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Editorial overview: Growth and development: eukaryotes
Available online at www.sciencedirect.com
ScienceDirect Editorial overview: Growth and development: eukaryotes Michael Bo¨lker Current Opinion in Microbiology 2014, 22:v–vii For a complete overview see the Issue Available online 19th November 2014 http://dx.doi.org/10.1016/j.mib.2014.10.006 1369-5274/# 2014 Elsevier Ltd. All right reserved.
Michael Bo¨lker Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany e-mail: [email protected] Michael Bo¨lker is Professor at the Genetics Institute of the Marburg University and member of the LOEWE Center for Synthetic Microbiology (SYNMIKRO). Research in the Bo¨lker group focuses on investigating the molecular and cellular biology of the plant pathogenic fungus Ustilago maydis, with an emphasis on the role of small GTPases during morphogenetic transitions. In addition, the lab studies secondary metabolism in U. maydis. Recently, his team discovered cryptic peroxisomal targeting of metabolic enzymes via ribosomal readthrough of stop codons both in fungi and in animals.
Eukaryotic microbes are compartmentalized and have been successfully used to study the molecular and biochemical properties of organelles. In the focus of this issue, however, are not only the common principles that organelles of eukaryotic microbes share with their ‘higher’ cousins, plants and animals. Here, also the specialized functions of organelles are addressed that extend the biochemical and biological abilities and often provide functions highly adaptive to the specific life-styles of eukaryotic microorganisms. The spectrum reaches from the metabolic activity of peroxisomes in primary and secondary metabolism to the unique intracellular organization of plastids derived from secondary endosymbiosis. In their review Zimorski et al. describe that all eukaryotes have or at least have had a mitochondrium in their past. This reflects not only the endosymbiotic origin of eukaryotic organelles but also the birth of eukaryotes as such. It is generally accepted that mitochondria and chloroplasts are each derived from a single endosymbiotic event. The best evidence for the singularity of primary endosymbiosis is the universal conservation of the two protein import machineries that translocate proteins into mitochondria and plastids, respectively. For secondary endosymbiosis events, it is not so easy to tell whether the resulting complex organelles are derived from a singular event. Since these organelles could have been incorporated into a specific organism by a tertiary event, it is not clear which of these organisms might have been the first and original host. Here, conflicting phylogenetic data from genome comparisons so far did not allow a unified and uncontested hypothesis. Another serious problem for any hypothesis on the origin and timing of single and multiple endosymbiotic events is the fact that single cells have a genome, but the corresponding species has a pangenome which is much bigger than any of the particular genomes. Since it was a single cell that has been taken up in the initial symbiotic event one has to take into account that its genome may significantly different from the pangenome of that species. The universal and essential function of mitochondria for eukaryotes has been established by elucidating their critical role for iron sulfur (Fe/S) cluster biogenesis, which is reviewed in this issue by Lill et al. Inside mitochondria Fe/S clusters are generated by an assembly machinery similar to that of bacteria. But interestingly, mitochondrial Fe/S cluster assembly is also critical for iron–sulfur protein biogenesis outside of mitochondria. A central player for biogenesis of cytosolic and nuclear Fe/S proteins is the mitochondrial ABC transporter Atm1. It has long been assumed that it exports a substrate necessary for Fe/S cluster formation in the cytosol but the exact nature of this presumed sulfur containing compound X-S is still unknown. The review focuses on this central question and discusses the latest results concerning this problem. Based on the finding that the export reaction
www.sciencedirect.com
Current Opinion in Microbiology 2014, 22:v–vii
vi Growth and development: eukaryotes
