1
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Ibe CN, Bailey SL, Korolev AV, Brett P, Saunders DGO. Isocitrate lyase promotes Puccinia striiformis f. sp. tritici susceptibility in wheat (Triticum aestivum) by suppressing accumulation of glyoxylate cycle intermediates. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38949911 DOI: 10.1111/tpj.16908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 06/16/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024]
Abstract
Plant fungal parasites manipulate host metabolism to support their own survival. Among the many central metabolic pathways altered during infection, the glyoxylate cycle is frequently upregulated in both fungi and their host plants. Here, we examined the response of the glyoxylate cycle in bread wheat (Triticum aestivum) to infection by the obligate biotrophic fungal pathogen Puccinia striiformis f. sp. tritici (Pst). Gene expression analysis revealed that wheat genes encoding the two unique enzymes of the glyoxylate cycle, isocitrate lyase (TaICL) and malate synthase, diverged in their expression between susceptible and resistant Pst interactions. Focusing on TaICL, we determined that the TaICL B homoeolog is specifically upregulated during early stages of a successful Pst infection. Furthermore, disruption of the B homoeolog alone was sufficient to significantly perturb Pst disease progression. Indeed, Pst infection of the TaICL-B disruption mutant (TaICL-BY400*) was inhibited early during initial penetration, with the TaICL-BY400* line also accumulating high levels of malic acid, citric acid, and aconitic acid. Exogenous application of malic acid or aconitic acid also suppressed Pst infection, with trans-aconitic acid treatment having the most pronounced effect by decreasing fungal biomass 15-fold. Thus, enhanced TaICL-B expression during Pst infection may lower accumulation of malic acid and aconitic acid to promote Pst proliferation. As exogenous application of aconitic acid and malic acid has previously been shown to inhibit other critical pests and pathogens, we propose TaICL as a potential target for disruption in resistance breeding that could have wide-reaching protective benefits for wheat and beyond.
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Affiliation(s)
- Carol N Ibe
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sarah L Bailey
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Paul Brett
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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2
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Zhang Y, Li H, Shen Y, Wang S, Tian L, Yin H, Shi J, Xing A, Zhang J, Ali U, Sami A, Chen X, Gao C, Zhao Y, Lyu Y, Wang X, Chen Y, Tian Z, Wu SB, Wu L. Readthrough events in plants reveal plasticity of stop codons. Cell Rep 2024; 43:113723. [PMID: 38300801 DOI: 10.1016/j.celrep.2024.113723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 10/02/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor tRNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of basic transcription factor 3. Furthermore, the SCR events exhibit non-conserved signature, and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.
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Affiliation(s)
- Yuqian Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China; School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Hehuan Li
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yanting Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shunxi Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Lei Tian
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Haoqiang Yin
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Jiawei Shi
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Anqi Xing
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
| | - Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Usman Ali
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Abdul Sami
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Xueyan Chen
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Chenxuan Gao
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yangtao Zhao
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yajing Lyu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Xiaoxu Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yanhui Chen
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shu-Biao Wu
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
| | - Liuji Wu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China; School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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3
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Bittner E, Stehlik T, Lam J, Dimitrov L, Heimerl T, Schöck I, Harberding J, Dornes A, Heymons N, Bange G, Schuldiner M, Zalckvar E, Bölker M, Schekman R, Freitag J. Proteins that carry dual targeting signals can act as tethers between peroxisomes and partner organelles. PLoS Biol 2024; 22:e3002508. [PMID: 38377076 PMCID: PMC10906886 DOI: 10.1371/journal.pbio.3002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/01/2024] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Peroxisomes are organelles with crucial functions in oxidative metabolism. To correctly target to peroxisomes, proteins require specialized targeting signals. A mystery in the field is the sorting of proteins that carry a targeting signal for peroxisomes and as well as for other organelles, such as mitochondria or the endoplasmic reticulum (ER). Exploring several of these proteins in fungal model systems, we observed that they can act as tethers bridging organelles together to create contact sites. We show that in Saccharomyces cerevisiae this mode of tethering involves the peroxisome import machinery, the ER-mitochondria encounter structure (ERMES) at mitochondria and the guided entry of tail-anchored proteins (GET) pathway at the ER. Our findings introduce a previously unexplored concept of how dual affinity proteins can regulate organelle attachment and communication.
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Affiliation(s)
- Elena Bittner
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thorsten Stehlik
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jason Lam
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Lazar Dimitrov
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Thomas Heimerl
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Isabelle Schöck
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jannik Harberding
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Anita Dornes
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Nikola Heymons
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Bölker
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Randy Schekman
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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4
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Wang YY, Head DJ, Hauser BA. During Water Stress, Fertility Modulated by ROS Scavengers Abundant in Arabidopsis Pistils. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112182. [PMID: 37299161 DOI: 10.3390/plants12112182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
Hours after watering plants with 75 mM NaCl, the water potential of reproductive structures precipitously decreases. In flowers with mature gametes, this change in water potential did not alter the rate of fertilization but caused 37% of the fertilized ovules to abort. We hypothesize that the accumulation of reactive oxygen species (ROS) in ovules is an early physiological manifestation associated with seed failure. In this study, we characterize ROS scavengers that were differentially expressed in stressed ovules to determine whether any of these genes regulate ROS accumulation and/or associate with seed failure. Mutants in an iron-dependent superoxide dismutase (FSD2), ascorbate peroxidase (APX4), and three peroxidases (PER17, PER28, and PER29) were evaluated for changes in fertility. Fertility was unchanged in apx4 mutants, but the other mutants grown under normal conditions averaged a 140% increase in seed failure. In pistils, PER17 expression increases three-fold after stress, while the other genes decreased two-fold or more following stress; this change in expression accounts for differences in fertility between healthy and stressed conditions for different genotypes. In pistils, H2O2 levels rose in per mutants, but only in the triple mutant was there a significant increase, indicating that other ROS or their scavengers be involved in seed failure.
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Affiliation(s)
- Ya-Ying Wang
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Donald J Head
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Bernard A Hauser
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
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5
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Samanta I, Roy PC, Das E, Mishra S, Chowdhary G. Plant Peroxisomal Polyamine Oxidase: A Ubiquitous Enzyme Involved in Abiotic Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2023; 12:652. [PMID: 36771734 PMCID: PMC9919379 DOI: 10.3390/plants12030652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Polyamines (PAs) are positively charged amines that are present in all organisms. In addition to their functions specific to growth and development, they are involved in responding to various biotic and abiotic stress tolerance functions. The appropriate concentration of PA in the cell is maintained by a delicate balance between the catabolism and anabolism of PAs, which is primarily driven by two enzymes, namely diamine oxidase and polyamine oxidase (PAO). PAOs have been found to be localized in multiple subcellular locations, including peroxisomes. This paper presents a holistic account of peroxisomal PAOs. PAOs are flavin adenine dinucleotide-dependent enzymes with varying degrees of substrate specificity. They are expressed differentially upon various abiotic stress conditions, namely heat, cold, salinity, and dehydration. It has also been observed that in a particular species, the various PAO isoforms are expressed differentially with a spatial and temporal distinction. PAOs are targeted to peroxisome via a peroxisomal targeting signal (PTS) type 1. We conducted an extensive bioinformatics analysis of PTS1s present in various peroxisomal PAOs and present a consensus peroxisome targeting signal present in PAOs. Furthermore, we also propose an evolutionary perspective of peroxisomal PAOs. PAOs localized in plant peroxisomes are of potential importance in abiotic stress tolerance since peroxisomes are one of the nodal centers of reactive oxygen species (ROS) homeostasis and an increase in ROS is a major indicator of the plant being in stress conditions; hence, in the future, PAO enzymes could be used as a key candidate for generating abiotic stress tolerant crops.
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Affiliation(s)
- Ishita Samanta
- Plant Molecular Biology Laboratory, School of Biotechnology, KIIT, Bhubaneswar 751024, India
| | - Pamela Chanda Roy
- Plant Molecular Biology Laboratory, School of Biotechnology, KIIT, Bhubaneswar 751024, India
| | - Eshani Das
- Plant Molecular Biology Laboratory, School of Biotechnology, KIIT, Bhubaneswar 751024, India
| | - Sasmita Mishra
- Department of Biology, Kean University, 1000 Morris Avenue, Union, NJ 07083, USA
| | - Gopal Chowdhary
- Plant Molecular Biology Laboratory, School of Biotechnology, KIIT, Bhubaneswar 751024, India
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6
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Kunze M. Computational Evaluation of Peroxisomal Targeting Signals in Metazoa. Methods Mol Biol 2023; 2643:391-404. [PMID: 36952201 DOI: 10.1007/978-1-0716-3048-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Most soluble proteins enclosed in peroxisomes encode either type-1 or type-2 peroxisomal targeting signals (PTS1 or PTS2), which act as postal codes and define the proteins' intracellular destination. Thus, various computational programs have been developed to evaluate the probability of specific peptide sequences for being a functional PTS or to scan the primary sequence of proteins for such signals. Among these prediction algorithms the PTS1-predictor ( https://mendel.imp.ac.at/pts1/ ) has been amply used, but the research logic of this and other PTS1 prediction tools is occasionally misjudged giving rise to characteristic pitfalls. Here, a proper utilization of the PTS1-predictor is introduced together with a framework of additional tests to increase the validity of the interpretation of results. Moreover, a list of possible causes for a mismatch between results of such predictions and experimental outcomes is provided. However, the foundational arguments apply to other prediction tools for PTS1 motifs as well.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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7
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Hochreiter B, Schmid JA, Berger J, Kunze M. Estimating the Interaction Strength Between PTS1-Peptides and Their Receptor PEX5 in Living Cells Using Flow-Cytometer-Based FRET (flowFRET) Measurements. Methods Mol Biol 2023; 2643:413-434. [PMID: 36952203 DOI: 10.1007/978-1-0716-3048-8_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The import of many peroxisomal matrix proteins is initiated by the interaction of type-1 peroxisomal targeting signals (PTS1) residing at the extreme C-terminus of cargo proteins and their receptor protein PEX5. This interaction has been amply investigated by biophysical methods using isolated proteins and peptides or heterologous systems such as two-hybrid assays. However, a recently developed novel application of Fluorescence resonance energy transfer (FRET) allows a quantifying measurement of this interaction in living cells. This method combines the systematic measurement of FRET-efficiency in a high number of cells with a well-suited normalization protocol and a fitting algorithm, which together allow the estimation of numerical values for the apparent interaction strength that correlates with other measures of binding strength but can be obtained under rather physiological conditions.
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Affiliation(s)
- Bernhard Hochreiter
- Institute for Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria.
| | - Johannes A Schmid
- Institute for Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Medical University of Vienna, Vienna, Austria
| | - Markus Kunze
- Department of Pathobiology of the Nervous System, Medical University of Vienna, Vienna, Austria.
