Research, Research Reports
Polyadenylated versions of small non-coding RNAs in Saccharomyces cerevisiae are degraded by Rrp6p/Rrp47p independent of the core nuclear exosome
Anusha Chaudhuri1,#, Soumita Paul2,#, Mayukh Banerjea2 and Biswadip Das2
In this investigation, we unveiled a novel functional role of the major nuclear 3′→5′ exoribonuclease, Rrp6p, and its cofactor Rrp47p in the degradation of polyadenylated versions of several mature sncRNAs, including 5S, 5.8S rRNAs, all sn- and some select snoRNAs in the baker’s yeast S. cerevisiae.
Exploring carbon source related localization and phosphorylation in the Snf1/Mig1 network using population and single cell-based approaches
Svenja Braam1, Farida Tripodi2, Linnea Österberg1,3, Sebastian Persson1, Niek Welkenhuysen1, Paola Coccetti2 and Marija Cvijovic1
In this work we set out to explore the relationship between the subcellular localization and regulation of kinases in the context of carbon source signaling. The data presented in this paper reinforce the notion that not only the activation/inactivation of kinases but also their subcellular localization and that of their targets influence fate decisions in response to environmental changes.
A Modular Cloning Toolkit for the production of recombinant proteins in Leishmania tarentolae
Katrin Hieronimus1,2,#, Tabea Donauer1,2,#, Jonas Klein1,#, Bastian Hinkel1,#, Julia Vanessa Spänle1,#, Anna Probst1,#, Justus Niemeyer1,#, Salina Kibrom1, Anna Maria Kiefer1, Luzia Schneider2, Britta Husemann2, Eileen Bischoff2, Sophie Möhring2, Nicolas Bayer1, Dorothée Klein1, Adrian Engels1, Benjamin Gustav Ziehmer2, Julian Stieß3, Pavlo Moroka1, Michael Schroda1, and Marcel Deponte2
Modular Cloning (MoClo) is based on libraries of standardized genetic parts that can be directionally assembled via Golden Gate cloning in one-pot reactions into transcription units and multigene constructs. We established a MoClo toolkit and exemplified its application for the production of recombinant proteins in L. tarentolae.
A metagenomic approach to unveil the association between fecal gut microbiota and short-chain fatty acids in diarrhea caused by diarrheagenic Escherichia coli in children
Pablo Gallardo1,2, Mariana Izquierdo2, Tomeu Viver3, Esteban Bustos-Caparros3, Dana Piras2, Roberto M. Vidal4, Hermie J.M. Harmsen1 and Mauricio J. Farfan2
Diarrheagenic Escherichia coli (DEC) is the main cause of diarrhea in children under five years old. The virulence of DEC is tightly regulated by environmental signals influenced by the gut microbiota and its metabolites. Our results increase the knowledge of the association between short chain fatty acids during diarrhea and changes in the microbiota composition associated with the presence of DEC pathogens.
The effect of multiple sclerosis therapy on gut microbiota dysbiosis: a longitudinal prospective study
Andreea-Cristina Paraschiv1,a, Vitalie Vacaras1,2,a, Cristina Nistor1,2, Cristiana Vacaras3, Stefan Strilciuc1 and Dafin F Muresanu1,2
The gut microbiota, a complex ecosystem with various immune functions, plays a significant role in MS, and its response to different treatments is highlighted in this study. In clinical practice, maintaining a healthy microbiota is crucial for individuals with MS.
Comparison of microbial communities and the profile of sulfate-reducing bacteria in patients with ulcerative colitis and their association with bowel diseases: a pilot study
Ivan Kushkevych1, Kristýna Martínková1, Lenka Mráková1, Francesco Giudici2, Simone Baldi2, David Novak3, Márió Gajdács4, Monika Vítězová1, Dani Dordevic5, Amedeo Amedei2 and Simon K.-M. R. Rittmann6
Considerable evidence has accumulated regarding the molecular relationship between gut microbiota (GM) composition and the onset (clinical presentation and prognosis) of ulcerative colitis UC. Our findings highlight, among other observations, significant variations in the gut microbial composition among patients with varying disease severity and activity.
Replicative aging in yeast involves dynamic intron retention patterns associated with mRNA processing/export and protein ubiquitination
Jesús Gómez-Montalvo1, Alvaro de Obeso Fernández del Valle1, Luis Fernando De la Cruz Gutiérrez1, Jose Mario Gonzalez-Meljem1 and Christian Quintus Scheckhuber1
Saccharomyces cerevisiae has yielded relevant insights into some of the basic mechanisms of organismal aging. Among these are genomic instability, oxidative stress, caloric restriction and mitochondrial dysfunction. Our work uncovers a previously unexplored layer of the transcriptional program of yeast aging and, more generally, expands the knowledge on the occurrence of alternative splicing in baker´s yeast.
