, Guido Kroemer2-4 and Frank Madeo1,5,6
Viral, bacterial, fungal and protozoal biology is of cardinal importance for the evolutionary history of life, ecology, biotechnology and infectious diseases. Various microbiological model systems have fundamentally contributed to the understanding of molecular and cellular processes, including the cell cycle, cell death, mitochondrial biogenesis, vesicular fusion and autophagy, among many others. Microbial interactions within the environment have profound effects on many fields of biology, from ecological diversity to the highly complex and multifaceted impact of the microbiome on human health. Also, biotechnological innovation and corresponding industrial operations strongly depend on microbial engineering. With this wide range of impact in mind, the peer-reviewed (…)
Yeast goes viral: probing SARS-CoV-2 biology using S. cerevisiae
Brandon Ho1, Raphael Loll-Krippleber1 and Grant W. Brown1
The budding yeast Saccharomyces cerevisiae has long been an outstanding platform for understanding the biology of eukaryotic cells. Robust genetics, cell biology, molecular biology, and biochemistry complement deep and detailed genome annotation, a multitude of genome-scale strain collections for functional genomics, and substantial gene conservation with Metazoa to comprise a powerful model for modern biological research. Recently, the yeast model has demonstrated its utility in a perhaps unexpected area, that of eukaryotic virology. Here we discuss three innovative applications of the yeast model system to reveal functions and investigate variants of proteins encoded by the SARS-CoV-2 virus.
Murals meet microbes: at the crossroads of microbiology and cultural heritage
Maria A. Bauer1, Katharina Kainz1, Christoph Ruckenstuhl1, Frank Madeo1-3 and Didac Carmona-Gutierrez1
This article comments on the duality of microorganisms in the conservation and restoration of cultural heritage, which encompasses the negative impact of damaging microorganisms and recent advances in using specific microorganisms and microbial-based technologies for cultural heritage preservation.
Urm1, not quite a ubiquitin-like modifier?
Lars Kaduhr1, Cindy Brachmann1, Keerthiraju Ethiraju Ravichandran2,3, James D. West4, Sebastian Glatt2 and Raffael Schaffrath1
This article comments on work published by Brachmann et al. (Redox Biol, 2020), which studied urmylation of the yeast 2-Cys peroxiredoxin Ahp1, uncovering that promiscuous lysine target sites and specific redox requirements determine the Urm1 acceptor activity of the peroxiredoxin.
Microbial Cell
is an open-access, peer-reviewed journal that publishes exceptionally relevant research works that implement the use of unicellular organisms (and multicellular microorganisms) to understand cellular responses to internal and external stimuli and/or human diseases.
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Peer-reviewed, open-access research using unicellular organisms (and multicellular microorganisms) to understand cellular responses and human disease.
The journal (founded in 2014) is led by its Editors-in-Chief Frank Madeo, Didac Carmona-Gutierrez, and Guido Kroemer
Microbial Cell has been publishing original scientific literature since 2014, and from the very beginning has been managed by active scientists through an independent Publishing House (Shared science Publishers). The journal was conceived as a platform to acknowledge the importance of unicellular organisms, both as model systems as well as in the biological context of human health and disease.
Ever since, Microbial Cell has very positively developed and strongly grown into a respected journal in the unicellular research community and even beyond. This scientific impact is reflected in the yearly number of citations obtained by articles published in Microbial Cell, as recorded by the Web of Science (Clarivate, formerly Thomson/Reuters):
The scientific impact of Microbial Cell is also mirrored in a series of milestones:
2015: Microbial Cell is included in the Emerging Sources Citation Index (ESCI), a selection of developing journals drafted by Clarivate Analytics based on the candidate’s publishing standards, quality, editorial content, and citation data. Note: As an ESCI-selected journal, Microbial Cell is currently being evaluated in a rigorous and long process to determine an inclusion in the Science Citation Index Expanded (SCIE), which allows the official calculation of Clarivate Analytics’ impact factor.
2016: Microbial Cell is awarded the so-called DOAJ Seal by the selective Directory of Open Access Journals (DOAJ). The DOAJ Seal is an exclusive mark of certification for open access journals granted by DOAJ to journals that adhere to outstanding best practice and achieve an extra high and clear commitment to open access and high publishing standards.
2017: Microbial Cell is included in Pubmed Central (PMC), allowing the archiving of all the journal’s articles in PMC and PubMed.
2019: Microbial Cell is indexed in the prestigious abstract and citation database Scopus after a thorough selection process. This also means that Microbial Cell obtains, for the first time, an official Scopus CiteScore as well as an official journal ranking in the Scimago Journal and Country Ranking.
2022: Microbial Cell’s CiteScore reaches a value of 7.2 for the year 2021, positioning Microbial Cell among the top microbiology journals (previously available CiteScores: 2019: 5.4; 2020: 5.1).
2022: Microbial Cell is indexed in the highly selective Science Citation Index Expanded™, which covers approx. 9,500 of the world’s most impactful journals across 178 scientific disciplines. In their journal selection and curation process, Clarivate´s editors apply 24 ‘quality’ criteria and four ‘impact’ criteria to select the most influential journals in their respective fields. This selection is also a pre-requisite for inclusion in the JCR, which features the impact factor.
2022: Microbial Cell is listed in the Journal Citation Reports™ (JCR), and obtains its first official Journal Impact Factor™ (JIF) for the year 2021: 5.316.Check Article Types and Manuscript Preparation guidelines. Submit online via Scholastica.
It takes four to tango: the cooperative adventure of scientific publishing
Didac Carmona-Gutierrez1,2, Katharina Kainz1 and Frank Madeo1-3
This Editorial is the 500th article published in Microbial Cell, a journey that started in 2014 and has seen the journal grow steadily and maintain itself as a respected community platform. The foundation that has allowed for and driven this development – as for any responsible journal – is composed of four essential pillars: the readers, the authors, the editors and the referees.