requires glutathione (GSH) and on recent insights from crystallization studies it is assumed that a GSH derived compound might be the long-sought component X-S. Another complication results from the fact that the core ISC machinery is required to generate X-S. Two possible explanations are discussed: (i) a Fe–S containing mitochondrial enzyme might be required for production of X-S or (ii) a 2Fe–2S cluster itself is part of the exported molecule. Concerning the first hypothesis there are some hints that glutathione persulfide (GSSH) or polysulfide (GSSSG) might be interesting candidates for compound X-S. It is known for a long time that mitochondria play an important role in aging. We learn from Bernhardt et al. that the production of reactive oxygen species (ROS) during the respiratory activity of mitochondria is one of the major factors that influence both chronological and replicative aging. Interestingly, enhanced respiration results in lower ROS production (at least per O2 consumed) and thus extends lifespan. Another factor affecting aging is the protein quality control system (PQS) in mitochondria that deals with oxidized and damaged proteins. This system detects and degrades defective mitochondrial proteins. Interestingly, some of these proteins are ‘retro-translocated’ to the outer membrane before being degraded. ROS does not only affect proteins but also cause damage and alteration of mitochondrial DNA. This poses a serious challenge for the fungal cell: spore progeny has to be produced before onset of aging processes that affect the integrity of the mitochondrial DNA. The review by Grosche et al. focuses on the complex compartmentalization of secondary endosymbionts. In contrast to the monophyletic origins of mitochondria and plastids, engulfment of a eukaryotic cell by another eukaryote has occurred several times independently during evolution. This allows observing the different fates of these endosymbionts in a variety of species. While some of these endosymbionts have retained their nuclear genome in a minimized state others have lost it completely. Another aspect of secondary endosymbiosis is the occurrence of the periplastidal compartment (PPC), derived from the cytoplasm of the endosymbiont. This unique and interesting compartment can vary between being nearly devoid of proteins or — in case of nucleomorph-containing endosymbionts — still maintain a whole set of proteins involved in transcription and translation. The study of this minimized compartment and its genetic interconnection with the ‘other cytoplasms’ in the same cell is exciting not only for basic research but also as guidance for approaches to minimize cells in synthetic biology. Recognition of ambient pH and elicitation of proper cellular responses are crucial for cellular survival. In recent years the signaling pathways triggering the reaction to alkaline conditions have been studied in several eukaryotic microbes. In this issue, Pen˜alva et al. give an Current Opinion in Microbiology 2014, 22:v–vii
overview on recent findings obtained in the yeast Saccharomyces cerevisiae and in the filamentous fungus Aspergillus nidulans. The critical module involved in pH sensing comprises a considerable number of different proteins. The final active component is a zinc-finger protein, PacC, which is proteolytically cleaved and then acts as transcription factor for pH regulated genes. Components of the endosomal sorting complexes required for transport (ESCRT) machinery have been previously found to be involved in pH sensing and signaling. This suggested that the pH signaling machinery might localize to endosomes. However, several new publications challenge this model. Cells containing mutant variants of Vps27 are defective for effective recruitment of ESCRT to endosomes but still able to sense pH. Interestingly, an arrestin-like protein, PalF appears to be the critical factor for membrane localization of the Pal signaling complex. Pal F becomes activated by ubiquitination and only PalFUb is complexed with Vps23. Therefore, ubiquitination of PalF is the toggle switch which allows pH-signaling. Wolf and Casadevall review the generation and function of extracellular vesicles (EV) released by eukaryotic microbes. EV are produced by many different species including bacteria, archea, protozoa and fungi. Despite their different phylogenetic origin and mechanism of production all EV are remarkably similar in size. In pathogens, EV were often found to play a role during infection. There they might provide an opportunity to transport concentrated sets of enzymes and virulence factors to hit cells also located farther away. By using vesicles instead of simple protein secretion dilution of the cargo is prevented. Recent studies have revealed that EV do not form a uniform population but consist of different