Quantifying yeast lipidomics by high-performance thin-layer chromatography (HPTLC) and comparison to mass spectrometry-based shotgun lipidomics
Thorsten Meyer1, Oskar Knittelfelder2, Martin Smolnig1 and Patrick Rockenfeller1
Lipidomic analysis in diverse biological settings has become a frequent tool to increase our understanding of the processes of life. Here we describe a method to analyse basic lipidomics in yeast using HPTLC and offer comparison to measurement of the same samples with MS-based shotgun lipidomics.
A cobalt concentration sensitive Btu-like system facilitates cobalamin uptake in Anabaena sp. PCC 7120
Julia Graf1, Leonard Fresenborg1,2, Hans-Michael Seitz2,3, Rafael Pernil1 and Enrico Schleiff1,2,4,5
Metal homeostasis is central to all forms of life, as metals are essential micronutrients with toxic effects at elevated levels. Our results provide novel information on the uptake of cobalamin and the regulation of the cellular cobalt content in cyanobacteria.
Valine biosynthesis in Saccharomyces cerevisiae is regulated by the mitochondrial branched-chain amino acid aminotransferase Bat1
March 21, 2018
In Saccharomyces cerevisiae, the yeast, the Bat1 and Bat2 proteins, which are branched-chain amino acid aminotransferases, play distinct roles in valine biosynthesis and cell growth regulation, with Bat1 primarily located in the mitochondria and Bat2 in the cytosol, and the mitochondria being identified as the major site of valine biosynthesis in this yeast.
Microbial competition between Escherichia coli and Candida albicans reveals a soluble fungicidal factor
March 7, 2018
Localized and systemic fungal infections caused by Candida albicans can lead to significant mortality and morbidity. Here, Cabral et al. show that E. coli produces a soluble factor that kills C. albicans in a magnesium-dependent fashion such that depletion of available magnesium is essential for toxicity.
Impact of F1Fo-ATP-synthase dimer assembly factors on mitochondrial function and organismic aging
January 30, 2018
In aerobic organisms, mitochondrial F1Fo-ATP-synthase is the major site of ATP production. Here, Rampello et al. report on the role of the two dimer assembly factors PaATPE and PaATPG of the aging model Podospora anserina validating a model that links mitochondrial membrane remodeling to aging and identify specific molecular components triggering this process.
Yeast quiescence exit swiftness is influenced by cell volume and chronological age
December 6, 2017
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.
The neuroprotective steroid progesterone promotes mitochondrial uncoupling, reduces cytosolic calcium and augments stress resistance in yeast cells
May 31, 2017
Progesterone, known for its role in the reproductive system, also acts as a neurosteroid and has been suggested to aid recovery from traumatic brain injury; a study using yeast models shows that progesterone can protect against apoptosis, reduce oxidative stress and calcium spikes, and increase mitochondrial function, independent of traditional progesterone receptors or calcium transporters.
A simple microfluidic platform to study age-dependent protein abundance and localization changes in Saccharomyces cerevisiae
April 13, 2017
We have developed a user-friendly microfluidic system paired with a genetic approach to enrich and study ageing mother yeast cells, enabling the monitoring of protein abundance and localization changes during the crucial first half of their replicative lifespan, leading to the discovery of novel age-dependent protein behaviors.
The frequency of yeast [PSI+] prion formation is increased during chronological ageing
March 27, 2017
Aging is marked by a decline in cellular functions and the increased formation of the yeast [PSI+] prion, an altered translation termination factor, which suggests that autophagy suppresses age-related prion development. Interestingly, yeast cells that adopt the [PSI+] form exhibit better survival through aging, indicating that [PSI+] formation, linked to enhanced autophagy, may confer advantages such as reduced protein aggregation and improved cell viability.
A multigene family encoding surface glycoproteins in Trypanosoma congolense
March 2, 2017
Trypanosoma congolense, the causative agent of the most important livestock disease in Africa, expresses specific surface proteins involved in its parasitic lifestyle. By mining the T. congolense genome database, we identified a novel family of lectin-like glycoproteins (TcoClecs).
The transcription factors ADR1 or CAT8 are required for RTG pathway activation and evasion from yeast acetic acid-induced programmed cell death in raffinose
December 2, 2016
Yeast Saccharomyces cerevisiae grown on glucose undergoes programmed cell death (PCD) induced by acetic acid (AA-PCD), but evades PCD when grown in raffinose. This is due to concomitant relief of carbon catabolite repression (CCR) and activation of mitochondrial retrograde signaling. In this work, we investigated the relationships between the RTG and CCR pathways in the modulation of AA-PCD sensitivity under glucose repression or de-repression conditions. Our data show that simultaneous mitochondrial retrograde pathway activation and SNF1-dependent relief of CCR have a key role in central carbon metabolism reprogramming which modulates the yeast acetic acid-stress response.