Vol. 06, 2019

Sulfur dioxide resistance in Saccharomyces cerevisiae: beyond SSU1

Estéfani García-Ríos¹ and José Manuel Guillamón¹

This article discusses the importance of understanding sulfite resistance in Saccharomyces cerevisiae due to its use in winemaking and the potential role of the transcription factor Com2. While the SSU1 gene and its activity have been correlated with sulfite tolerance, the work by Lage et al. (2019) indicates that Com2 might control a large percentage of the genes activated by SO2 and contribute to the yeast's protective response, offering new insights into the molecular factors influencing this oenological trait.

Metabolic reprogramming of Salmonella infected macrophages and its modulation by iron availability and the mTOR pathway

Julia Telser^1,2,#, Chiara Volani^1,3,#, Richard Hilbe^1,2, Markus Seifert^1,2, Natascha Brigo¹, Giuseppe Paglia⁴ and Günter Weiss^1,2

This article shows that iron plays a critical role in both the immune response and metabolic reprogramming of macrophages during infection, influencing the TCA cycle and mTOR pathway, with implications for the growth of intracellular bacteria like Salmonella.

Tribal warfare: Commensal Neisseria kill pathogen Neisseria gonorrhoeae using its DNA

Magdalene So¹ and Maria A. Rendón¹

This article comments on work published by Kim et al (Cell Host Microbe, 2019), which adds a new dimension to the concept of commensal protection. It shows that commensal Neisseria kill the closely related pathogen N. gonorrhoeae through an unexpected mechanism, one that involves genetic competence, DNA methylation state and recombination.

Yet another job for the bacterial ribosome

Andrea Origi^1,2, Ana Natriashivili^1,2, Lara Knüpffer¹, Clara Fehrenbach¹, Kärt Denks^1,2, Rosella Asti¹ and Hans-Georg Koch¹

This article comments on work published by Knüpffer et al (mBio, 2019), which revealed the intricate interaction of uL23 with yet another essential player in bacteria, the ATPase SecA, which is best known for its role during post-translational secretion of proteins across the bacterial SecYEG translocon

Type II-Metacaspases are involved in cell stress but not in cell death in the unicellular green alga Dunaliella tertiolecta

M. Teresa Mata^1,&, Armando Palma¹, Candela García-Gómez^1,#, María López-Parages¹, Víctor Vázquez¹, Iván Cheng-Sánchez², Francisco Sarabia², Félix López-Figueroa¹, Carlos Jiménez¹ and María Segovia¹

This article shows that in the green alga Dunaliella tertiolecta, Type-II metacaspases are involved in the stress response to ultraviolet radiation but are not linked to cell death, suggesting their role in survival strategies under stressful environmental conditions.

Transcriptomic and chemogenomic analyses unveil the essential role of Com2-regulon in response and tolerance of Saccharomyces cerevisiae to stress induced by sulfur dioxide

Patrícia Lage^1,2, Belém Sampaio-Marques^3,4, Paula Ludovico^3,4, Nuno P. Mira⁵ and Ana Mendes-Ferreira^1,2

This article shows that in the presence of sulfur dioxide (SO2), the transcription factor Com2 plays a critical role in the tolerance and response of Saccharomyces cerevisiae, affecting the expression of a majority of SO2-activated genes and contributing to the protection against stress induced by SO2 at an enologically relevant pH.

Gut microbial metabolites in depression: understanding the biochemical mechanisms

Giorgia Caspani¹, Sidney Kennedy^2-5, Jane A. Foster⁶ and Jonathan Swann¹

This article shows how the gut microbiota contributes to the pathophysiology of depression and examines the mechanisms by which microbially-derived molecules may influence depressive behavior, highlighting the potential of dietary interventions as novel therapeutic strategies.

Proline metabolism regulates replicative lifespan in the yeast Saccharomyces cerevisiae

Yukio Mukai¹, Yuka Kamei¹, Xu Liu¹, Shan Jiang¹, Yukiko Sugimoto², Noreen Suliani binti Mat Nanyan², Daisuke Watanabe² and Hiroshi Takagi²

This article shows that intracellular proline levels in the budding yeast Saccharomyces cerevisiae are correlated with its replicative lifespan, suggesting a protective role of proline against cellular senescence due to various stresses.

The multiple functions of the numerous Chlamydia trachomatis secreted proteins: the tip of the iceberg

Joana N. Bugalhão¹ and Luís Jaime Mota¹

CThis article shows an in-depth review on the current knowledge and outstanding questions about secreted proteins from Chlamydia trachomatis, detailing their roles in host cell interaction and immune response evasion.

Yeast AP-1 like transcription factors (Yap) and stress response: a current overview

Claudina Rodrigues-Pousada¹, Frédéric Devaux², Soraia M. Caetano¹, Catarina Pimentel¹, Sofia da Silva¹, Ana Carolina Cordeiro¹ and Catarina Amaral¹

This review summarizes current understanding of the eight Yap transcription factors in Saccharomyces cerevisiae, detailing their activation by specific stress conditions and discussing their function and evolution across various fungal species.

