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Skowyra ML, Feng P, Rapoport TA. Towards solving the mystery of peroxisomal matrix protein import. Trends Cell Biol 2024; 34:388-405. [PMID: 37743160 PMCID: PMC10957506 DOI: 10.1016/j.tcb.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Peroxisomes are vital metabolic organelles that import their lumenal (matrix) enzymes from the cytosol using mobile receptors. Surprisingly, the receptors can even import folded proteins, but the underlying mechanism has been a mystery. Recent results reveal how import receptors shuttle cargo into peroxisomes. The cargo-bound receptors move from the cytosol across the peroxisomal membrane completely into the matrix by a mechanism that resembles transport through the nuclear pore. The receptors then return to the cytosol through a separate retrotranslocation channel, leaving the cargo inside the organelle. This cycle concentrates imported proteins within peroxisomes, and the energy for cargo import is supplied by receptor export. Peroxisomal protein import thus fundamentally differs from other previously known mechanisms for translocating proteins across membranes.
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Affiliation(s)
- Michael L Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Peiqiang Feng
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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2
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Call D, Pizarro SS, Tovey E, Knight E, Baumgardner C, Christensen KA, Morris JC. Measuring Dynamic Glycosomal pH Changes in Living Trypanosoma brucei. J Vis Exp 2024:10.3791/66279. [PMID: 38314910 PMCID: PMC10879817 DOI: 10.3791/66279] [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] [Indexed: 02/07/2024] Open
Abstract
Glucose metabolism is critical for the African trypanosome, Trypanosoma brucei, as an essential metabolic process and regulator of parasite development. Little is known about the cellular responses generated when environmental glucose levels change. In both bloodstream and procyclic form (insect stage) parasites, glycosomes house most of glycolysis. These organelles are rapidly acidified in response to glucose deprivation, which likely results in the allosteric regulation of glycolytic enzymes such as hexokinase. In previous work, localizing the chemical probe used to make pH measurements was challenging, limiting its utility in other applications. This paper describes the development and use of parasites that express glycosomally localized pHluorin2, a heritable protein pH biosensor. pHluorin2 is a ratiometric pHluorin variant that displays a pH (acid)-dependent decrease in excitation at 395 nm while simultaneously yielding an increase in excitation at 475 nm. Transgenic parasites were generated by cloning the pHluorin2 open reading frame into the trypanosome expression vector pLEW100v5, enabling inducible protein expression in either lifecycle stage. Immunofluorescence was used to confirm the glycosomal localization of the pHluorin2 biosensor, comparing the localization of the biosensor to the glycosomal resident protein aldolase. The sensor responsiveness was calibrated at differing pH levels by incubating cells in a series of buffers that ranged in pH from 4 to 8, an approach we have previously used to calibrate a fluorescein-based pH sensor. We then measured pHluorin2 fluorescence at 405 nm and 488 nm using flow cytometry to determine glycosomal pH. We validated the performance of the live transgenic pHluorin2-expressing parasites, monitoring pH over time in response to glucose deprivation, a known trigger of glycosomal acidification in PF parasites. This tool has a range of potential applications, including potentially being used in high-throughput drug screening. Beyond glycosomal pH, the sensor could be adapted to other organelles or used in other trypanosomatids to understand pH dynamics in the live cell setting.
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Affiliation(s)
- Daniel Call
- Department Chemistry and Biochemistry, Brigham Young University
| | - Sabrina S Pizarro
- Eukaryotic Pathogens Innovation Center, Clemson University; Department of Genetics and Biochemistry, Clemson University
| | - Erica Tovey
- Department Chemistry and Biochemistry, Brigham Young University
| | - Emily Knight
- Eukaryotic Pathogens Innovation Center, Clemson University; Department of Genetics and Biochemistry, Clemson University
| | - Carrie Baumgardner
- Eukaryotic Pathogens Innovation Center, Clemson University; Department of Physics and Astronomy, Clemson University
| | | | - James C Morris
- Eukaryotic Pathogens Innovation Center, Clemson University;
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Gao Y, Skowyra ML, Feng P, Rapoport TA. Protein import into peroxisomes occurs through a nuclear pore-like phase. Science 2022; 378:eadf3971. [PMID: 36520918 PMCID: PMC9795577 DOI: 10.1126/science.adf3971] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peroxisomes are ubiquitous organelles whose dysfunction causes fatal human diseases. Most peroxisomal proteins are imported from the cytosol in a folded state by the soluble receptor PEX5. How folded cargo crosses the membrane is unknown. Here, we show that peroxisomal import is similar to nuclear transport. The peroxisomal membrane protein PEX13 contains a conserved tyrosine (Y)- and glycine (G)-rich YG domain, which forms a selective phase resembling that formed by phenylalanine-glycine (FG) repeats within nuclear pores. PEX13 resides in the membrane in two orientations that oligomerize and suspend the YG meshwork within the lipid bilayer. Purified YG domains form hydrogels into which PEX5 selectively partitions, by using conserved aromatic amino acid motifs, bringing cargo along. The YG meshwork thus forms an aqueous conduit through which PEX5 delivers folded proteins into peroxisomes.
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Affiliation(s)
- Yuan Gao
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael L. Skowyra
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Peiqiang Feng
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tom A. Rapoport
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA.,Corresponding author.