types. The review gives an overview on how many different ways they can be generated and how fungi deal with the challenge to deliver EV through a dense cell wall. The aspect of protein quality control in peroxisomes is in the focus of the review by Kumar et al. Autophagy of peroxisomes (pexophagy) is a common phenomenon to get rid of defective peroxisomes. Thus pexophagy deals more with the death of peroxisomes than with keeping them healthy. Neither, the signals nor other aspects as to how peroxisomes maintain their activity and cope with stress are fully understood. However, it is becoming more and more obvious that a very important part of peroxisomal protein quality control does not only happen inside of peroxisomes but already occurs before import. Correct folding of imported proteins and timing of import is critical to avoid accumulation of wrongly folded protein aggregates inside of peroxisomes. This is underlined by the fact that classic chaperones of the Hsp family that assist protein folding are not found inside of peroxisomes. Instead, peroxisomes contain a Lon protease, which appears to be able to recognize and to degrade misfolded www.sciencedirect.com
Editorial overview Bo¨lker vii
proteins. Interestingly, failure in degradation of unfolded proteins less affect growth rate but chronological lifespan. Protein degradation and pexophagy seem to collaborate since deletion of both resulted in even more pronounced reduction of chronological lifespan. Trypanosomatide parasites contain a very unusual form of peroxisomes, termed glycosomes, harboring the majority of glycolytic enzymes. Although it is known for a long time that in these organisms glycolysis has been relocated from the cytosol to these specialized peroxisomes, the adaptive value of this reorganization is not fully understood yet. The review by Szoor et al. addresses the metabolic function of glycosomes during the parasitic life-cycle and discusses different hypotheses to explain this unusual compartmentalization of glycolysis. This organization is necessary since allosteric regulation of enzyme activity does not occur in glycosomes. This fact, however, cannot explain why this unique compartmentalization has happened during evolution. Here, the interesting hypothesis is favored, that compartmentalization of glycolysis into glycosomes allows rapid downregulation of
www.sciencedirect.com
this pathway by selective degradation of these organelles through autophagy. Since environmental conditions change very rapidly during the parasitic life cycle, downregulation of this highly active pathway would pose a problem if these abundant and stable enzymes were located in the cytosol. The last review by Stehlik et al. focuses on the metabolic capacity of fungal peroxisomes. Until recently, peroxisomes were considered mainly as site where fatty acids are degraded and where hydrogen peroxide generated during this process is detoxified. Recently, more and unexpected metabolic enzymes were detected in peroxisomes. In fungi several glycolytic enzymes harbor cryptic peroxisomal targeting signals that are unveiled by differential splicing or ribosomal readthrough of stop codons. In addition, a large diversity of further metabolic functions reaching from primary to secondary metabolism has been discovered to reside in peroxisomes. This metabolic flexibility makes these organelles even interesting for synthetic biology. Since they are non-essential in fungi they can easily be redesigned to harbor tailor-made metabolic pathways.
Current Opinion in Microbiology 2014, 22:v–vii
ScienceDirect Editorial overview: Growth and development: eukaryotes Michael Bo¨lker Current Opinion in Microbiology 2014, 22:v–vii For a complete overview see the Issue Available online 19th November 2014 http://dx.doi.org/10.1016/j.mib.2014.10.006 1369-5274/# 2014 Elsevier Ltd. All right reserved.
Michael Bo¨lker Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany e-mail: [email protected] Michael Bo¨lker is Professor at the Genetics Institute of the Marburg University and member of the LOEWE Center for Synthetic Microbiology (SYNMIKRO). Research in the Bo¨lker group focuses on investigating the molecular and cellular biology of the plant pathogenic fungus Ustilago maydis, with an emphasis on the role of small GTPases during morphogenetic transitions. In addition, the lab studies secondary metabolism in U. maydis. Recently, his team discovered cryptic peroxisomal targeting of metabolic enzymes via ribosomal readthrough of stop codons both in fungi and in animals.
