Vol. 05, 2018

pH homeostasis links the nutrient sensing PKA/TORC1/Sch9 ménage-à-trois to stress tolerance and longevity

Marie-Anne Deprez^1,°, Elja Eskes^1,°, Tobias Wilms¹, Paula Ludovico², Joris Winderickx¹

In this article, Deprez et al. discuss accumulating evidence indicates that pH homeostasis plays a prominent role in the determination of ageing and longevity, thereby providing new perspectives and avenues to explore the underlying molecular mechanisms.

Guidelines and recommendations on yeast cell death nomenclature

Didac Carmona-Gutierrez^1,‡,*, Maria Anna Bauer^1,‡, Andreas Zimmermann¹, Andrés Aguilera², Nicanor Austriaco³, Kathryn Ayscough⁴, Rena Balzan⁵, Shoshana Bar-Nun⁶, Antonio Barrientos^7,8, Peter Belenky⁹, Marc Blondel¹⁰, Ralf J. Braun¹¹, Michael Breitenbach¹², William C. Burhans¹³, Sabrina Büttner^1,14, Duccio Cavalieri¹⁵, Michael Chang¹⁶, Katrina F. Cooper¹⁷, Manuela Côrte-Real¹⁸, Vítor Costa^19–21, Christophe Cullin²², Ian Dawes²³, Jörn Dengjel²⁴, Martin B. Dickman²⁵, Tobias Eisenberg^1,26, Birthe Fahrenkrog²⁷, Nicolas Fasel²⁸, Kai-Uwe Fröhlich¹, Ali Gargouri²⁹, Sergio Giannattasio³⁰, Paola Goffrini³¹, Campbell W. Gourlay³², Chris M. Grant³³, Michael T. Greenwood³⁴, Nicoletta Guaragnella³⁰, Thomas Heger³⁵, Jürgen Heinisch³⁶, Eva Herker³⁷, Johannes M. Herrmann³⁸, Sebastian Hofer¹, Antonio Jiménez-Ruiz³⁹, Helmut Jungwirth¹, Katharina Kainz¹, Dimitrios P. Kontoyiannis⁴⁰, Paula Ludovico^41,42, Stéphen Manon⁴³, Enzo Martegani⁴⁴, Cristina Mazzoni⁴⁵, Lynn A. Megeney^46–48, Chris Meisinger⁴⁹, Jens Nielsen^50–52, Thomas Nyström⁵³, Heinz D. Osiewacz⁵⁴, Tiago F. Outeiro^55–58, Hay-Oak Park⁵⁹, Tobias Pendl¹, Dina Petranovic^50,51, Stephane Picot^60,61, Peter Polčic⁶², Ted Powers⁶³, Mark Ramsdale⁶⁴, Mark Rinnerthaler⁶⁵, Patrick Rockenfeller^1,32, Christoph Ruckenstuhl¹, Raffael Schaffrath⁶⁶, Maria Segovia⁶⁷, Fedor F. Severin⁶⁸, Amir Sharon⁶⁹, Stephan J. Sigrist⁷⁰, Cornelia Sommer-Ruck¹, Maria João Sousa¹⁸, Johan M. Thevelein^71,72, Karin Thevissen⁷³, Vladimir Titorenko⁷⁴, Michel B. Toledano⁷⁵, Mick Tuite³², F.-Nora Vögtle⁴⁹, Benedikt Westermann¹¹, Joris Winderickx⁷⁶, Silke Wissing⁷⁷, Stefan Wölfl⁷⁸, Zhaojie J. Zhang⁷⁹, Richard Y. Zhao⁸⁰, Bing Zhou⁸¹, Lorenzo Galluzzi^82–84,*, Guido Kroemer^84–90,*, Frank Madeo^1,26,*

In this review, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of yeast.

Burkholderia gladioli strain NGJ1 deploys a prophage tail-like protein for mycophagy

Rahul Kumar¹, Sunil Kumar Yadav¹, Durga Madhab Swain¹ and Gopaljee Jha¹

In this article, the authors comment on the study "A prophage tail-like protein is deployed by Burkholderia bacteria to feed on fungi" by Swain et al. (Nature Communications, 2017), discussing that a prophage tail-like protein (Bg_9562) is essential for mycophagy. The protein may help the bacteria to survive in certain ecological niches and, considering its broad-spectrum antifungal activity, may be potentially useful in biotechnological applications to control fungal diseases.

Fat storage-inducing transmembrane (FIT or FITM) proteins are related to lipid phosphatase/phosphotransferase enzymes

Matthew J Hayes¹, Vineet Choudhary², Namrata Ojha², John JH Shin³, Gil-Soo Han⁴, George M. Carman⁴, Christopher JR Loewen³, William A Prinz² and Timothy P Levine¹

Fat storage-inducing transmembrane (FIT or FITM) proteins have been implicated in the partitioning of triacylglycerol to lipid droplets and the budding of lipid droplets from the ER. Saccharomyces cerevisiae has two FITM homologues and the presented results suggest that Scs3p and Yft2p as well as FITMs in general are lipid phosphatase/phosphotransferase (LPT) enzymes involved in an as yet unknown critical step in phospholipid metabolism.