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8
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Lacroux J, Atteia A, Brugière S, Couté Y, Vallon O, Steyer JP, van Lis R. Proteomics unveil a central role for peroxisomes in butyrate assimilation of the heterotrophic Chlorophyte alga Polytomella sp. Front Microbiol 2022; 13:1029828. [PMID: 36353459 PMCID: PMC9637915 DOI: 10.3389/fmicb.2022.1029828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/05/2022] [Indexed: 09/08/2023] Open
Abstract
Volatile fatty acids found in effluents of the dark fermentation of biowastes can be used for mixotrophic growth of microalgae, improving productivity and reducing the cost of the feedstock. Microalgae can use the acetate in the effluents very well, but butyrate is poorly assimilated and can inhibit growth above 1 gC.L-1. The non-photosynthetic chlorophyte alga Polytomella sp. SAG 198.80 was found to be able to assimilate butyrate fast. To decipher the metabolic pathways implicated in butyrate assimilation, quantitative proteomics study was developed comparing Polytomella sp. cells grown on acetate and butyrate at 1 gC.L-1. After statistical analysis, a total of 1772 proteins were retained, of which 119 proteins were found to be overaccumulated on butyrate vs. only 46 on acetate, indicating that butyrate assimilation necessitates additional metabolic steps. The data show that butyrate assimilation occurs in the peroxisome via the β-oxidation pathway to produce acetyl-CoA and further tri/dicarboxylic acids in the glyoxylate cycle. Concomitantly, reactive oxygen species defense enzymes as well as the branched amino acid degradation pathway were strongly induced. Although no clear dedicated butyrate transport mechanism could be inferred, several membrane transporters induced on butyrate are identified as potential condidates. Metabolic responses correspond globally to the increased needs for central cofactors NAD, ATP and CoA, especially in the peroxisome and the cytosol.
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Affiliation(s)
| | - Ariane Atteia
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Sabine Brugière
- Univ Grenoble Alpes, CEA, INSERM, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
| | - Yohann Couté
- Univ Grenoble Alpes, CEA, INSERM, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
| | - Olivier Vallon
- Institut de Biologie Physico-Chimique, UMR7141 CNRS-Sorbonne Université, Paris, France
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9
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Tarafdar S, Chowdhary G. Translating the Arabidopsis thaliana Peroxisome Proteome Insights to Solanum lycopersicum: Consensus Versus Diversity. Front Cell Dev Biol 2022; 10:909604. [PMID: 35912119 PMCID: PMC9328179 DOI: 10.3389/fcell.2022.909604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Peroxisomes are small, single-membrane specialized organelles present in all eukaryotic organisms. The peroxisome is one of the nodal centers of reactive oxygen species homeostasis in plants, which are generated in a high amount due to various stress conditions. Over the past decade, there has been extensive study on peroxisomal proteins and their signaling pathways in the model plant Arabidopsis thaliana, and a lot has been deciphered. However, not much impetus has been given to studying the peroxisome proteome of economically important crops. Owing to the significance of peroxisomes in the physiology of plants during normal and stress conditions, understating its proteome is of much importance. Hence, in this paper, we have made a snapshot of putative peroxisomal matrix proteins in the economically important vegetable crop tomato (Solanum lycopersicum, (L.) family Solanaceae). First, a reference peroxisomal matrix proteome map was generated for Arabidopsis thaliana using the available proteomic and localization studies, and proteins were categorized into various groups as per their annotations. This was used to create the putative peroxisomal matrix proteome map for S. lycopersicum. The putative peroxisome proteome in S. lycopersicum retains the basic framework: the bulk of proteins had peroxisomal targeting signal (PTS) type 1, a minor group had PTS2, and the catalase family retained its characteristic internal PTS. Apart from these, a considerable number of S. lycopersicum orthologs did not contain any “obvious” PTS. The number of PTS2 isoforms was found to be reduced in S. lycopersicum. We further investigated the PTS1s in the case of both the plant species and generated a pattern for canonical and non-canonical PTS1s. The number of canonical PTS1 proteins was comparatively lesser in S. lycopersicum. The non-canonical PTS1s were found to be comparable in both the plant species; however, S. lycopersicum showed greater diversity in the composition of the signal tripeptide. Finally, we have tried to address the lacunas and probable strategies to fill those gaps.
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10
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Vasilev J, Mix AK, Heimerl T, Maier UG, Moog D. Inferred Subcellular Localization of Peroxisomal Matrix Proteins of Guillardia theta Suggests an Important Role of Peroxisomes in Cryptophytes. FRONTIERS IN PLANT SCIENCE 2022; 13:889662. [PMID: 35783940 PMCID: PMC9244630 DOI: 10.3389/fpls.2022.889662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes participate in several important metabolic processes in eukaryotic cells, such as the detoxification of reactive oxygen species (ROS) or the degradation of fatty acids by β-oxidation. Recently, the presence of peroxisomes in the cryptophyte Guillardia theta and other "chromalveolates" was revealed by identifying proteins for peroxisomal biogenesis. Here, we investigated the subcellular localization of candidate proteins of G. theta in the diatom Phaeodactylum tricornutum, either possessing a putative peroxisomal targeting signal type 1 (PTS1) sequence or factors lacking a peroxisomal targeting signal but known to be involved in β-oxidation. Our results indicate important contributions of the peroxisomes of G. theta to the carbohydrate, ether phospholipid, nucleotide, vitamin K, ROS, amino acid, and amine metabolisms. Moreover, our results suggest that in contrast to many other organisms, the peroxisomes of G. theta are not involved in the β-oxidation of fatty acids, which exclusively seems to occur in the cryptophyte's mitochondria.
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Affiliation(s)
- Jana Vasilev
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ann-Kathrin Mix
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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11
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Záhonová K, Treitli SC, Le T, Škodová-Sveráková I, Hanousková P, Čepička I, Tachezy J, Hampl V. Anaerobic derivates of mitochondria and peroxisomes in the free-living amoeba Pelomyxa schiedti revealed by single-cell genomics. BMC Biol 2022; 20:56. [PMID: 35227266 PMCID: PMC8887013 DOI: 10.1186/s12915-022-01247-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/03/2022] [Indexed: 01/15/2023] Open
Abstract
Background Mitochondria and peroxisomes are the two organelles that are most affected during adaptation to microoxic or anoxic environments. Mitochondria are known to transform into anaerobic mitochondria, hydrogenosomes, mitosomes, and various transition stages in between, collectively called mitochondrion-related organelles (MROs), which vary in enzymatic capacity. Anaerobic peroxisomes were identified only recently, and their putatively most conserved function seems to be the metabolism of inositol. The group Archamoebae includes anaerobes bearing both anaerobic peroxisomes and MROs, specifically hydrogenosomes in free-living Mastigamoeba balamuthi and mitosomes in the human pathogen Entamoeba histolytica, while the organelles within the third lineage represented by Pelomyxa remain uncharacterized. Results We generated high-quality genome and transcriptome drafts from Pelomyxa schiedti using single-cell omics. These data provided clear evidence for anaerobic derivates of mitochondria and peroxisomes in this species, and corresponding vesicles were tentatively identified in electron micrographs. In silico reconstructed MRO metabolism harbors respiratory complex II, electron-transferring flavoprotein, a partial TCA cycle running presumably in the reductive direction, pyruvate:ferredoxin oxidoreductase, [FeFe]-hydrogenases, a glycine cleavage system, a sulfate activation pathway, and an expanded set of NIF enzymes for iron-sulfur cluster assembly. When expressed in the heterologous system of yeast, some of these candidates localized into mitochondria, supporting their involvement in the MRO metabolism. The putative functions of P. schiedti peroxisomes could be pyridoxal 5′-phosphate biosynthesis, amino acid and carbohydrate metabolism, and hydrolase activities. Unexpectedly, out of 67 predicted peroxisomal enzymes, only four were also reported in M. balamuthi, namely peroxisomal processing peptidase, nudix hydrolase, inositol 2-dehydrogenase, and d-lactate dehydrogenase. Localizations in yeast corroborated peroxisomal functions of the latter two. Conclusions This study revealed the presence and partially annotated the function of anaerobic derivates of mitochondria and peroxisomes in P. schiedti using single-cell genomics, localizations in yeast heterologous systems, and transmission electron microscopy. The MRO metabolism resembles that of M. balamuthi and most likely reflects the state in the common ancestor of Archamoebae. The peroxisomal metabolism is strikingly richer in P. schiedti. The presence of myo-inositol 2-dehydrogenase in the predicted peroxisomal proteome corroborates the situation in other Archamoebae, but future experimental evidence is needed to verify additional functions of this organelle. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01247-w.
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Affiliation(s)
- Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic. .,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
| | | | - Tien Le
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Pavla Hanousková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.
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12
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Kamoshita M, Kumar R, Anteghini M, Kunze M, Islinger M, Martins dos Santos V, Schrader M. Insights Into the Peroxisomal Protein Inventory of Zebrafish. Front Physiol 2022; 13:822509. [PMID: 35295584 PMCID: PMC8919083 DOI: 10.3389/fphys.2022.822509] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022] Open
Abstract
Peroxisomes are ubiquitous, oxidative subcellular organelles with important functions in cellular lipid metabolism and redox homeostasis. Loss of peroxisomal functions causes severe disorders with developmental and neurological abnormalities. Zebrafish are emerging as an attractive vertebrate model to study peroxisomal disorders as well as cellular lipid metabolism. Here, we combined bioinformatics analyses with molecular cell biology and reveal the first comprehensive inventory of Danio rerio peroxisomal proteins, which we systematically compared with those of human peroxisomes. Through bioinformatics analysis of all PTS1-carrying proteins, we demonstrate that D. rerio lacks two well-known mammalian peroxisomal proteins (BAAT and ZADH2/PTGR3), but possesses a putative peroxisomal malate synthase (Mlsl) and verified differences in the presence of purine degrading enzymes. Furthermore, we revealed novel candidate peroxisomal proteins in D. rerio, whose function and localisation is discussed. Our findings confirm the suitability of zebrafish as a vertebrate model for peroxisome research and open possibilities for the study of novel peroxisomal candidate proteins in zebrafish and humans.
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Affiliation(s)
- Maki Kamoshita
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rechal Kumar
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Marco Anteghini
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Markus Kunze
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Markus Islinger
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vítor Martins dos Santos
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
- *Correspondence: Michael Schrader,
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13
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Rudić J, Dragićević MB, Momčilović I, Simonović AD, Pantelić D. In Silico Study of Superoxide Dismutase Gene Family in Potato and Effects of Elevated Temperature and Salicylic Acid on Gene Expression. Antioxidants (Basel) 2022; 11:antiox11030488. [PMID: 35326138 PMCID: PMC8944489 DOI: 10.3390/antiox11030488] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
Potato (Solanum tuberosum L.) is the most important vegetable crop globally and is very susceptible to high ambient temperatures. Since heat stress causes the accumulation of reactive oxygen species (ROS), investigations regarding major enzymatic components of the antioxidative system are of the essence. Superoxide dismutases (SODs) represent the first line of defense against ROS but detailed in silico analysis and characterization of the potato SOD gene family have not been performed thus far. We have analyzed eight functional SOD genes, three StCuZnSODs, one StMnSOD, and four StFeSODs, annotated in the updated version of potato genome (Spud DB DM v6.1). The StSOD genes and their respective proteins were analyzed in silico to determine the exon-intron organization, splice variants, cis-regulatory promoter elements, conserved domains, signals for subcellular targeting, 3D-structures, and phylogenetic relations. Quantitative PCR analysis revealed higher induction of StCuZnSODs (the major potato SODs) and StFeSOD3 in thermotolerant cultivar Désirée than in thermosensitive Agria and Kennebec during long-term exposure to elevated temperature. StMnSOD was constitutively expressed, while expression of StFeSODs was cultivar-dependent. The effects of salicylic acid (10−5 M) on StSODs expression were minor. Our results provide the basis for further research on StSODs and their regulation in potato, particularly in response to elevated temperatures.