Eukaryotic microbes are compartmentalized and have been successfully used to study the molecular and biochemical properties of organelles. In the focus of this issue, however, are not only the common principles that organelles of eukaryotic microbes share with their ‘higher’ cousins, plants and animals. Here, also the specialized functions of organelles are addressed that extend the biochemical and biological abilities and often provide functions highly adaptive to the specific life-styles of eukaryotic microorganisms. The spectrum reaches from the metabolic activity of peroxisomes in primary and secondary metabolism to the unique intracellular organization of plastids derived from secondary endosymbiosis. In their review Zimorski et al. describe that all eukaryotes have or at least have had a mitochondrium in their past. This reflects not only the endosymbiotic origin of eukaryotic organelles but also the birth of eukaryotes as such. It is generally accepted that mitochondria and chloroplasts are each derived from a single endosymbiotic event. The best evidence for the singularity of primary endosymbiosis is the universal conservation of the two protein import machineries that translocate proteins into mitochondria and plastids, respectively. For secondary endosymbiosis events, it is not so easy to tell whether the resulting complex organelles are derived from a singular event. Since these organelles could have been incorporated into a specific organism by a tertiary event, it is not clear which of these organisms might have been the first and original host. Here, conflicting phylogenetic data from genome comparisons so far did not allow a unified and uncontested hypothesis. Another serious problem for any hypothesis on the origin and timing of single and multiple endosymbiotic events is the fact that single cells have a genome, but the corresponding species has a pangenome which is much bigger than any of the particular genomes. Since it was a single cell that has been taken up in the initial symbiotic event one has to take into account that its genome may significantly different from the pangenome of that species. The universal and essential function of mitochondria for eukaryotes has been established by elucidating their critical role for iron sulfur (Fe/S) cluster biogenesis, which is reviewed in this issue by Lill et al. Inside mitochondria Fe/S clusters are generated by an assembly machinery similar to that of bacteria. But interestingly, mitochondrial Fe/S cluster assembly is also critical for iron–sulfur protein biogenesis outside of mitochondria. A central player for biogenesis of cytosolic and nuclear Fe/S proteins is the mitochondrial ABC transporter Atm1. It has long been assumed that it exports a substrate necessary for Fe/S cluster formation in the cytosol but the exact nature of this presumed sulfur containing compound X-S is still unknown. The review focuses on this central question and discusses the latest results concerning this problem. Based on the finding that the export reaction
www.sciencedirect.com
Current Opinion in Microbiology 2014, 22:v–vii
vi Growth and development: eukaryotes
requires glutathione (GSH) and on recent insights from crystallization studies it is assumed that a GSH derived compound might be the long-sought component X-S. Another complication results from the fact that the core ISC machinery is required to generate X-S. Two possible explanations are discussed: (i) a Fe–S containing mitochondrial enzyme might be required for production of X-S or (ii) a 2Fe–2S cluster itself is part of the exported molecule. Concerning the first hypothesis there are some hints that glutathione persulfide (GSSH) or polysulfide (GSSSG) might be interesting candidates for compound X-S. It is known for a long time that mitochondria play an important role in aging. We learn from Bernhardt et al. that the production of reactive oxygen species (ROS) during the respiratory activity of mitochondria is one of the major factors that influence both chronological and replicative aging. Interestingly, enhanced respiration results in lower ROS production (at least per O2 consumed) and thus extends lifespan. Another factor affecting aging is the protein quality control system (PQS) in mitochondria that deals with oxidized and damaged proteins. This system detects and degrades defective mitochondrial proteins. Interestingly, some of these proteins are ‘retro-translocated’ to the outer membrane before being degraded. ROS does not only affect proteins but also cause damage and alteration of mitochondrial DNA. This poses a serious challenge for the fungal cell: spore progeny has to be produced before onset of aging processes that affect the integrity of the mitochondrial DNA. The review by Grosche et al. focuses on the complex compartmentalization of secondary endosymbionts. In contrast to the monophyletic origins of mitochondria and plastids, engulfment of a eukaryotic cell by another eukaryote has occurred several times independently during evolution. This allows observing the different fates of these endosymbionts in a variety of species. While some of these endosymbionts have retained their nuclear genome in a minimized state others have lost it completely. Another aspect of secondary endosymbiosis is the occurrence of the periplastidal compartment (PPC), derived from the cytoplasm of the endosymbiont. This unique and interesting compartment can vary between being nearly devoid of proteins or — in case of nucleomorph-containing endosymbionts — still maintain a whole set of proteins involved in transcription and translation. The study of this minimized compartment and its genetic interconnection with the ‘other cytoplasms’ in the same cell is exciting not only for basic research but also as guidance for approaches to minimize cells in synthetic biology. Recognition of ambient pH and elicitation of proper cellular responses are crucial for cellular survival. In recent years the signaling pathways triggering the reaction to alkaline conditions have been studied in several eukaryotic microbes. In this issue, Pen˜alva et al. give an Current Opinion in Microbiology 2014, 22:v–vii