Ras signalling in pathogenic yeasts

Daniel R. Pentland¹, Elliot Piper-Brown¹, Fritz A. Mühlschlegel^1,2 and Campbell W. Gourlay¹

In this article Pentland et al. review the roles of Ras protein function and signalling in the major human yeast pathogens Candida albicans and Cryptococcus neoformans and discuss the potential for targeting Ras as a novel approach to anti-fungal therapy.

The logics of metabolic regulation in bacteria challenges biosensor-based metabolic engineering

Matthieu Jules¹

In this article, the authors comment on the study "Molecular and Physiological Logics of the Pyruvate-Induced Response of a Novel Transporter in Bacillus subtilis" by Charbonnier et al. (mBio, 2017), which identified and characterized a pyruvate transport system in the Gram-positive (G+ve) bacterium Bacillus subtilis, a well-established biotechnological workhorse for the production of enzymes, fine chemicals and antibiotics.

A novel basolateral type IV secretion model for the CagA oncoprotein of Helicobacter pylori

Silja Wessler¹ and Steffen Backert²

In this article, the authors comment on the study "Helicobacter pylori Employs a Unique Basolateral Type IV Secretion Mechanism for CagA Delivery" by Tegtmeyer et al. (Cell Host Microbe, 2017), discussing that the finding of a T4SS receptor suggests the presence of a sophisticated control mechanism for the injection of CagA and the possible impact of this novel signaling cascade on pathogenesis during infection with Helicobacter pylori.

Yeast quiescence exit swiftness is influenced by cell volume and chronological age

Damien Laporte¹, Laure Jimenez¹, Laëtitia Gouleme¹, Isabelle Sagot¹

Quiescence exit swiftness is crucial not only for micro-organisms in competition for an environmental niche, such as yeast, but also for the maintenance of tissue homeostasis in multicellular species. Here, Laporte et al. explore the effect of replicative and chronological age on Saccharomyces cerevisiae quiescence exit efficiency. Overall, their data illustrate that the quiescent state is a continuum evolving with time, early and deep quiescence being distinguishable by the cell’s proficiency to re-enter the proliferation cycle.

Exploring the mechanism of amebic trogocytosis: the role of amebic lysosomes

Allissia A. Gilmartin¹ and William A. Petri, Jr^1,2,3

In this article, the authors comment on the study "Inhibition of Amebic Lysosomal Acidification Blocks Amebic Trogocytosis and Cell Killing" by Gilmartin et al. (MBio, 2017), discussing the the role of amebic lysosomes in Trogocytosis, the intracellular transfer of fragments of cell material.

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Temporal analysis of the autophagic and apoptotic phenotypes in Leishmania parasites

Louise Basmaciyan¹, Laurence Berry², Julie Gros³, Nadine Azas³ and Magali Casanova³

This article details a comprehensive analysis of miltefosine-induced cell death and autophagy in Leishmania major, providing criteria for clear identification of apoptotic and autophagic cells, demonstrating the sequential nature of autophagy followed by apoptosis in nutrient-deprived conditions, and cautioning against using the generic kinase inhibitor staurosporine as a Leishmania apoptosis inducer, with the aim of improving the understanding of these processes and their targeting for new anti-leishmanial drugs.

A global view of substrate phosphorylation and dephosphorylation during budding yeast mitotic exit

Sandra A. Touati¹ and Frank Uhlmann¹

In this article, the authors comment on the study "Phosphoproteome dynamics during mitotic exit in budding yeast" by Touati (EMBO J, 2018) that described a time-resolved global phosphoproteome analysis during a cell cycle phase known as mitotic exit in budding yeast revealed the principles of phosphoregulation governing the ordered sequence of events such as spindle elongation, chromosome decondensation, and completion of cell division.

Gammaretroviruses tether to mitotic chromatin by directly binding nucleosomal histone proteins

Madushi Wanaguru¹ and Kate N. Bishop¹

In this article, the authors comment on the study "Murine leukemia virus p12 tethers the capsid-containing pre-integration complex to chromatin by binding directly to host nucleosomes in mitosis" by Wanaguruet al. (PLoS Pathog, 2018) that highlights the essential role of the gammaretroviral gag cleavage product, p12, at both early and late stages of the virus life cycle, particularly in the integration of the viral DNA into the host cell chromatin to form a provirus. It also emphasizes the recent findings regarding the N- and C-terminal domains of p12, revealing their direct binding to the viral capsid lattice and nucleosomal histone proteins, respectively, thus elucidating the mechanism by which p12 links the viral pre-integration complex to mitotic chromatin.