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14
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Hooper CM, Castleden IR, Tanz SK, Grasso SV, Millar AH. Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1346:67-89. [PMID: 35113396 DOI: 10.1007/978-3-030-80352-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In eukaryotic organisms, subcellular protein location is critical in defining protein function and understanding sub-functionalization of gene families. Some proteins have defined locations, whereas others have low specificity targeting and complex accumulation patterns. There is no single approach that can be considered entirely adequate for defining the in vivo location of all proteins. By combining evidence from different approaches, the strengths and weaknesses of different technologies can be estimated, and a location consensus can be built. The Subcellular Location of Proteins in Arabidopsis database ( http://suba.live/ ) combines experimental data sets that have been reported in the literature and is analyzing these data to provide useful tools for biologists to interpret their own data. Foremost among these tools is a consensus classifier (SUBAcon) that computes a proposed location for all proteins based on balancing the experimental evidence and predictions. Further tools analyze sets of proteins to define the abundance of cellular structures. Extending these types of resources to plant crop species has been complex due to polyploidy, gene family expansion and contraction, and the movement of pathways and processes within cells across the plant kingdom. The Crop Proteins of Annotated Location database ( http://crop-pal.org/ ) has developed a range of subcellular location resources including a species-specific voting consensus for 12 plant crop species that offers collated evidence and filters for current crop proteomes akin to SUBA. Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways. Together SUBA and cropPAL created reference subcellulomes for plants as well as species-specific subcellulomes for cross-species data mining. These data collections are increasingly used by the research community to provide a subcellular protein location layer, inform models of compartmented cell function and protein-protein interaction network, guide future molecular crop breeding strategies, or simply answer a specific question-where is my protein of interest inside the cell?
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Affiliation(s)
- Cornelia M Hooper
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Ian R Castleden
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sandra K Tanz
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sally V Grasso
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - A Harvey Millar
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia.
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15
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Neofunctionalization of Glycolytic Enzymes: An Evolutionary Route to Plant Parasitism in the Oomycete Phytophthora nicotianae. Microorganisms 2022; 10:microorganisms10020281. [PMID: 35208735 PMCID: PMC8879444 DOI: 10.3390/microorganisms10020281] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/12/2022] [Accepted: 01/23/2022] [Indexed: 02/04/2023] Open
Abstract
Oomycetes, of the genus Phytophthora, comprise of some of the most devastating plant pathogens. Parasitism of Phytophthora results from evolution from an autotrophic ancestor and adaptation to a wide range of environments, involving metabolic adaptation. Sequence mining showed that Phytophthora spp. display an unusual repertoire of glycolytic enzymes, made of multigene families and enzyme replacements. To investigate the impact of these gene duplications on the biology of Phytophthora and, eventually, identify novel functions associated to gene expansion, we focused our study on the first glycolytic step on P. nicotianae, a broad host range pathogen. We reveal that this step is committed by a set of three glucokinase types that differ by their structure, enzymatic properties, and evolutionary histories. In addition, they are expressed differentially during the P. nicotianae life cycle, including plant infection. Last, we show that there is a strong association between the expression of a glucokinase member in planta and extent of plant infection. Together, these results suggest that metabolic adaptation is a component of the processes underlying evolution of parasitism in Phytophthora, which may possibly involve the neofunctionalization of metabolic enzymes.
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16
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Leissring MA. Insulin-Degrading Enzyme: Paradoxes and Possibilities. Cells 2021; 10:cells10092445. [PMID: 34572094 PMCID: PMC8472535 DOI: 10.3390/cells10092445] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/31/2022] Open
Abstract
More than seven decades have passed since the discovery of a proteolytic activity within crude tissue extracts that would become known as insulin-degrading enzyme (IDE). Certainly much has been learned about this atypical zinc-metallopeptidase; at the same time, however, many quite fundamental gaps in our understanding remain. Herein, I outline what I consider to be among the most critical unresolved questions within the field, many presenting as intriguing paradoxes. For instance, where does IDE, a predominantly cytosolic protein with no signal peptide or clearly identified secretion mechanism, interact with insulin and other extracellular substrates? Where precisely is IDE localized within the cell, and what are its functional roles in these compartments? How does IDE, a bowl-shaped protein that completely encapsulates its substrates, manage to avoid getting “clogged” and thus rendered inactive virtually immediately? Although these paradoxes are by definition unresolved, I offer herein my personal insights and informed speculations based on two decades working on the biology and pharmacology of IDE and suggest specific experimental strategies for addressing these conundrums. I also offer what I believe to be especially fruitful avenues for investigation made possible by the development of new technologies and IDE-specific reagents. It is my hope that these thoughts will contribute to continued progress elucidating the physiology and pathophysiology of this important peptidase.
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Affiliation(s)
- Malcolm A Leissring
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine (UCI MIND), Irvine, CA 92697, USA
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17
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Horváthová L, Žárský V, Pánek T, Derelle R, Pyrih J, Motyčková A, Klápšťová V, Vinopalová M, Marková L, Voleman L, Klimeš V, Petrů M, Vaitová Z, Čepička I, Hryzáková K, Harant K, Gray MW, Chami M, Guilvout I, Francetic O, Franz Lang B, Vlček Č, Tsaousis AD, Eliáš M, Doležal P. Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. Nat Commun 2021; 12:2947. [PMID: 34011950 PMCID: PMC8134430 DOI: 10.1038/s41467-021-23046-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them are present in mitochondria, and their behaviour in biochemical assays is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). We additionally identified 23 protein families co-occurring with miT2SS in eukaryotes. Seven of these proteins could be directly linked to the core miT2SS by functional data and/or sequence features, whereas others may represent different parts of a broader functional pathway, possibly also involving the peroxisome. Its distribution in eukaryotes and phylogenetic evidence together indicate that the miT2SS-centred pathway is an ancestral eukaryotic trait. Our findings thus have direct implications for the functional properties of the early mitochondrion. Bacteria use the type 2 secretion system to secrete enzymes and toxins across the outer membrane to the environment. Here the authors analyse the T2SS pathway in three protist lineages and suggest that the early mitochondrion may have been capable of secreting proteins into the cytosol.
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Affiliation(s)
- Lenka Horváthová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vojtěch Žárský
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Tomáš Pánek
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic.,Faculty of Science, Department of Zoology, Charles University, Prague 2, Czech Republic
| | - Romain Derelle
- School of Biosciences, University of Birmingham, Edgbaston, UK
| | - Jan Pyrih
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury, UK.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Alžběta Motyčková
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Veronika Klápšťová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Martina Vinopalová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Lenka Marková
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Luboš Voleman
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Klimeš
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Markéta Petrů
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Zuzana Vaitová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Čepička
- Faculty of Science, Department of Zoology, Charles University, Prague 2, Czech Republic
| | - Klára Hryzáková
- Faculty of Science, Department of Genetics and Microbiology, Charles University, Prague 2, Czech Republic
| | - Karel Harant
- Faculty of Science, Proteomic core facility, Charles University, BIOCEV, Vestec, Czech Republic
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, University of Basel, Basel, Switzerland
| | - Ingrid Guilvout
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montreal, QC, Canada
| | - Čestmír Vlček
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague 4, Czech Republic
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury, UK
| | - Marek Eliáš
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic.
| | - Pavel Doležal
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic.
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18
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BiFC Method Based on Intraorganellar Protein Crowding Detects Oleate-Dependent Peroxisomal Targeting of Pichia pastoris Malate Dehydrogenase. Int J Mol Sci 2021; 22:ijms22094890. [PMID: 34063066 PMCID: PMC8124512 DOI: 10.3390/ijms22094890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/24/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Abstract
The maintenance of intracellular NAD+/NADH homeostasis across multiple, subcellular compartments requires the presence of NADH-shuttling proteins, which circumvent the lack of permeability of organelle membranes to these cofactors. Very little is known regarding these proteins in the methylotrophic yeast, Pichia pastoris. During the study of the subcellular locations of these shuttling proteins, which often have dual subcellular locations, it became necessary to develop new ways to detect the weak peroxisomal locations of some of these proteins. We have developed a novel variation of the traditional Bimolecular Fluorescence Complementation (BiFC), called divergent BiFC, to detect intraorganellar colocalization of two noninteracting proteins based on their proximity-based protein crowding within a small subcellular compartment, rather than on the traditional protein–protein interactions expected for BiFC. This method is used to demonstrate the partially peroxisomal location of one such P. pastoris NADH-shuttling protein, malate dehydrogenase B, only when cells are grown in oleate, but not when grown in methanol or glucose. We discuss the mode of NADH shuttling in P. pastoris and the physiological basis of the medium-dependent compartmentalization of PpMdhB.
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19
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Mondal DK, Pal DS, Abbasi M, Datta R. Functional partnership between carbonic anhydrase and malic enzyme in promoting gluconeogenesis in
Leishmania major. FEBS J 2021; 288:4129-4152. [DOI: 10.1111/febs.15720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/29/2020] [Accepted: 01/15/2021] [Indexed: 12/24/2022]
Affiliation(s)
- Dipon Kumar Mondal
- Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur India
| | - Dhiman Sankar Pal
- Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur India
| | - Mazharul Abbasi
- Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur India
| | - Rupak Datta
- Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur India
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20
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Hochreiter B, Chong CS, Hartig A, Maurer-Stroh S, Berger J, Schmid JA, Kunze M. A Novel FRET Approach Quantifies the Interaction Strength of Peroxisomal Targeting Signals and Their Receptor in Living Cells. Cells 2020; 9:cells9112381. [PMID: 33143123 PMCID: PMC7693011 DOI: 10.3390/cells9112381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 02/02/2023] Open
Abstract
Measuring Förster–resonance–energy–transfer (FRET) efficiency allows the investigation of protein–protein interactions (PPI), but extracting quantitative measures of affinity necessitates highly advanced technical equipment or isolated proteins. We demonstrate the validity of a recently suggested novel approach to quantitatively analyze FRET-based experiments in living mammalian cells using standard equipment using the interaction between different type-1 peroxisomal targeting signals (PTS1) and their soluble receptor peroxin 5 (PEX5) as a model system. Large data sets were obtained by flow cytometry coupled FRET measurements of cells expressing PTS1-tagged EGFP together with mCherry fused to the PTS1-binding domain of PEX5, and were subjected to a fitting algorithm extracting a quantitative measure of the interaction strength. This measure correlates with results obtained by in vitro techniques and a two-hybrid assay, but is unaffected by the distance between the fluorophores. Moreover, we introduce a live cell competition assay based on this approach, capable of depicting dose- and affinity-dependent modulation of the PPI. Using this system, we demonstrate the relevance of a sequence element next to the core tripeptide in PTS1 motifs for the interaction strength between PTS1 and PEX5, which is supported by a structure-based computational prediction of the binding energy indicating a direct involvement of this sequence in the interaction.
