Table of contents

Volume 1, Issue 4, pp. 110 - 139, April 2014

Issue cover
Cover: Electron tomogram of a section of a Hansenula polymorpha pex3 atg1 cell showing preperoxisomal structures in the vicinity of the nuclear envelope. Picture by Kèvin Knoops and Ida van der Klei (University of Groningen, The Netherlands). The cover is published under the Creative Commons Attribution (CC BY) license. Enlarge issue cover

Editorial

Metabolites in aging and autophagy

Sabrina Schroeder, Andreas Zimmermann, Didac Carmona-Gutierrez, Tobias Eisenberg, Christoph Ruckenstuhl, Aleksandra Andryushkova, Tobias Pendl, Alexandra Harger, Frank Madeo

page 110-114 | 10.15698/mic2014.04.142 | Full text | PDF |

News and Thoughts

Only functional localization is faithful localization

Roland Lill

page 115-117 | 10.15698/mic2014.04.141 | Full text | PDF |

Reviews

Longevity pathways and maintenance of the proteome: the role of autophagy and mitophagy during yeast ageing

Belém Sampaio-Marques, William C. Burhans, Paula Ludovico

page 118-127 | 10.15698/mic2014.04.136 | Full text | PDF | Abstract

Ageing is a complex and multi-factorial process that results in the progressive accumulation of molecular alterations that disrupt different cellular functions. The budding yeast Saccharomyces cerevisiae is an important model organism that has significantly contributed to the identification of conserved molecular and cellular determinants of ageing. The nutrient-sensing pathways are well-recognized modulators of longevity from yeast to mammals, but their downstream effectors and outcomes on different features of ageing process are still poorly understood. A hypothesis that is attracting increased interest is that one of the major functions of these “longevity pathways” is to contribute to the maintenance of the proteome during ageing. In support of this hypothesis, evidence shows that TOR/Sch9 and Ras/PKA pathways are important regulators of autophagy that in turn are essential for healthy cellular ageing. It is also well known that mitochondria homeostasis and function regulate lifespan, but how mitochondrial dynamics, mitophagy and biogenesis are regulated during ageing remains to be elucidated. This review describes recent findings that shed light on how longevity pathways and metabolic status impact maintenance of the proteome in both yeast ageing paradigms. These findings demonstrate that yeast remain a powerful model system for elucidating these relationships and their influence on ageing regulation.

Microreviews

De novo peroxisome biogenesis revisited

Marten Veenhuis, Ida J. van der Klei

page 128-130 | 10.15698/mic2014.04.138 | Full text | PDF | Abstract

We describe an alternative peroxisome formation pathway in yeast pex3 and pex19 cells, which relies on the existence of small peroxisomal remnants that are present in these cells. This groundbreaking result challenges current models prescribing that peroxisomes derive de novo from the ER. Our data also has major implications for the sorting pathway of specific peroxisomal membrane proteins (PMPs). We propose a novel sorting pathway for the PMPs Pex13 and Pex14 that is independent of the known Pex3/Pex19 machinery.

The Parkinson’s disease-associated protein α-synuclein disrupts stress signaling – a possible implication for methamphetamine use?

Shaoxiao Wang, Stephan N. Witt

page 131-132 | 10.15698/mic2014.04.137 | Full text | PDF | Abstract

The human neuronal protein α-synuclein (α-syn) has been linked by a plethora of studies as a causative factor in sporadic Parkinson’s disease (PD). To speed the pace of discovery about the biology and pathobiology of α-syn, organisms such as yeast, worms, and flies have been used to investigate the mechanisms by which elevated levels of α-syn are toxic to cells and to screen for drugs and genes that suppress this toxicity. We recently reported [Wang et al. Proc. Natl. Acad. Sci. (2012) 109: 16119–16124] that human α-syn, at high expression levels, disrupts stress-activated signal transduction pathways in both yeast and human neuroblastoma cells. Disruption of these signaling pathways ultimately leads to vulnerability to stress and to cell death. Here we discuss how the disruption of cell signaling by α-syn may have relevance to the parkinsonism that is associated with the abuse of the drug methamphetamine (meth).

Transcriptional and genomic mayhem due to aging-induced nucleosome loss in budding yeast

Zheng Hu, Kaifu Chen, Wei Li, Jessica K. Tyler

page 133-136 | 10.15698/mic2014.04.139 | Full text | PDF | Abstract

All eukaryotic genomes are assembled into a nucleoprotein structure termed chromatin, which is comprised of regular arrays of nucleosomes. Each nucleosome consists of eight core histone protein molecules around which the DNA is wrapped 1.75 times. The ultimate consequence of packaging the genome into chromatin is that the DNA sequences are relatively inaccessible. This allows the cell to use a comprehensive toolbox of chromatin-altering machineries to reveal access to the DNA sequence at the right time and right place in order to allow genomic processes, such as DNA repair, transcription and replication, to occur in a tightly-regulated manner. In other words, chromatin provides the framework that allows the regulation of all genomic processes, because the machineries that mediate transcription, repair and DNA replication themselves are relatively non-sequence specific and if the genome were naked, they would presumably perform their tasks in a random and unregulated manner. We recently provided support for this prediction in Zheng et al., [Genes and Development (2014) 28:396-408] by investigating a physiologically relevant scenario in which we had found that cells lose half of the core histone proteins, that is, during the mitotic aging (also called replicative aging) of budding yeast. Using new spike-in normalization techniques, we found that the occupancy of nucleosomes at most DNA sequences is reduced by 50%, leading to transcriptional induction of every single gene. This loss of histones during aging was also accompanied by a significantly-increased frequency of genomic instability including DNA breaks, chromosomal translocations, retrotransposition, and transfer of mitochondrial DNA into the nuclear genome (Figure 1).

Secondary structures involving the poly(A) tail and other 3’ sequences are major determinants of mRNA isoform stability in yeast

Zarmik Moqtaderi, Joseph V. Geisberg and Kevin Struhl

page 137-139 | 10.15698/mic2014.04.140 | Full text | PDF | Abstract

In Saccharomyces cerevisiae, previous measurements of mRNA stabilities have been determined on a per-gene basis. We and others have recently shown that yeast genes give rise to a highly heterogeneous population of mRNAs due to extensive alternative 3’ end formation. Typical genes can have fifty or more distinct mRNA isoforms with 3’ endpoints differing by as little as one and as many as hundreds of nucleotides. In our recent paper [Geisberg et al. Cell (2014) 156: 812-824] we measured half-lives of individual mRNA isoforms in Saccharomyces cerevisiae by using the anchor away method for the rapid removal of Rpb1, the largest subunit of RNA Polymerase II, from the nucleus, followed by direct RNA sequencing of the cellular mRNA population over time. Combining these two methods allowed us to determine half-lives for more than 20,000 individual mRNA isoforms originating from nearly 5000 yeast genes. We discovered that different 3’ mRNA isoforms arising from the same gene can have widely different stabilities, and that such half-life variability across mRNA isoforms from a single gene is highly prevalent in yeast cells. Determining half-lives for many different mRNA isoforms from the same genes allowed us to identify hundreds of RNA sequence elements involved in the stabilization and destabilization of individual isoforms. In many cases, the poly(A) tail is likely to participate in the formation of stability-enhancing secondary structures at mRNA 3’ ends. Our results point to an important role for mRNA structure at 3’ termini in governing transcript stability, likely by reducing the interaction of the mRNA with the degradation apparatus.