Snf1 cooperates with the CWI MAPK pathway to mediate the degradation of Med13 following oxidative stress

Stephen D. Willis¹, David C. Stieg¹, Kai Li Ong², Ravina Shah^1,3, Alexandra K. Strich^1,4, Julianne H. Grose² and Katrina F. Cooper¹

This article explores the response of eukaryotic cells to environmental stress, highlighting the role of the conserved cyclin C-Cdk8 kinase in determining pro-survival or pro-death programs. Specifically, it discusses how oxidative stress triggers the destruction of Med13 by the SCFGrr1 ubiquitin ligase, releasing cyclin C to promote mitochondrial fission and cell death in Saccharomyces cerevisiae. Additionally, it reveals that the AMP kinase Snf1 activates a separate degron in Med13, contributing to the complex regulation of Med13 degradation following H2O2 stress through the coordination of the cell wall integrity and MAPK pathways.

Importance of polyphosphate in the Leishmania life cycle

Kid Kohl¹, Haroun Zangger¹, Matteo Rossi¹, Nathalie Isorce¹, Lon-Fye Lye², Katherine L. Owens², Stephen M. Beverley², Andreas Mayer¹ and Nicolas Fasel¹

This article explores the importance of polyphosphate (polyP) in Leishmania parasites, emphasizing the role of the polyP polymerase VTC4 and its impact on parasite survival at higher temperatures. Additionally, it discusses the effects of VTC4 knockout in mouse infections, noting a delay in lesion formation and strong pathology in L. major VTC4 knockout, without confirmation through complementation and no alteration in L. guyanensis infections in mice with VTC4 knockdown.

Methodologies for in vitro and in vivo evaluation of efficacy of antifungal and antibiofilm agents and surface coatings against fungal biofilms

Patrick Van Dijck^1,2,‡, Jelmer Sjollema^3,‡, Bruno P.A. Cammue^4,5, Katrien Lagrou^6,7, Judith Berman⁸, Christophe d’Enfert⁹, David R. Andes^10,11, Maiken C. Arendrup^12-14, Axel A. Brakhage¹⁵, Richard Calderone¹⁶, Emilia Cantón¹⁷, Tom Coenye^18,19, Paul Cos²⁰, Leah E. Cowen²¹, Mira Edgerton²², Ana Espinel-Ingroff²³, Scott G. Filler²⁴, Mahmoud Ghannoum²⁵, Neil A.R. Gow²⁶, Hubertus Haas²⁷, Mary Ann Jabra-Rizk²⁸, Elizabeth M. Johnson²⁹, Shawn R. Lockhart³⁰, Jose L. Lopez-Ribot³¹, Johan Maertens³², Carol A. Munro²⁶, Jeniel E. Nett³³, Clarissa J. Nobile³⁴, Michael A. Pfaller^35,36, Gordon Ramage^19,37, Dominique Sanglard³⁸, Maurizio Sanguinetti³⁹, Isabel Spriet⁴⁰, Paul E. Verweij⁴¹, Adilia Warris⁴², Joost Wauters⁴³, Michael R. Yeaman⁴⁴, Sebastian A.J. Zaat⁴⁵, Karin Thevissen^4,*

This article highlights the critical importance of accurate susceptibility testing methods and the discovery of novel antifungal and antibiofilm agents in combating invasive fungal infections associated with biofilm formation on medical devices, thereby emphasizing the need for advancements in medical mycology research to address these complex diseases.

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Helicobacter hepaticus polysaccharide induces an anti-inflammatory response in intestinal macrophages

Camille Danne¹ and Fiona Powrie¹

In this article, the authors comment on the study "A Large Polysaccharide Produced by Helicobacter hepaticus Induces an Anti-inflammatory Gene Signature in Macrophages. " by Danne et al, (Cell Host Microbe 2017), discussing the interactions between H. hepaticus and intestinal macrophages that promote mutualism.

Endolysosomal pathway activity protects cells from neurotoxic TDP-43

Christine Leibiger^1,#, Jana Deisel^1,#, Andreas Aufschnaiter², Stefanie Ambros¹, Maria Tereshchenko¹, Bert M. Verheijen^3,4, Sabrina Büttner^2,5, and Ralf J. Braun¹

In this article, the authors comment on the study "TDP-43 controls lysosomal pathways thereby determining its own clearance and cytotoxicity" by Leibiger et al. (Hum Mol Genet, 2018), proposing that ameliorating endolysosomal pathway activity enhances cell survival in TDP‑43-associated diseases.