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Affiliation(s)
- Bernhard Hochreiter
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, 1090 Vienna, Austria;
| | - Cheng-Shoong Chong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; (C.-S.C.); (S.M.-S.)
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Andreas Hartig
- Department of Biochemistry and Cell Biology, Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria;
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; (C.-S.C.); (S.M.-S.)
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Johannes Berger
- Center for Brain Research, Department of Pathobiology of the Nervous System, Medical University of Vienna, 1090 Vienna, Austria;
| | - Johannes A. Schmid
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, 1090 Vienna, Austria;
- Correspondence: (J.A.S.); (M.K.)
| | - Markus Kunze
- Center for Brain Research, Department of Pathobiology of the Nervous System, Medical University of Vienna, 1090 Vienna, Austria;
- Correspondence: (J.A.S.); (M.K.)
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21
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González-Robles A, González-Lázaro M, Lagunes-Guillén AE, Omaña-Molina M, Lares-Jiménez LF, Lares-Villa F, Martínez-Palomo A. Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans. Genome Biol Evol 2020; 12:1734-1750. [PMID: 32602891 PMCID: PMC7549135 DOI: 10.1093/gbe/evaa129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
Peroxisomes perform various metabolic processes that are primarily related to the elimination of reactive oxygen species and oxidative lipid metabolism. These organelles are present in all major eukaryotic lineages, nevertheless, information regarding the presence of peroxisomes in opportunistic parasitic protozoa is scarce and in many cases it is still unknown whether these organisms have peroxisomes at all. Here, we performed ultrastructural, cytochemical, and bioinformatic studies to investigate the presence of peroxisomes in three genera of free-living amoebae from two different taxonomic groups that are known to cause fatal infections in humans. By transmission electron microscopy, round structures with a granular content limited by a single membrane were observed in Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba polyphaga, Acanthamoeba royreba, Balamuthia mandrillaris (Amoebozoa), and Naegleria fowleri (Heterolobosea). Further confirmation for the presence of peroxisomes was obtained by treating trophozoites in situ with diaminobenzidine and hydrogen peroxide, which showed positive reaction products for the presence of catalase. We then performed comparative genomic analyses to identify predicted peroxin homologues in these organisms. Our results demonstrate that a complete set of peroxins-which are essential for peroxisome biogenesis, proliferation, and protein import-are present in all of these amoebae. Likewise, our in silico analyses allowed us to identify a complete set of peroxins in Naegleria lovaniensis and three novel peroxin homologues in Naegleria gruberi. Thus, our results indicate that peroxisomes are present in these three genera of free-living amoebae and that they have a similar peroxin complement despite belonging to different evolutionary lineages.
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Affiliation(s)
- Arturo González-Robles
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Mónica González-Lázaro
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Anel Edith Lagunes-Guillén
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Maritza Omaña-Molina
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlanepantla, Estado de México, Mexico
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Adolfo Martínez-Palomo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
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22
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Stehlik T, Kremp M, Kahnt J, Bölker M, Freitag J. Peroxisomal targeting of a protein phosphatase type 2C via mitochondrial transit. Nat Commun 2020; 11:2355. [PMID: 32398688 PMCID: PMC7217942 DOI: 10.1038/s41467-020-16146-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 04/16/2020] [Indexed: 11/16/2022] Open
Abstract
Correct intracellular distribution of proteins is critical for the function of eukaryotic cells. Certain proteins are targeted to more than one cellular compartment, e.g. to mitochondria and peroxisomes. The protein phosphatase Ptc5 from Saccharomyces cerevisiae contains an N-terminal mitochondrial presequence followed by a transmembrane domain, and has been detected in the mitochondrial intermembrane space. Here we show mitochondrial transit of Ptc5 to peroxisomes. Translocation of Ptc5 to peroxisomes depended both on the C-terminal peroxisomal targeting signal (PTS1) and N-terminal cleavage by the mitochondrial inner membrane peptidase complex. Indirect targeting of Ptc5 to peroxisomes prevented deleterious effects of its phosphatase activity in the cytosol. Sorting of Ptc5 involves simultaneous interaction with import machineries of both organelles. We identify additional mitochondrial proteins with PTS1, which localize in both organelles and can increase their physical association. Thus, a tug-of-war-like mechanism can influence the interaction and communication of two cellular compartments.
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Affiliation(s)
- Thorsten Stehlik
- Department of Biology, Philipps University Marburg, Marburg, Germany
| | - Marco Kremp
- Department of Biology, Philipps University Marburg, Marburg, Germany
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Bölker
- Department of Biology, Philipps University Marburg, Marburg, Germany.
- LOEWE Center for Synthetic Microbiology, Marburg, Germany.
| | - Johannes Freitag
- Department of Biology, Philipps University Marburg, Marburg, Germany.
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23
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A Global Analysis of Enzyme Compartmentalization to Glycosomes. Pathogens 2020; 9:pathogens9040281. [PMID: 32290588 PMCID: PMC7237986 DOI: 10.3390/pathogens9040281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/28/2022] Open
Abstract
In kinetoplastids, the first seven steps of glycolysis are compartmentalized into a glycosome along with parts of other metabolic pathways. This organelle shares a common ancestor with the better-understood eukaryotic peroxisome. Much of our understanding of the emergence, evolution, and maintenance of glycosomes is limited to explorations of the dixenous parasites, including the enzymatic contents of the organelle. Our objective was to determine the extent that we could leverage existing studies in model kinetoplastids to determine the composition of glycosomes in species lacking evidence of experimental localization. These include diverse monoxenous species and dixenous species with very different hosts. For many of these, genome or transcriptome sequences are available. Our approach initiated with a meta-analysis of existing studies to generate a subset of enzymes with highest evidence of glycosome localization. From this dataset we extracted the best possible glycosome signal peptide identification scheme for in silico identification of glycosomal proteins from any kinetoplastid species. Validation suggested that a high glycosome localization score from our algorithm would be indicative of a glycosomal protein. We found that while metabolic pathways were consistently represented across kinetoplastids, individual proteins within those pathways may not universally exhibit evidence of glycosome localization.
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24
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Zhang C, Ma Y, Miao H, Tang X, Xu B, Wu Q, Mu Y, Huang Z. Transcriptomic Analysis of Pichia pastoris ( Komagataella phaffii) GS115 During Heterologous Protein Production Using a High-Cell-Density Fed-Batch Cultivation Strategy. Front Microbiol 2020; 11:463. [PMID: 32265887 PMCID: PMC7098997 DOI: 10.3389/fmicb.2020.00463] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/04/2020] [Indexed: 12/27/2022] Open
Abstract
Pichia pastoris (Komagataella phaffii) is a methylotrophic yeast that is widely used in industry as a host system for heterologous protein expression. Heterologous gene expression is typically facilitated by strongly inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters. However, protein production is usually accomplished by a fed-batch induction process, which is known to negatively affect cell physiology, resulting in limited protein yields and quality. To assess how yields of exogenous proteins can be increased and to further understand the physiological response of P. pastoris to the carbon conversion of glycerol and methanol, as well as the continuous induction of methanol, we analyzed recombinant protein production in a 10,000-L fed-batch culture. Furthermore, we investigated gene expression during the yeast cell culture phase, glycerol feed phase, glycerol-methanol mixture feed (GM) phase, and at different time points following methanol induction using RNA-Seq. We report that the addition of the GM phase may help to alleviate the adverse effects of methanol addition (alone) on P. pastoris cells. Secondly, enhanced upregulation of the mitogen-activated protein kinase (MAPK) signaling pathway was observed in P. pastoris following methanol induction. The MAPK signaling pathway may be related to P. pastoris cell growth and may regulate the alcohol oxidase1 (AOX1) promoter via regulatory factors activated by methanol-mediated stimulation. Thirdly, the unfolded protein response (UPR) and ER-associated degradation (ERAD) pathways were not significantly upregulated during the methanol induction period. These results imply that the presence of unfolded or misfolded phytase protein did not represent a serious problem in our study. Finally, the upregulation of the autophagy pathway during the methanol induction phase may be related to the degradation of damaged peroxisomes but not to the production of phytase. This work describes the metabolic characteristics of P. pastoris during heterologous protein production under high-cell-density fed-batch cultivation. We believe that the results of this study will aid further in-depth studies of P. pastoris heterologous protein expression, regulation, and secretory mechanisms.
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Affiliation(s)
- Chengbo Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
| | - Yu Ma
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Huabiao Miao
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Bo Xu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Yuelin Mu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
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25
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Nerstedt A, Kurhe Y, Cansby E, Caputo M, Gao L, Vorontsov E, Ståhlman M, Nuñez-Durán E, Borén J, Marschall HU, Mashek DG, Saunders DN, Sihlbom C, Hoy AJ, Mahlapuu M. Lipid droplet-associated kinase STK25 regulates peroxisomal activity and metabolic stress response in steatotic liver. J Lipid Res 2019; 61:178-191. [PMID: 31857389 DOI: 10.1194/jlr.ra119000316] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/05/2019] [Indexed: 12/18/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) are emerging as leading causes of liver disease worldwide and have been recognized as one of the major unmet medical needs of the 21st century. Our recent translational studies in mouse models, human cell lines, and well-characterized patient cohorts have identified serine/threonine kinase (STK)25 as a protein that coats intrahepatocellular lipid droplets (LDs) and critically regulates liver lipid homeostasis and progression of NAFLD/NASH. Here, we studied the mechanism-of-action of STK25 in steatotic liver by relative quantification of the hepatic LD-associated phosphoproteome from high-fat diet-fed Stk25 knockout mice compared with their wild-type littermates. We observed a total of 131 proteins and 60 phosphoproteins that were differentially represented in STK25-deficient livers. Most notably, a number of proteins involved in peroxisomal function, ubiquitination-mediated proteolysis, and antioxidant defense were coordinately regulated in Stk25 -/- versus wild-type livers. We confirmed attenuated peroxisomal biogenesis and protection against oxidative and ER stress in STK25-deficient human liver cells, demonstrating the hepatocyte-autonomous manner of STK25's action. In summary, our results suggest that regulation of peroxisomal function and metabolic stress response may be important molecular mechanisms by which STK25 controls the development and progression of NAFLD/NASH.