Septin clearance from the division site triggers cytokinesis in budding yeast

Davide Tamborrini¹ and Simonetta Piatti¹

This article comments on work published by Tamborrini et al (Nat Commun., 2019), which shows that septin displacement during splitting is an essential prerequisite for contractile actomyosin ring constriction during mitosis.

Functional link between mitochondria and Rnr3, the minor catalytic subunit of yeast ribonucleotide reductase

Isaac Corcoles-Saez¹, Jean-Luc Ferat², Michael Costanzo³, Charles M. Boone³ and Rita S. Cha¹

This article shows that the carbon source affects the abundance of ribonucleotide reductase (RNR) subunits in yeast, with a novel Mec1 signaling axis regulating Rnr3 independently of known DNA damage response pathways, and reveals Rnr3's unexpected role in mitochondrial function.

The influence of the microbiota on immune development, chronic inflammation, and cancer in the context of aging

Taylor N. Tibbs^1,#, Lacey R. Lopez^1,#, and Janelle C. Arthur^1,2,3

This article shows that the microbiota is crucial for immune system development and that its relationship with the immune system during aging and the pathogenesis of age-related diseases, including cancer, needs further research to inform disease treatment and prevention.

Targeting GATA transcription factors – a novel strategy for anti-aging interventions?

Andreas Zimmermann¹, Katharina Kainz^1,2, Sebastian J. Hofer^1,3, Maria A. Bauer¹, Sabrina Schroeder¹, Jörn Dengjel⁴, Federico Pietrocola⁵, Oliver Kepp^6-9, Christoph Ruckenstuhl¹, Tobias Eisenberg^1,3,10,11, Stephan J. Sigrist¹², Frank Madeo^1,3,10, Guido Kroemer^{6-9, 13-15} and Didac Carmona-Gutierrez¹

This article comments on work published by Carmona-Gutierrez et al. (Nat Commun., 2019), which identified a natural compound, 4,4'-dimethoxychalcone, inducing autophagy and prolonging lifespan in different organisms through a mechanism that involves GATA transcription factors.

Ser/Thr protein phosphatases in fungi: structure, regulation and function

Joaquín Ariño¹, Diego Velázquez¹ and Antonio Casamayor¹

In this work we present the members of this family in S. cerevisiae and other fungal species, and review the most recent findings concerning their regulation and the roles they play in the most diverse aspects of cell biology.

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Adaptive bacterial response to low level chlorhexidine exposure and its implications for hand hygiene

Günter Kampf¹

This article shows that bacteria can adapt to low levels of Chlorhexidine digluconate (CHG), resulting in increased tolerance and cross-resistance to other antimicrobials, suggesting caution in the widespread use of CHG to minimize avoidable selection pressure for resistance.

Microevolution of the pathogenic yeasts Candida albicans and Candida glabrata during antifungal therapy and host infection

Pedro Pais^1,2,#, Mónica Galocha^1,2,#, Romeu Viana^1,2, Mafalda Cavalheiro^1,2, Diana Pereira^1,2, Miguel Cacho Teixeira^1,2

This review explores how Candida albicans and Candida glabrata, common fungal pathogens resistant to antifungal therapy, adapt and evolve within different environments, aiming to identify stable adaptive mechanisms as potential drug targets.

The extracellular matrix of mycobacterial biofilms: could we shorten the treatment of mycobacterial infections?

Poushali Chakraborty¹ and Ashwani Kumar^{1, 2}

The article discusses the challenges presented by biofilms formed by non-tuberculous mycobacteria (NTM) species, which can lead to persistent infections that are difficult to treat due to phenotypic drug tolerance. The role of various cell wall components in mycobacterial biofilm formation is outlined, with a particular focus on Mycobacterium tuberculosis.

Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways

Hannah L. Klein¹, Giedrė Bačinskaja², Jun Che³, Anais Cheblal⁴, Rajula Elango⁵, Anastasiya Epshtein¹, Devon M. Fitzgerald^6-9, Belén Gómez-González¹⁰, Sharik R. Khan¹¹, Sandeep Kumar⁷, Bryan A. Leland¹², Léa Marie¹³, Qian Mei¹⁴, Judith Miné-Hattab^16,17, Alicja Piotrowska¹⁸, Erica J. Polleys¹⁹, Christopher D. Putnam^20,21, Elina A. Radchenko¹⁹, Anissia Ait Saada^22,23, Cynthia J. Sakofsky²⁴, Eun Yong Shim³, Mathew Stracy²⁵, Jun Xia^6-9, Zhenxin Yan⁷, Yi Yin²⁶, Andrés Aguilera¹⁰, Juan Lucas Argueso²⁷, Catherine H. Freudenreich^19,28, Susan M. Gasser⁴, Dmitry A. Gordenin²⁴, James E. Haber²⁹, Grzegorz Ira⁷, Sue Jinks-Robertson³⁰, Megan C. King¹², Richard D. Kolodner^{20, 31-33}, Andrei Kuzminov¹¹, Sarah AE Lambert^22,23, Sang Eun Lee³, Kyle M. Miller^6,15, Sergei M. Mirkin¹⁹, Thomas D. Petes²⁶, Susan M. Rosenberg^6-9,14, Rodney Rothstein³⁴, Lorraine S. Symington¹³, Pawel Zawadzki¹⁸, Nayun Kim³⁵, Michael Lisby² and Anna Malkova⁵

DNA recombination, repair and mutagenesis assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.

Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes

Hannah L Klein¹, Kenny K.H. Ang², Michelle R. Arkin², Emily C. Beckwitt^3,4, Yi-Hsuan Chang⁵, Jun Fan⁶, Youngho Kwon^7,8, Michael J. Morten¹, Sucheta Mukherjee⁹, Oliver J. Pambos⁶, Hafez el Sayyed⁶, Elizabeth S. Thrall¹⁰, João P. Vieira-da-Rocha⁹, Quan Wang¹¹, Shuang Wang^12,13, Hsin-Yi Yeh⁵, Julie S. Biteen¹⁴, Peter Chi^5,15, Wolf-Dietrich Heyer^9,16, Achillefs N. Kapanidis⁶, Joseph J. Loparo¹⁰, Terence R. Strick^12,13,17, Patrick Sung^7,8, Bennett Van Houten^3,18,19, Hengyao Niu¹¹ and Eli Rothenberg¹

Mechanistic assays of DNA repair processes are a powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.

Imbalance in gut microbes from babies born to obese mothers increases gut permeability and myeloid cell adaptations that provoke obesity and NAFLD

Taylor K. Soderborg¹ and Jacob E. Friedman^1,2,3

This article comments on work published by Soderborg et al. (Nat Commun, 2018), which demonstrates a causative role of early life microbiome dysbiosis in infants born to mothers with obesity in novel pathways that promote developmental programming of NAFLD.

Sulfur dioxide resistance in Saccharomyces cerevisiae: beyond SSU1

Estéfani García-Ríos¹ and José Manuel Guillamón¹

Targeting GATA transcription factors – a novel strategy for anti-aging interventions?

In the beginning was the word: How terminology drives our understanding of endosymbiotic organelles

Miroslav Oborník ^1,2

This In the Pit article argues that the naming conventions for biological entities influence research perspectives and methodologies, advocating for mitochondria and plastids to be classified and named as bacteria due to their endosymbiotic origins, with potential implications for our understanding of bacterial prevalence, definitions of the microbiome and multicellularity, and the concept of endosymbiotic domestication.

What’s in a name? How organelles of endosymbiotic origin can be distinguished from endosymbionts

Ansgar Gruber¹

This In the Pit article suggests redefining the relationship between hosts and endosymbionts, like mitochondria and plastids, as a single species based on "sexual symbiont integration," the loss of independent speciation, and congruence in genetic recombination and population sizes, rather than solely on historic classifications or structural properties.

Diverse conditions support near-zero growth in yeast: Implications for the study of cell lifespan

August 20, 2019

This review discusses alternative cultivation methods for baker's yeast to study its chronological lifespan, with the aim of better understanding the ageing of non-dividing cells and their potential implications for the lifespan of multicellular eukaryotes such as humans.

Evolution of the bacterial nucleosidase PpnN and its relation to the stringent response

July 16, 2019

This article comments on work published by Zhang et al (Mol Cell, 2019), which discovered an interesting mode of regulation of purine metabolism unique to Proteobacteria.

Integrins in disguise – mechanosensors in Saccharomyces cerevisiae as functional integrin analogues

July 15, 2019

This article shows that although yeast lack integrin-like proteins, they possess WSC- and MID-type mechanosensors that functionally resemble integrins in animal cells, playing a role in sensing external mechanical stimuli and activating the conserved PKC1-SLT1 cell wall integrity pathway, with potential implications for understanding mechanosensing in yeast biology.

Network dynamics of the yeast methyltransferome

July 9, 2019

This article presents a systematic genetic analysis of methyltransferases (MTases) under normal and stress conditions, uncovering the complex and adaptive nature of the methyltransferome and discovering a potential connection between phospholipid methylation and histone methylation, suggesting interplay between lipid homeostasis and epigenetic regulation.

Bacterial maze runners reveal hidden diversity in chemotactic performance

July 1, 2019

This article comments on work published by Salek et al. (Nat Commun, 2019), which combined microfluidic experiments with mathematical modeling to demonstrate that even in clonal populations, bacteria are individuals with different abilities to climb chemical gradients.

Beyond cells – The virome in the human holobiont

July 1, 2019

This article provides an overview of viromics—viral metagenomics—and its evolution, highlighting the complexity and dynamic nature of viruses beyond their traditional view as pathogens. It acknowledges the technological advancements in molecular biology and sequencing that have allowed the field to grow, while also noting that viromic research still faces significant challenges and is not as developed as bacterial metagenomics. The review underscores the importance of viruses in various ecosystems, their role in shaping the genetic landscape, and their potential impact, and looks forward to future directions in viromic research.

Laundry and textile hygiene in healthcare and beyond

July 1, 2019

This article shows that while institutional laundering is regulated to ensure hygiene, the trend towards energy-efficient washing at lower temperatures raises concerns about the antimicrobial efficacy of domestic laundering, with a focus on addressing microbial contamination in both clinical and home settings.