overview on recent findings obtained in the yeast Saccharomyces cerevisiae and in the filamentous fungus Aspergillus nidulans. The critical module involved in pH sensing comprises a considerable number of different proteins. The final active component is a zinc-finger protein, PacC, which is proteolytically cleaved and then acts as transcription factor for pH regulated genes. Components of the endosomal sorting complexes required for transport (ESCRT) machinery have been previously found to be involved in pH sensing and signaling. This suggested that the pH signaling machinery might localize to endosomes. However, several new publications challenge this model. Cells containing mutant variants of Vps27 are defective for effective recruitment of ESCRT to endosomes but still able to sense pH. Interestingly, an arrestin-like protein, PalF appears to be the critical factor for membrane localization of the Pal signaling complex. Pal F becomes activated by ubiquitination and only PalFUb is complexed with Vps23. Therefore, ubiquitination of PalF is the toggle switch which allows pH-signaling. Wolf and Casadevall review the generation and function of extracellular vesicles (EV) released by eukaryotic microbes. EV are produced by many different species including bacteria, archea, protozoa and fungi. Despite their different phylogenetic origin and mechanism of production all EV are remarkably similar in size. In pathogens, EV were often found to play a role during infection. There they might provide an opportunity to transport concentrated sets of enzymes and virulence factors to hit cells also located farther away. By using vesicles instead of simple protein secretion dilution of the cargo is prevented. Recent studies have revealed that EV do not form a uniform population but consist of different types. The review gives an overview on how many different ways they can be generated and how fungi deal with the challenge to deliver EV through a dense cell wall. The aspect of protein quality control in peroxisomes is in the focus of the review by Kumar et al. Autophagy of peroxisomes (pexophagy) is a common phenomenon to get rid of defective peroxisomes. Thus pexophagy deals more with the death of peroxisomes than with keeping them healthy. Neither, the signals nor other aspects as to how peroxisomes maintain their activity and cope with stress are fully understood. However, it is becoming more and more obvious that a very important part of peroxisomal protein quality control does not only happen inside of peroxisomes but already occurs before import. Correct folding of imported proteins and timing of import is critical to avoid accumulation of wrongly folded protein aggregates inside of peroxisomes. This is underlined by the fact that classic chaperones of the Hsp family that assist protein folding are not found inside of peroxisomes. Instead, peroxisomes contain a Lon protease, which appears to be able to recognize and to degrade misfolded www.sciencedirect.com
Editorial overview Bo¨lker vii
proteins. Interestingly, failure in degradation of unfolded proteins less affect growth rate but chronological lifespan. Protein degradation and pexophagy seem to collaborate since deletion of both resulted in even more pronounced reduction of chronological lifespan. Trypanosomatide parasites contain a very unusual form of peroxisomes, termed glycosomes, harboring the majority of glycolytic enzymes. Although it is known for a long time that in these organisms glycolysis has been relocated from the cytosol to these specialized peroxisomes, the adaptive value of this reorganization is not fully understood yet. The review by Szoor et al. addresses the metabolic function of glycosomes during the parasitic life-cycle and discusses different hypotheses to explain this unusual compartmentalization of glycolysis. This organization is necessary since allosteric regulation of enzyme activity does not occur in glycosomes. This fact, however, cannot explain why this unique compartmentalization has happened during evolution. Here, the interesting hypothesis is favored, that compartmentalization of glycolysis into glycosomes allows rapid downregulation of
www.sciencedirect.com
this pathway by selective degradation of these organelles through autophagy. Since environmental conditions change very rapidly during the parasitic life cycle, downregulation of this highly active pathway would pose a problem if these abundant and stable enzymes were located in the cytosol. The last review by Stehlik et al. focuses on the metabolic capacity of fungal peroxisomes. Until recently, peroxisomes were considered mainly as site where fatty acids are degraded and where hydrogen peroxide generated during this process is detoxified. Recently, more and unexpected metabolic enzymes were detected in peroxisomes. In fungi several glycolytic enzymes harbor cryptic peroxisomal targeting signals that are unveiled by differential splicing or ribosomal readthrough of stop codons. In addition, a large diversity of further metabolic functions reaching from primary to secondary metabolism has been discovered to reside in peroxisomes. This metabolic flexibility makes these organelles even interesting for synthetic biology. Since they are non-essential in fungi they can easily be redesigned to harbor tailor-made metabolic pathways.
Current Opinion in Microbiology 2014, 22:v–vii