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Affiliation(s)
- Annika Nerstedt
- Departments of Chemistry and Molecular Biology University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Yeshwant Kurhe
- Departments of Chemistry and Molecular Biology University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Emmelie Cansby
- Departments of Chemistry and Molecular Biology University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mara Caputo
- Departments of Chemistry and Molecular Biology University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lei Gao
- Departments of Chemistry and Molecular Biology University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Egor Vorontsov
- Proteomics Core Facility, University of Gothenburg, Gothenburg, Sweden
| | - Marcus Ståhlman
- Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Esther Nuñez-Durán
- Departments of Chemistry and Molecular Biology University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jan Borén
- Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Hanns-Ulrich Marschall
- Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Douglas G Mashek
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - Darren N Saunders
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Carina Sihlbom
- Proteomics Core Facility, University of Gothenburg, Gothenburg, Sweden
| | - Andrew J Hoy
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Margit Mahlapuu
- Departments of Chemistry and Molecular Biology University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
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26
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Chong CS, Kunze M, Hochreiter B, Krenn M, Berger J, Maurer-Stroh S. Rare Human Missense Variants can affect the Function of Disease-Relevant Proteins by Loss and Gain of Peroxisomal Targeting Motifs. Int J Mol Sci 2019; 20:E4609. [PMID: 31533369 PMCID: PMC6770196 DOI: 10.3390/ijms20184609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/06/2019] [Accepted: 09/14/2019] [Indexed: 12/30/2022] Open
Abstract
Single nucleotide variants (SNVs) resulting in amino acid substitutions (i.e., missense variants) can affect protein localization by changing or creating new targeting signals. Here, we studied the potential of naturally occurring SNVs from the Genome Aggregation Database (gnomAD) to result in the loss of an existing peroxisomal targeting signal 1 (PTS1) or gain of a novel PTS1 leading to mistargeting of cytosolic proteins to peroxisomes. Filtering down from 32,985 SNVs resulting in missense mutations within the C-terminal tripeptide of 23,064 human proteins, based on gene annotation data and computational prediction, we selected six SNVs for experimental testing of loss of function (LoF) of the PTS1 motif and five SNVs in cytosolic proteins for gain in PTS1-mediated peroxisome import (GoF). Experimental verification by immunofluorescence microscopy for subcellular localization and FRET affinity measurements for interaction with the receptor PEX5 demonstrated that five of the six predicted LoF SNVs resulted in loss of the PTS1 motif while three of five predicted GoF SNVs resulted in de novo PTS1 generation. Overall, we showed that a complementary approach incorporating bioinformatics methods and experimental testing was successful in identifying SNVs capable of altering peroxisome protein import, which may have implications in human disease.
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Affiliation(s)
- Cheng-Shoong Chong
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.
- National University of Singapore Graduate School for Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore 119077, Singapore.
| | - Markus Kunze
- Medical University of Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, 1090 Vienna, Austria.
| | - Bernhard Hochreiter
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, 1090 Vienna, Austria.
| | - Martin Krenn
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria.
- Institute of Human Genetics, Technical University Munich, 81675 Munich, Germany.
| | - Johannes Berger
- Medical University of Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, 1090 Vienna, Austria.
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.
- National University of Singapore Graduate School for Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore 119077, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.
- Innovations in Food and Chemical Safety Programme (IFCS), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.
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27
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Abstract
Ever since the signal hypothesis was proposed in 1971, the exact nature of signal peptides has been a focus point of research. The prediction of signal peptides and protein subcellular location from amino acid sequences has been an important problem in bioinformatics since the dawn of this research field, involving many statistical and machine learning technologies. In this review, we provide a historical account of how position-weight matrices, artificial neural networks, hidden Markov models, support vector machines and, lately, deep learning techniques have been used in the attempts to predict where proteins go. Because the secretory pathway was the first one to be studied both experimentally and through bioinformatics, our main focus is on the historical development of prediction methods for signal peptides that target proteins for secretion; prediction methods to identify targeting signals for other cellular compartments are treated in less detail.
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Affiliation(s)
- Henrik Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Konstantinos D Tsirigos
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Søren Brunak
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kgs. Lyngby, Denmark
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Science for Life Laboratory, Stockholm University, Solna, Sweden
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28
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Vincow ES, Thomas RE, Merrihew GE, Shulman NJ, Bammler TK, MacDonald JW, MacCoss MJ, Pallanck LJ. Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective. Autophagy 2019; 15:1592-1605. [PMID: 30865561 DOI: 10.1080/15548627.2019.1586258] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The destruction of mitochondria through macroautophagy (autophagy) has been recognised as a major route of mitochondrial protein degradation since its discovery more than 50 years ago, but fundamental questions remain unanswered. First, how much mitochondrial protein turnover occurs through auto-phagy? Mitochondrial proteins are also degraded by nonautophagic mechanisms, and the proportion of mitochondrial protein turnover that occurs through autophagy is still unknown. Second, does auto-phagy degrade mitochondrial proteins uniformly or selectively? Autophagy was originally thought to degrade all mitochondrial proteins at the same rate, but recent work suggests that mitochondrial autophagy may be protein selective. To investigate these questions, we used a proteomics-based approach in the fruit fly Drosophila melanogaster, comparing mitochondrial protein turnover rates in autophagy-deficient Atg7 mutants and controls. We found that ~35% of mitochondrial protein turnover occurred via autophagy. Similar analyses using parkin mutants revealed that parkin-dependent mitophagy accounted for ~25% of mitochondrial protein turnover, suggesting that most mitochondrial autophagy specifically eliminates dysfunctional mitochondria. We also found that our results were incompatible with uniform autophagic turnover of mitochondrial proteins and consistent with protein-selective autophagy. In particular, the autophagic turnover rates of individual mitochondrial proteins varied widely, and only a small amount of the variation could be attributed to tissue differences in mitochondrial composition and autophagy rate. Furthermore, analyses comparing autophagy-deficient and control human fibroblasts revealed diverse autophagy-dependent turnover rates even in homogeneous cells. In summary, our work indicates that autophagy acts selectively on mitochondrial proteins, and that most mitochondrial protein turnover occurs through non-autophagic processes. Abbreviations: Atg5: Autophagy-related 5 (Drosophila); ATG5: autophagy related 5 (human); Atg7: Autophagy-related 7 (Drosophila); ATG7: autophagy related 7 (human); DNA: deoxyribonucleic acid; ER: endoplasmic reticulum; GFP: green fluorescent protein; MS: mass spectrometry; park: parkin (Drosophila); Pink1: PTEN-induced putative kinase 1 (Drosophila); PINK1: PTEN-induced kinase 1 (human); PRKN: parkin RBR E3 ubiquitin protein ligase (human); RNA: ribonucleic acid; SD: standard deviation; Ub: ubiquitin/ubiquitinated; WT: wild-type; YME1L: YME1 like ATPase (Drosophila); YME1L1: YME1 like 1 ATPase (human).
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Affiliation(s)
- Evelyn S Vincow
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Ruth E Thomas
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Gennifer E Merrihew
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Nicholas J Shulman
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Theo K Bammler
- b Department of Environmental and Occupational Health Sciences, University of Washington , Seattle , WA , USA
| | - James W MacDonald
- b Department of Environmental and Occupational Health Sciences, University of Washington , Seattle , WA , USA
| | - Michael J MacCoss
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Leo J Pallanck
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
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29
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Krombach S, Reissmann S, Kreibich S, Bochen F, Kahmann R. Virulence function of the Ustilago maydis sterol carrier protein 2. THE NEW PHYTOLOGIST 2018; 220:553-566. [PMID: 29897130 DOI: 10.1111/nph.15268] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/14/2018] [Indexed: 05/06/2023]
Abstract
The peroxisomal sterol carrier protein 2 (Scp2) of the biotrophic maize pathogen Ustilago maydis was detected in apoplastic fluid, suggesting that it might function as a secreted effector protein. Here we analyze the role of the scp2 gene during plant colonization. We used reverse genetics approaches to delete the scp2 gene, determined stress sensitivity and fatty acid utilization of mutants, demonstrated secretion of Scp2, used quantitative reverse transcription polymerase chain reaction for expression analysis and expressed GFP-Scp2 fusion proteins for protein localization. scp2 mutants were strongly attenuated in virulence and this defect manifested itself during penetration. Scp2 localized to peroxisomes and peroxisomal targeting was necessary for its virulence function. Deletion of scp2 in U. maydis interfered neither with growth nor with peroxisomal β-oxidation. Conventionally secreted Scp2 protein could not rescue the virulence defect. scp2 mutants displayed an altered localization of peroxisomes. Our results show a virulence function for Scp2 during penetration that is probably carried out by Scp2 in peroxisomes. We speculate that Scp2 affects the lipid composition of membranes and in this way ensures the even cellular distribution of peroxisomes.
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Affiliation(s)
- Sina Krombach
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany
| | - Stefanie Reissmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany
| | - Saskia Kreibich
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany
| | - Florian Bochen
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany
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30
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Thomas RE, Vincow ES, Merrihew GE, MacCoss MJ, Davis MY, Pallanck LJ. Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles. PLoS Genet 2018; 14:e1007694. [PMID: 30256786 PMCID: PMC6175534 DOI: 10.1371/journal.pgen.1007694] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/08/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022] Open
Abstract
Mutations in the glucosylceramidase beta (GBA) gene are strongly associated with neurodegenerative diseases marked by protein aggregation. GBA encodes the lysosomal enzyme glucocerebrosidase, which breaks down glucosylceramide. A common explanation for the link between GBA mutations and protein aggregation is that lysosomal accumulation of glucosylceramide causes impaired autophagy. We tested this hypothesis directly by measuring protein turnover and abundance in Drosophila mutants with deletions in the GBA ortholog Gba1b. Proteomic analyses revealed that known autophagy substrates, which had severely impaired turnover in autophagy-deficient Atg7 mutants, showed little to no overall slowing of turnover or increase in abundance in Gba1b mutants. Likewise, Gba1b mutants did not have the marked impairment of mitochondrial protein turnover seen in mitophagy-deficient parkin mutants. Proteasome activity, microautophagy, and endocytic degradation also appeared unaffected in Gba1b mutants. However, we found striking changes in the turnover and abundance of proteins associated with extracellular vesicles (EVs), which have been proposed as vehicles for the spread of protein aggregates in neurodegenerative disease. These changes were specific to Gba1b mutants and did not represent an acceleration of normal aging. Western blotting of isolated EVs confirmed the increased abundance of EV proteins in Gba1b mutants, and nanoparticle tracking analysis revealed that Gba1b mutants had six times as many EVs as controls. Genetic perturbations of EV production in Gba1b mutants suppressed protein aggregation, demonstrating that the increase in EV abundance contributed to the accumulation of protein aggregates. Together, our findings indicate that glucocerebrosidase deficiency causes pathogenic changes in EV metabolism and may promote the spread of protein aggregates through extracellular vesicles.
