Vol. 06, 2019

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.

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

Tarek Elhasi¹ and Anders Blomberg¹

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

Guri Giaever¹, Elena Lissina¹and Corey Nislow¹

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

M. Mehdi Salek^1,#, Francesco Carrara^1,#, Vicente Fernandez¹ and Roman Stocker¹

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

Rodrigo García-López^1,2,3, Vicente Pérez-Brocal^1,2,3 and Andrés Moya^1,2,3

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

Dirk P. Bockmühl¹, Jan Schages¹ and Laura Rehberg¹

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.

Bacterial pathogens under high-tension: Staphylococcus aureus adhesion to von Willebrand factor is activated by force

Felipe Viela¹, Pietro Speziale^2,3, Giampiero Pietrocola² and Yves F. Dufrêne^1,4

This article comments on work published by Viela et al (mBio, 2019), which shows that the bacterial cell surface protein A to the large plasma glycoprotein von Willebrand factor interaction is tightly regulated by mechanical force.

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Beyond cells – The virome in the human holobiont

Rodrigo García-López^1,2,3, Vicente Pérez-Brocal^1,2,3 and Andrés Moya^1,2,3

Laundry and textile hygiene in healthcare and beyond

Dirk P. Bockmühl¹, Jan Schages¹ and Laura Rehberg¹

Bacterial pathogens under high-tension: Staphylococcus aureus adhesion to von Willebrand factor is activated by force

Felipe Viela¹, Pietro Speziale^2,3, Giampiero Pietrocola² and Yves F. Dufrêne^1,4

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.

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.

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.

Forty-five-year evolution of probiotic therapy

Scarlett Puebla-Barragan^1,2 and Gregor Reid^1,2

The field of probiotics has greatly expanded over the past 45 years, driven by the need for safer alternatives to drugs, interest in natural microbial products, and clinical proof of effectiveness, with scientific formulations increasingly defining the market and promising applications for various health areas expected in the future.

Role of pheromone recognition systems in creating new species of fission yeast

Taisuke Seike¹ and Chikashi Shimoda²

This article comments on work published by Seike at al. (PloS Biol., 2019), which demonstrated an “asymmetric” pheromone recognition system in the fission yeast Schizosaccharomyces pombe.

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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.

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.

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.