Two distinct penicillin binding proteins promote cell division in different Salmonella lifestyles

Sónia Castanheira¹, Juan J. Cestero¹, Francisco García-del Portillo¹, M. Graciela Pucciarelli^1,2,3

In this article, the authors comment on the study "A Specialized Peptidoglycan Synthase Promotes Salmonella Cell Division inside Host Cells" by Castanheira et al. (mBio, 2017), discussing insights in two distinct penicillin binding proteins that promote cell division in different Salmonella lifestyles.

New perspectives from South-Y-East, not all about death
A report of the 12th lnternational Meeting on Yeast Apoptosis in Bari, Italy, May 14th-18th, 2017

Nicoletta Guaragnella^1,#, Mariarita Stirpe^2,#, William Burhans³, Manuela Côrte-Real⁴, Campbell Gourlay⁵, Paula Ludovico^6,7, Frank Madeo^8,9, Dina Petranovic¹⁰, Joris Winderickx¹¹, Cristina Mazzoni² and Sergio Giannattasio¹

In this article Guaragnella et al. report on the 12th International Meeting on Yeast Apoptosis (IMYA12), which was held in Bari, Italy from May 14th to 18th, 2017, where more than 100 participants, among which senior and young scientists from Europe, USA, North Africa and Japan, had an intense and open exchange of achievements and ideas in the field of yeast regulated cell death (RCD).

pH homeostasis links the nutrient sensing PKA/TORC1/Sch9 ménage-à-trois to stress tolerance and longevity

Marie-Anne Deprez^1,°, Elja Eskes^1,°, Tobias Wilms¹, Paula Ludovico², Joris Winderickx¹

Guidelines and recommendations on yeast cell death nomenclature

Burkholderia gladioli strain NGJ1 deploys a prophage tail-like protein for mycophagy

Rahul Kumar¹, Sunil Kumar Yadav¹, Durga Madhab Swain¹ and Gopaljee Jha¹

Ras signalling in pathogenic yeasts

Daniel R. Pentland¹, Elliot Piper-Brown¹, Fritz A. Mühlschlegel^1,2 and Campbell W. Gourlay¹

The logics of metabolic regulation in bacteria challenges biosensor-based metabolic engineering

Matthieu Jules¹

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Microbial wars: competition in ecological niches and within the microbiome

Maria A. Bauer¹, Katharina Kainz¹, Didac Carmona-Gutierrez¹ and Frank Madeo^1,2

In this Editorial Bauer et al. provide a brief overview on microbial competition and discuss some of its roles and consequences that directly affect humans.

Exploring the mechanism of amebic trogocytosis: the role of amebic lysosomes

Allissia A. Gilmartin¹ and William A. Petri, Jr^1,2,3

Non-canonical regulation of glutathione and trehalose biosynthesis characterizes non-Saccharomyces wine yeasts with poor performance in active dry yeast production

January 26, 2018

Several yeast species, belonging to Saccharomyces and non-Saccharomyces genera, play fundamental roles during spontaneous must grape fermentation, and recent studies have shown that mixed fermentations, co-inoculated with S. cerevisiae and non-Saccharomyces strains, can improve wine organoleptic properties. Here, Gamero-Sandemetrio et al. present findings that non-canonical regulation of glutathione and trehalose biosynthesis could cause poor fermentative performance after active dry yeast (ADY) production, as it corroborates the corrective effect of antioxidant treatments, during biomass propagation, with both pure chemicals and food-grade argan oil.

New perspectives from South-Y-East, not all about death
A report of the 12th lnternational Meeting on Yeast Apoptosis in Bari, Italy, May 14th-18th, 2017

January 16, 2018

Molecular signature of the imprintosome complex at the mating-type locus in fission yeast

January 16, 2018

Genetic and molecular studies have indicated that an epigenetic imprint at mat1, the sexual locus of fission yeast, initiates mating type switching. Here, Raimondi et al. characterized the recruitment of early players of mating type switching at the mat1 region and suggest a nucleoprotein protective structure defined as imprintosome.

Leishmania guyanensis parasites block the activation of the inflammasome by inhibiting maturation of IL-1β

January 14, 2018

The various symptomatic outcomes of cutaneous leishmaniasis relates to the type and potency of its underlying inflammatory responses mediated by Toll-Like-Receptor-3 (TLR3). Here, Hartely et al. investigated other innate pattern recognition receptors capable of reacting to dsRNA and potentially contributing to LRV1-mediated inflammatory pathology. They postulate that avoidance of the inflammasome pathways is likely an important mechanism of virulence in Leishmania infection irrespective of the LRV1-status.

A novel system to monitor mitochondrial translation in yeast

January 13, 2018

In this study Suhm et al. present a novel system to monitor mitochondrial translation by detection of mitochondrial GFP-translation through fluorescence microscopy and flow cytometry in functional mitochondria. This novel tool allows the investigation of the function and regulation of mitochondrial translation during stress signaling, aging and mitochondrial biogenesis.