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Affiliation(s)
- Ruth E. Thomas
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Evelyn S. Vincow
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Marie Y. Davis
- Department of Neurology, University of Washington, Seattle, WA, United States of America
- Department of Neurology, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States of America
| | - Leo J. Pallanck
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
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31
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Kim I, Bang WY, Kim S, Jin SM, Hyun JY, Han EH, Lee E. Peroxisome-targeted Supramolecular Nanoprobes Assembled with Pyrene-labelled Peptide Amphiphiles. Chem Asian J 2018; 13:3485-3490. [PMID: 29956888 DOI: 10.1002/asia.201800863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 11/09/2022]
Abstract
Despite the versatile metabolic functions of peroxisomes such as lipid synthesis and fatty acid oxidation and their relevance to genetically inherited diseases, namely, peroxisome biogenesis disorders and peroxisomal enzyme deficiency, there is not much research on peroxisome-targeting therapeutics. Herein we present supramolecular nanostructured probes based on the self-assembly of peptide amphiphiles (PAs) having peroxisome-targeting ability in mammalian cells. The PA was designed to include the peroxisome-targeting tripeptide (SKL) and a fluorescent dye (pyrene). It was revealed that the presence of the SKL-appended carboxyl terminal group of PA, the extent of α-helical nature of the peptide block, and the fibrillar morphology of nano-assemblies affected the targeting efficiency of PA supramolecular nanoprobe. The simple modification of PAs by the peroxisome-targeting strength prediction showed an enhanced peroxisome specificity, as expected. This work provides important insights into designing subcellular organelle-targeting nanoparticles for next-generation nanomedicines.
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Affiliation(s)
- Inhye Kim
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Woo-Young Bang
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Sooyong Kim
- Graduate School of Analytical Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Seon-Mi Jin
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Ju-Yong Hyun
- Drug & Disease Target Research Team, Division of Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea.,Department of Bio-Microsystem Technology, Korea University, 145 Anam-ro, Sungbuk-gu, Seoul, 02841, Republic of Korea
| | - Eun Hee Han
- Drug & Disease Target Research Team, Division of Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Eunji Lee
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
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Phylogenetic analysis of cnidarian peroxiredoxins and stress-responsive expression in the estuarine sea anemone Nematostella vectensis. Comp Biochem Physiol A Mol Integr Physiol 2018; 221:32-43. [PMID: 29567405 DOI: 10.1016/j.cbpa.2018.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 02/08/2023]
Abstract
Peroxiredoxins (PRXs) are a family of antioxidant enzymes present in all domains of life. To date, the diversity and function of peroxiredoxins within animals have only been studied in a few model species. Thus, we sought to characterize peroxiredoxin diversity in cnidarians and to gain insight into their function in one cnidarian-the sea anemone Nematostella vectensis. Phylogenetic analysis using all six known PRX subfamilies (PRX1-4, PRX5, PRX6, PRXQ/AHPE1, TPX, BCP-PRXQ) revealed that like bilaterians, cnidarians contain representatives from three subfamilies (PRX1-4, PRX5, PRX6). Within the PRX1-4 subfamily, cnidarian sequences fall into two clades: PRX4, and a cnidarian-specific clade, which we term CNID-PRX. This phylogenetic analysis demonstrates that the three PRX subfamilies present in Bilateria were also present in the last common ancestor of the Cnidaria and Bilateria, and further that diversification of the PRX1-4 subfamily has occurred within the cnidarian lineage. We next examined the impact of decreased salinity, increased temperature, and peroxide exposure on the expression of four prx genes in N. vectensis (cnid-prx, prx4, prx5, and prx6). These genes exhibited unique expression patterns in response to these environmental stressors. Expression of prx4 decreased with initial exposure to elevated temperature, cnid-prx increased with exposure to elevated temperatures as well as with hydrogen peroxide exposure, and expression of all prxs transiently decreased with reduced salinity. Predicted subcellular localization patterns also varied among PRX proteins. Together these results provide evidence that peroxiredoxins in N. vectensis serve distinct physiological roles and lay a groundwork for understanding how peroxiredoxins mediate cnidarian developmental processes and environmental responses.
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Moog D, Przyborski JM, Maier UG. Genomic and Proteomic Evidence for the Presence of a Peroxisome in the Apicomplexan Parasite Toxoplasma gondii and Other Coccidia. Genome Biol Evol 2018; 9:3108-3121. [PMID: 29126146 PMCID: PMC5737649 DOI: 10.1093/gbe/evx231] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2017] [Indexed: 02/06/2023] Open
Abstract
Apicomplexans are successful parasites responsible for severe human diseases including malaria, toxoplasmosis, and cryptosporidiosis. For many years, it has been discussed whether these parasites are in possession of peroxisomes, highly variable eukaryotic organelles usually involved in fatty acid degradation and cellular detoxification. Conflicting experimental data has been published. With the age of genomics, ever more high quality apicomplexan genomes have become available, that now allow a new assessment of the dispute. Here, we provide bioinformatic evidence for the presence of peroxisomes in Toxoplasma gondii and other coccidians. For these organisms, we have identified a complete set of peroxins, probably responsible for peroxisome biogenesis, division, and protein import. Moreover, via a global screening for peroxisomal targeting signals, we were able to show that a complete set of fatty acid β-oxidation enzymes is equipped with either PTS1 or PTS2 sequences, most likely mediating transport of these factors to putative peroxisomes in all investigated Coccidia. Our results further imply a life cycle stage-specific presence of peroxisomes in T. gondii and suggest several independent losses of peroxisomes during the evolution of apicomplexan parasites.
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Affiliation(s)
- Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Germany
| | - Jude M Przyborski
- Laboratory for Parasitology, Philipps University Marburg, Germany.,Centre for Infectious Diseases, Parasitology, Heidelberg University Medical School, INF324, Heidelberg, Germany
| | - Uwe G Maier
- Laboratory for Cell Biology, Philipps University Marburg, Germany.,LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University, Marburg, Germany
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34
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Freitag J, Stehlik T, Stiebler AC, Bölker M. The Obvious and the Hidden: Prediction and Function of Fungal Peroxisomal Matrix Proteins. Subcell Biochem 2018; 89:139-155. [PMID: 30378022 DOI: 10.1007/978-981-13-2233-4_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fungal peroxisomes are characterized by a number of specific biological functions. To understand the physiology and biochemistry of these organelles knowledge of the proteome content is crucial. Here, we address different strategies to predict peroxisomal proteins by bioinformatics approaches. These tools range from simple text searches to network based learning strategies. A complication of this analysis is the existence of cryptic peroxisomal proteins, which are overlooked in conventional bioinformatics queries. These include proteins where targeting information results from transcriptional and posttranscriptional alterations. But also proteins with low efficiency targeting motifs that are predominantly localized in the cytosol, and proteins lacking any canonical targeting information, can play important roles within peroxisomes. Many of these proteins are so far unpredictable. Detection and characterization of these cryptic peroxisomal proteins revealed the presence of novel peroxisomal enzymatic reaction networks in fungi.
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Affiliation(s)
- Johannes Freitag
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Thorsten Stehlik
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Alina C Stiebler
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Michael Bölker
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany.
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Abstract
Our knowledge of the proteome of plant peroxisomes is far from being complete, and the functional complexity and plasticity of this cell organelle are amazingly high particularly in plants, as exemplified by the model species Arabidopsis thaliana. Plant-specific peroxisome functions that have been uncovered only recently include, for instance, the participation of peroxisomes in phylloquinone and biotin biosynthesis. Experimental proteome studies have been proved very successful in defining the proteome of Arabidopsis peroxisomes but this approach also faces significant challenges and limitations. Complementary to experimental approaches, computational methods have emerged as important powerful tools to define the proteome of soluble matrix proteins of plant peroxisomes. Compared to other cell organelles such as mitochondria, plastids and the ER, the simultaneous operation of two major import pathways for soluble proteins in peroxisomes is rather atypical. Novel machine learning prediction approaches have been developed for peroxisome targeting signals type 1 (PTS1) and revealed high sensitivity and specificity, as validated by in vivo subcellular targeting analyses in diverse transient plant expression systems. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In contrast, the prediction of PTS2 proteins largely remains restricted to genome searches by conserved patterns contrary to more advanced machine learning methods. Here, we summarize and discuss the capabilities and accuracies of available prediction algorithms for PTS1 and PTS2 carrying proteins.
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Affiliation(s)
- Sigrun Reumann
- Department of Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
| | - Gopal Chowdhary
- KIIT School of Biotechnology, Campus XI, KIIT University, Bhubaneswar, 751024, India
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36
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Kunze M. Predicting Peroxisomal Targeting Signals to Elucidate the Peroxisomal Proteome of Mammals. Subcell Biochem 2018; 89:157-199. [PMID: 30378023 DOI: 10.1007/978-981-13-2233-4_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peroxisomes harbor a plethora of proteins, but the peroxisomal proteome as the entirety of all peroxisomal proteins is still unknown for mammalian species. Computational algorithms can be used to predict the subcellular localization of proteins based on their amino acid sequence and this method has been amply used to forecast the intracellular fate of individual proteins. However, when applying such algorithms systematically to all proteins of an organism the prediction of its peroxisomal proteome in silico should be possible. Therefore, a reliable detection of peroxisomal targeting signals (PTS ) acting as postal codes for the intracellular distribution of the encoding protein is crucial. Peroxisomal proteins can utilize different routes to reach their destination depending on the type of PTS. Accordingly, independent prediction algorithms have been developed for each type of PTS, but only those for type-1 motifs (PTS1) have so far reached a satisfying predictive performance. This is partially due to the low number of peroxisomal proteins limiting the power of statistical analyses and partially due to specific properties of peroxisomal protein import, which render functional PTS motifs inactive in specific contexts. Moreover, the prediction of the peroxisomal proteome is limited by the high number of proteins encoded in mammalian genomes, which causes numerous false positive predictions even when using reliable algorithms and buries the few yet unidentified peroxisomal proteins. Thus, the application of prediction algorithms to identify all peroxisomal proteins is currently ineffective as stand-alone method, but can display its full potential when combined with other methods.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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37
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Bersch K, Lobos Matthei I, Thoms S. Multiple Localization by Functional Translational Readthrough. Subcell Biochem 2018; 89:201-219. [PMID: 30378024 DOI: 10.1007/978-981-13-2233-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In a compartmentalized cell, correct protein localization is crucial for function of virtually all cellular processes. From the cytoplasm as a starting point, proteins are imported into organelles by specific targeting signals. Many proteins, however, act in more than one cellular compartment. In this chapter, we discuss mechanisms by which proteins can be targeted to multiple organelles with a focus on a novel gene regulatory mechanism, functional translational readthrough, that permits multiple targeting of proteins to the peroxisome and other organelles. In mammals, lactate and malate dehydrogenase are the best-characterized enzymes whose targeting is controlled by functional translational readthrough.
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Affiliation(s)
- Kristina Bersch
- Department of Child and Adolescent Health, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Ignacio Lobos Matthei
- Department of Child and Adolescent Health, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
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38
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Li G, Fan A, Peng G, Keyhani NO, Xin J, Cao Y, Xia Y. A bifunctional catalase-peroxidase,MakatG1, contributes to virulence ofMetarhizium acridumby overcoming oxidative stress on the host insect cuticle. Environ Microbiol 2017; 19:4365-4378. [DOI: 10.1111/1462-2920.13932] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 09/14/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Guohong Li
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
| | - Anni Fan
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
| | - Guoxiong Peng
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
| | - Nemat O. Keyhani
- School of Life Sciences; Chongqing University; Chongqing China
- Department of Microbiology and Cell Science; University of Florida; Gainesville FL USA
| | - Jiankang Xin
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
| | - Yueqing Cao
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
| | - Yuxian Xia
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
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39
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Kumar R, Kumari B, Kumar M. Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine. PeerJ 2017; 5:e3561. [PMID: 28890846 PMCID: PMC5588793 DOI: 10.7717/peerj.3561] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/20/2017] [Indexed: 12/15/2022] Open
Abstract
Background The endoplasmic reticulum plays an important role in many cellular processes, which includes protein synthesis, folding and post-translational processing of newly synthesized proteins. It is also the site for quality control of misfolded proteins and entry point of extracellular proteins to the secretory pathway. Hence at any given point of time, endoplasmic reticulum contains two different cohorts of proteins, (i) proteins involved in endoplasmic reticulum-specific function, which reside in the lumen of the endoplasmic reticulum, called as endoplasmic reticulum resident proteins and (ii) proteins which are in process of moving to the extracellular space. Thus, endoplasmic reticulum resident proteins must somehow be distinguished from newly synthesized secretory proteins, which pass through the endoplasmic reticulum on their way out of the cell. Approximately only 50% of the proteins used in this study as training data had endoplasmic reticulum retention signal, which shows that these signals are not essentially present in all endoplasmic reticulum resident proteins. This also strongly indicates the role of additional factors in retention of endoplasmic reticulum-specific proteins inside the endoplasmic reticulum. Methods This is a support vector machine based method, where we had used different forms of protein features as inputs for support vector machine to develop the prediction models. During training leave-one-out approach of cross-validation was used. Maximum performance was obtained with a combination of amino acid compositions of different part of proteins. Results In this study, we have reported a novel support vector machine based method for predicting endoplasmic reticulum resident proteins, named as ERPred. During training we achieved a maximum accuracy of 81.42% with leave-one-out approach of cross-validation. When evaluated on independent dataset, ERPred did prediction with sensitivity of 72.31% and specificity of 83.69%. We have also annotated six different proteomes to predict the candidate endoplasmic reticulum resident proteins in them. A webserver, ERPred, was developed to make the method available to the scientific community, which can be accessed at http://proteininformatics.org/mkumar/erpred/index.html. Discussion We found that out of 124 proteins of the training dataset, only 66 proteins had endoplasmic reticulum retention signals, which shows that these signals are not an absolute necessity for endoplasmic reticulum resident proteins to remain inside the endoplasmic reticulum. This observation also strongly indicates the role of additional factors in retention of proteins inside the endoplasmic reticulum. Our proposed predictor, ERPred, is a signal independent tool. It is tuned for the prediction of endoplasmic reticulum resident proteins, even if the query protein does not contain specific ER-retention signal.
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Affiliation(s)
- Ravindra Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India.,Current affiliation: Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Bandana Kumari
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
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40
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Siddiqui SS, Springer SA, Verhagen A, Sundaramurthy V, Alisson-Silva F, Jiang W, Ghosh P, Varki A. The Alzheimer's disease-protective CD33 splice variant mediates adaptive loss of function via diversion to an intracellular pool. J Biol Chem 2017; 292:15312-15320. [PMID: 28747436 DOI: 10.1074/jbc.m117.799346] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/20/2017] [Indexed: 12/25/2022] Open
Abstract
The immunomodulatory receptor Siglec-3/CD33 influences risk for late-onset Alzheimer's disease (LOAD), an apparently human-specific post-reproductive disease. CD33 generates two splice variants: a full-length CD33M transcript produced primarily by the "LOAD-risk" allele and a shorter CD33m isoform lacking the sialic acid-binding domain produced primarily from the "LOAD-protective" allele. An SNP that modulates CD33 splicing to favor CD33m is associated with enhanced microglial activity. Individuals expressing more protective isoform accumulate less brain β-amyloid and have a lower LOAD risk. How the CD33m isoform increases β-amyloid clearance remains unknown. We report that the protection by the CD33m isoform may not be conferred by what it does but, rather, from what it cannot do. Analysis of blood neutrophils and monocytes and a microglial cell line revealed that unlike CD33M, the CD33m isoform does not localize to cell surfaces; instead, it accumulates in peroxisomes. Cell stimulation and activation did not mobilize CD33m to the surface. Thus, the CD33m isoform may neither interact directly with amyloid plaques nor engage in cell-surface signaling. Rather, production and localization of CD33m in peroxisomes is a way of diminishing the amount of CD33M and enhancing β-amyloid clearance. We confirmed intracellular localization by generating a CD33m-specific monoclonal antibody. Of note, CD33 is the only Siglec with a peroxisome-targeting sequence, and this motif emerged by convergent evolution in toothed whales, the only other mammals with a prolonged post-reproductive lifespan. The CD33 allele that protects post-reproductive individuals from LOAD may have evolved by adaptive loss-of-function, an example of the less-is-more hypothesis.
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Affiliation(s)
- Shoib S Siddiqui
- From the Center for Academic Research and Training in Anthropogeny (CARTA) and Glycobiology Research and Training Center (GRTC) and.,Departments of Medicine and Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093 and
| | - Stevan A Springer
- From the Center for Academic Research and Training in Anthropogeny (CARTA) and Glycobiology Research and Training Center (GRTC) and.,Departments of Medicine and Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093 and
| | - Andrea Verhagen
- From the Center for Academic Research and Training in Anthropogeny (CARTA) and Glycobiology Research and Training Center (GRTC) and.,Departments of Medicine and Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093 and
| | - Venkatasubramaniam Sundaramurthy
- From the Center for Academic Research and Training in Anthropogeny (CARTA) and Glycobiology Research and Training Center (GRTC) and
| | - Frederico Alisson-Silva
- From the Center for Academic Research and Training in Anthropogeny (CARTA) and Glycobiology Research and Training Center (GRTC) and.,Departments of Medicine and Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093 and
| | | | - Pradipta Ghosh
- Departments of Medicine and Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093 and
| | - Ajit Varki
- From the Center for Academic Research and Training in Anthropogeny (CARTA) and Glycobiology Research and Training Center (GRTC) and .,Departments of Medicine and Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093 and
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41
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Tamayo D, Muñoz JF, Almeida AJ, Puerta JD, Restrepo Á, Cuomo CA, McEwen JG, Hernández O. Paracoccidioides spp. catalases and their role in antioxidant defense against host defense responses. Fungal Genet Biol 2017; 100:22-32. [PMID: 28093309 DOI: 10.1016/j.fgb.2017.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 12/20/2016] [Accepted: 01/12/2017] [Indexed: 11/30/2022]
Abstract
Dimorphic human pathogenic fungi interact with host effector cells resisting their microbicidal mechanisms. Yeast cells are able of surviving within the tough environment of the phagolysosome by expressing an antioxidant defense system that provides protection against host-derived reactive oxygen species (ROS). This includes the production of catalases (CATs). Here we identified and analyzed the role of CAT isoforms in Paracoccidioides, the etiological agent of paracoccidioidomycosis. Firstly, we found that one of these isoforms was absent in the closely related dimorphic pathogen Coccidioides and dermatophytes, but all of them were conserved in Paracoccidioides, Histoplasma and Blastomyces species. We probed the contribution of CATs in Paracoccidioides by determining the gene expression levels of each isoform through quantitative RT-qPCR, in both the yeast and mycelia phases, and during the morphological switch (transition and germination), as well as in response to oxidative agents and during interaction with neutrophils. PbCATP was preferentially expressed in the pathogenic yeast phase, and was associated to the response against exogenous H2O2. Therefore, we created and analyzed the virulence defects of a knockdown strain for this isoform, and found that CATP protects yeast cells from H2O2 generated in vitro and is relevant during lung infection. On the other hand, CATA and CATB seem to contribute to ROS homeostasis in Paracoccidioides cells, during endogenous oxidative stress. CAT isoforms in Paracoccidioides might be coordinately regulated during development and dimorphism, and differentially expressed in response to different stresses to control ROS homeostasis during the infectious process, contributing to the virulence of Paracoccidioides.
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Affiliation(s)
- Diana Tamayo
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia; School of Microbiology, Universidad de Antioquia, Medellín, Colombia
| | - José F Muñoz
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Agostinho J Almeida
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Department of Biological Sciences, School of Sciences, Universidad EAFIT, Medellín, Colombia; Instituto Universitario da Maia, Maia, Portugal
| | - Juan D Puerta
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - Ángela Restrepo
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | | | - Juan G McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Orville Hernández
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Microbiology, Universidad de Antioquia, Medellín, Colombia; MICROBA Research Group, School of Microbiology, Universidad de Antioquia, Medellín, Colombia.
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42
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Wang J, Wang Y, Gao C, Jiang L, Guo D. PPero, a Computational Model for Plant PTS1 Type Peroxisomal Protein Prediction. PLoS One 2017; 12:e0168912. [PMID: 28045983 PMCID: PMC5207514 DOI: 10.1371/journal.pone.0168912] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 12/08/2016] [Indexed: 11/19/2022] Open
Abstract
Well-defined motifs often make it easy to investigate protein function and localization. In plants, peroxisomal proteins are guided to peroxisomes mainly by a conserved type 1 (PTS1) or type 2 (PTS2) targeting signal, and the PTS1 motif is commonly used for peroxisome targeting protein prediction. Currently computational prediction of peroxisome targeted PTS1-type proteins are mostly based on the 3 amino acids PTS1 motif and the adjacent sequence which is less than 14 amino acid residue in length. The potential contribution of the adjacent sequences beyond this short region has never been well investigated in plants. In this work, we develop a bi-profile Bayesian SVM method to extract and learn position-based amino acid features for both PTS1 motifs and their extended adjacent sequences in plants. Our proposed model outperformed other implementations with similar applications and achieved the highest accuracy of 93.6% and 92.6% for Arabidosis and other plant species respectively. A large scale analysis for Arabidopsis, Rice, Maize, Potato, Wheat, and Soybean proteome was conducted using the proposed model and a batch of candidate PTS1 proteins were predicted. The DNA segments corresponding to the C-terminal sequences of 9 selected candidates were cloned and transformed into Arabidopsis for experimental validation, and 5 of them demonstrated peroxisome targeting.
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Affiliation(s)
- Jue Wang
- School of Life Sciences and State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Yejun Wang
- Department of Medical Genetics, Shenzhen University Health Science Center, Shenzhen, China
| | - Caiji Gao
- School of Life Sciences and State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Liwen Jiang
- School of Life Sciences and State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Dianjing Guo
- School of Life Sciences and State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
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43
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Bessho-Uehara M, Konishi K, Oba Y. Biochemical characteristics and gene expression profiles of two paralogous luciferases from the Japanese firefly Pyrocoelia atripennis (Coleoptera, Lampyridae, Lampyrinae): insight into the evolution of firefly luciferase genes. Photochem Photobiol Sci 2017; 16:1301-1310. [DOI: 10.1039/c7pp00110j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The same green luminescence is generated by two luciferase isoforms: PatLuc1 is used in lanterns of various stages, and PatLuc2 is used in the body of immobile/less-mobile stages.
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Affiliation(s)
- Manabu Bessho-Uehara
- Graduate School of Bioagricultural Sciences
- Nagoya University
- Nagoya 464-8601
- Japan
| | - Kaori Konishi
- Graduate School of Bioagricultural Sciences
- Nagoya University
- Nagoya 464-8601
- Japan
| | - Yuichi Oba
- Graduate School of Bioagricultural Sciences
- Nagoya University
- Nagoya 464-8601
- Japan
- Department of Environmental Biology
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44
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Davis A, Abbriano R, Smith SR, Hildebrand M. Clarification of Photorespiratory Processes and the Role of Malic Enzyme in Diatoms. Protist 2016; 168:134-153. [PMID: 28104538 DOI: 10.1016/j.protis.2016.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/03/2016] [Accepted: 10/08/2016] [Indexed: 11/20/2022]
Abstract
Evidence suggests that diatom photorespiratory metabolism is distinct from other photosynthetic eukaryotes in that there may be at least two routes for the metabolism of the photorespiratory metabolite glycolate. One occurs primarily in the mitochondria and is similar to the C2 photorespiratory pathway, and the other processes glycolate through the peroxisomal glyoxylate cycle. Genomic analysis has identified the presence of key genes required for glycolate oxidation, the glyoxylate cycle, and malate metabolism, however, predictions of intracellular localization can be ambiguous and require verification. This knowledge gap leads to uncertainties surrounding how these individual pathways operate, either together or independently, to process photorespiratory intermediates under different environmental conditions. Here, we combine in silico sequence analysis, in vivo protein localization techniques and gene expression patterns to investigate key enzymes potentially involved in photorespiratory metabolism in the model diatom Thalassiosira pseudonana. We demonstrate the peroxisomal localization of isocitrate lyase and the mitochondrial localization of malic enzyme and a glycolate oxidase. Based on these analyses, we propose an updated model for photorespiratory metabolism in T. pseudonana, as well as a mechanism by which C2 photorespiratory metabolism and its associated pathways may operate during silicon starvation and growth arrest.
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Affiliation(s)
- Aubrey Davis
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A
| | - Raffaela Abbriano
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A
| | - Sarah R Smith
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A.; J. Craig Venter Institute, La Jolla, CA, U.S.A
| | - Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A..
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45
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Jungreis I, Chan CS, Waterhouse RM, Fields G, Lin MF, Kellis M. Evolutionary Dynamics of Abundant Stop Codon Readthrough. Mol Biol Evol 2016; 33:3108-3132. [PMID: 27604222 PMCID: PMC5100048 DOI: 10.1093/molbev/msw189] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector, Anopheles gambiae, and of 51 additional Drosophila melanogaster stop codons, including several cases of double and triple readthrough and of readthrough of two adjacent stop codons. We find that most differences between the readthrough repertoires of the two species arose from readthrough gain or loss in existing genes, rather than birth of new genes or gene death; that readthrough-associated RNA structures are sometimes gained or lost while readthrough persists; that readthrough is more likely to be lost at TAA and TAG stop codons; and that readthrough is under continued purifying evolutionary selection in mosquito, based on population genetic evidence. We also determine readthrough-associated gene properties that predate readthrough, and identify differences in the characteristic properties of readthrough genes between clades. We estimate more than 600 functional readthrough stop codons in mosquito and 900 in fruit fly, provide evidence of readthrough control of peroxisomal targeting, and refine the phylogenetic extent of abundant readthrough as following divergence from centipede.
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Affiliation(s)
- Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Clara S Chan
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Robert M Waterhouse
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA.,Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, Geneva, Switzerland.,Swiss Institute of Bioinformatics, rue Michel-Servet 1, Geneva, Switzerland
| | | | | | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
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Nötzel C, Lingner T, Klingenberg H, Thoms S. Identification of New Fungal Peroxisomal Matrix Proteins and Revision of the PTS1 Consensus. Traffic 2016; 17:1110-24. [PMID: 27392156 DOI: 10.1111/tra.12426] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 12/20/2022]
Abstract
The peroxisomal targeting signal type 1 (PTS1) is a seemingly simple peptide sequence at the C-terminal end of most peroxisomal matrix proteins. PTS1 can be described as a tripeptide with the consensus motif [S/A/C] [K/R/H] L. However, this description is neither necessary nor sufficient. It does not cover all cases of PTS1 proteins, and some proteins in accordance with this consensus do not target to the peroxisome. In order to find new PTS proteins in yeast and to arrive at a more complete description of the PTS1 consensus motif, we developed a machine learning approach that involves orthologue expansion of the set of known peroxisomal proteins. We performed a genome-wide in silico screen, characterised several PTS1-containing peptides and identified two new peroxisomal matrix proteins, which we named Pxp1 (Yel020c) and Pxp2 (Yjr111c). Based on these in silico and in vivo analyses, we revised the yeast PTS1 consensus which now includes all known PTS1 proteins.
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Affiliation(s)
- Christopher Nötzel
- Department of Child and Adolescent Health, University Medical Center, University of Göttingen, Göttingen, Germany.,Current address: Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Thomas Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.,Current address: Microarray and Deep Sequencing Core Facility, University Medical Center, University of Göttingen, Göttingen, Germany
| | - Heiner Klingenberg
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center, University of Göttingen, Göttingen, Germany.
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Valli M, Tatto NE, Peymann A, Gruber C, Landes N, Ekker H, Thallinger GG, Mattanovich D, Gasser B, Graf AB. Curation of the genome annotation ofPichia pastoris(Komagataella phaffii) CBS7435 from gene level to protein function. FEMS Yeast Res 2016; 16:fow051. [DOI: 10.1093/femsyr/fow051] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2016] [Indexed: 11/14/2022] Open
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48
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Styles NA, Shonsey EM, Falany JL, Guidry AL, Barnes S, Falany CN. Carboxy-terminal mutations of bile acid CoA:N-acyltransferase alter activity and substrate specificity. J Lipid Res 2016; 57:1133-43. [PMID: 27230263 DOI: 10.1194/jlr.m064428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Indexed: 11/20/2022] Open
Abstract
Bile acid CoA:amino acid N-acyltransferase (BAAT) is the terminal enzyme in the synthesis of bile salts from cholesterol and catalyzes the conjugation of taurine or glycine to bile acid CoA thioesters to form bile acid N-acylamidates. BAAT has a dual localization to the cytosol and peroxisomes, possibly due to an inefficient carboxy-terminal peroxisomal targeting signal (PTS), -serine-glutamine-leucine (-SQL). Mutational analysis was used to define the role of the carboxy terminus in peroxisomal localization and kinetic activity. Amidation activity of BAAT and BAAT lacking the final two amino acids (AAs) (BAAT-S) were similar, whereas the activity of BAAT with a canonical PTS sequence (BAAT-SKL) was increased >2.5-fold. Kinetic analysis of BAAT and BAAT-SKL showed that BAAT-SKL had a lower Km for taurine and glycine as well as a greater Vmax There was no difference in the affinity for cholyl-CoA. In contrast to BAAT, BAAT-SKL forms bile acid N-acylamidates with β-alanine. BAAT-S immunoprecipitated when incubated with peroxisomal biogenesis factor 5 (Pex5) and rabbit anti-Pex5 antibodies; however, deleting the final 12 AAs prevented coimmunoprecipitation with Pex5, indicating the Pex5 interaction involves more than the -SQL sequence. These results indicate that even small changes in the carboxy terminus of BAAT can have significant effects on activity and substrate specificity.
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Affiliation(s)
- Nathan A Styles
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Erin M Shonsey
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Josie L Falany
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Amber L Guidry
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Stephen Barnes
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Charles N Falany
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294
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Morales J, Hashimoto M, Williams TA, Hirawake-Mogi H, Makiuchi T, Tsubouchi A, Kaga N, Taka H, Fujimura T, Koike M, Mita T, Bringaud F, Concepción JL, Hashimoto T, Embley TM, Nara T. Differential remodelling of peroxisome function underpins the environmental and metabolic adaptability of diplonemids and kinetoplastids. Proc Biol Sci 2016; 283:20160520. [PMID: 27170716 PMCID: PMC4874719 DOI: 10.1098/rspb.2016.0520] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/12/2016] [Indexed: 01/01/2023] Open
Abstract
The remodelling of organelle function is increasingly appreciated as a central driver of eukaryotic biodiversity and evolution. Kinetoplastids including Trypanosoma and Leishmania have evolved specialized peroxisomes, called glycosomes. Glycosomes uniquely contain a glycolytic pathway as well as other enzymes, which underpin the physiological flexibility of these major human pathogens. The sister group of kinetoplastids are the diplonemids, which are among the most abundant eukaryotes in marine plankton. Here we demonstrate the compartmentalization of gluconeogenesis, or glycolysis in reverse, in the peroxisomes of the free-living marine diplonemid, Diplonema papillatum Our results suggest that peroxisome modification was already under way in the common ancestor of kinetoplastids and diplonemids, and raise the possibility that the central importance of gluconeogenesis to carbon metabolism in the heterotrophic free-living ancestor may have been an important selective driver. Our data indicate that peroxisome modification is not confined to the kinetoplastid lineage, but has also been a factor in the success of their free-living euglenozoan relatives.
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Affiliation(s)
- Jorge Morales
- Department of Molecular and Cellular Parasitology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Muneaki Hashimoto
- Department of Molecular and Cellular Parasitology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Tom A Williams
- Institute for Cell and Molecular Biosciences, Newcastle University, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK School of Earth Sciences, University of Bristol, Bristol BS8 1TG, UK
| | - Hiroko Hirawake-Mogi
- Department of Molecular and Cellular Parasitology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Takashi Makiuchi
- Department of Molecular and Cellular Parasitology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Akiko Tsubouchi
- Department of Molecular and Cellular Parasitology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Naoko Kaga
- Division of Proteomics and Biomolecular Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Hikari Taka
- Division of Proteomics and Biomolecular Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Tsutomu Fujimura
- Division of Proteomics and Biomolecular Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Masato Koike
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Toshihiro Mita
- Department of Molecular and Cellular Parasitology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP) UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Juan L Concepción
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, Newcastle University, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Takeshi Nara
- Department of Molecular and Cellular Parasitology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
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50
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Reumann S, Chowdhary G, Lingner T. Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s). BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:790-803. [PMID: 26772785 DOI: 10.1016/j.bbamcr.2016.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups.
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Affiliation(s)
- S Reumann
- Department of Plant Biochemistry and Infection Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany; Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway.
| | - G Chowdhary
- Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India.
| | - T Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, D-37077 Goettingen, Germany.
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