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Andrade-Alviárez D, Bonive-Boscan AD, Cáceres AJ, Quiñones W, Gualdrón-López M, Ginger ML, Michels PAM. Delineating transitions during the evolution of specialised peroxisomes: Glycosome formation in kinetoplastid and diplonemid protists. Front Cell Dev Biol 2022; 10:979269. [PMID: 36172271 PMCID: PMC9512073 DOI: 10.3389/fcell.2022.979269] [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: 06/27/2022] [Accepted: 08/17/2022] [Indexed: 12/01/2022] Open
Abstract
One peculiarity of protists belonging to classes Kinetoplastea and Diplonemea within the phylum Euglenozoa is compartmentalisation of most glycolytic enzymes within peroxisomes that are hence called glycosomes. This pathway is not sequestered in peroxisomes of the third Euglenozoan class, Euglenida. Previous analysis of well-studied kinetoplastids, the ‘TriTryps’ parasites Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp., identified within glycosomes other metabolic processes usually not present in peroxisomes. In addition, trypanosomatid peroxins, i.e. proteins involved in biogenesis of these organelles, are divergent from human and yeast orthologues. In recent years, genomes, transcriptomes and proteomes for a variety of euglenozoans have become available. Here, we track the possible evolution of glycosomes by querying these databases, as well as the genome of Naegleria gruberi, a non-euglenozoan, which belongs to the same protist supergroup Discoba. We searched for orthologues of TriTryps proteins involved in glycosomal metabolism and biogenesis. Predicted cellular location(s) of each metabolic enzyme identified was inferred from presence or absence of peroxisomal-targeting signals. Combined with a survey of relevant literature, we refine extensively our previously postulated hypothesis about glycosome evolution. The data agree glycolysis was compartmentalised in a common ancestor of the kinetoplastids and diplonemids, yet additionally indicates most other processes found in glycosomes of extant trypanosomatids, but not in peroxisomes of other eukaryotes were either sequestered in this ancestor or shortly after separation of the two lineages. In contrast, peroxin divergence is evident in all euglenozoans. Following their gain of pathway complexity, subsequent evolution of peroxisome/glycosome function is complex. We hypothesize compartmentalisation in glycosomes of glycolytic enzymes, their cofactors and subsequently other metabolic enzymes provided selective advantage to kinetoplastids and diplonemids during their evolution in changing marine environments. We contend two specific properties derived from the ancestral peroxisomes were key: existence of nonselective pores for small solutes and the possibility of high turnover by pexophagy. Critically, such pores and pexophagy are characterised in extant trypanosomatids. Increasing amenability of free-living kinetoplastids and recently isolated diplonemids to experimental study means our hypothesis and interpretation of bioinformatic data are suited to experimental interrogation.
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Affiliation(s)
- Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Alejandro D. Bonive-Boscan
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Ana J. Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | | | - Michael L. Ginger
- School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Paul A. M. Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Paul A. M. Michels,
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Godar S, Oristian J, Hinsch V, Wentworth K, Lopez E, Amlashi P, Enverso G, Markley S, Alper JD. Light chain 2 is a Tctex-type related axonemal dynein light chain that regulates directional ciliary motility in Trypanosoma brucei. PLoS Pathog 2022; 18:e1009984. [PMID: 36155669 PMCID: PMC9536576 DOI: 10.1371/journal.ppat.1009984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/06/2022] [Accepted: 08/26/2022] [Indexed: 01/04/2023] Open
Abstract
Flagellar motility is essential for the cell morphology, viability, and virulence of pathogenic kinetoplastids. Trypanosoma brucei flagella beat with a bending wave that propagates from the flagellum's tip to its base, rather than base-to-tip as in other eukaryotes. Thousands of dynein motor proteins coordinate their activity to drive ciliary bending wave propagation. Dynein-associated light and intermediate chains regulate the biophysical mechanisms of axonemal dynein. Tctex-type outer arm dynein light chain 2 (LC2) regulates flagellar bending wave propagation direction, amplitude, and frequency in Chlamydomonas reinhardtii. However, the role of Tctex-type light chains in regulating T. brucei motility is unknown. Here, we used a combination of bioinformatics, in-situ molecular tagging, and immunofluorescence microscopy to identify a Tctex-type light chain in the procyclic form of T. brucei (TbLC2). We knocked down TbLC2 expression using RNAi in both wild-type and FLAM3, a flagellar attachment zone protein, knockdown cells and quantified TbLC2's effects on trypanosome cell biology and biophysics. We found that TbLC2 knockdown reduced the directional persistence of trypanosome cell swimming, induced an asymmetric ciliary bending waveform, modulated the bias between the base-to-tip and tip-to-base beating modes, and increased the beating frequency. Together, our findings are consistent with a model of TbLC2 as a down-regulator of axonemal dynein activity that stabilizes the forward tip-to-base beating ciliary waveform characteristic of trypanosome cells. Our work sheds light on axonemal dynein regulation mechanisms that contribute to pathogenic kinetoplastids' unique tip-to-base ciliary beating nature and how those mechanisms underlie dynein-driven ciliary motility more generally.
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Affiliation(s)
- Subash Godar
- Department of Physics and Astronomy, College of Science, Clemson University, Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - James Oristian
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Genetics and Biochemistry, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Valerie Hinsch
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Genetics and Biochemistry, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Katherine Wentworth
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Ethan Lopez
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Genetics and Biochemistry, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Parastoo Amlashi
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Gerald Enverso
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Samantha Markley
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Joshua Daniel Alper
- Department of Physics and Astronomy, College of Science, Clemson University, Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
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Michels PAM, Gualdrón-López M. Biogenesis and metabolic homeostasis of trypanosomatid glycosomes: new insights and new questions. J Eukaryot Microbiol 2022; 69:e12897. [PMID: 35175680 DOI: 10.1111/jeu.12897] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
Kinetoplastea and Diplonemea possess peroxisome-related organelles that, uniquely, contain most of the enzymes of the glycolytic pathway and are hence called glycosomes. Enzymes of several other core metabolic pathways have also been located in glycosomes, in addition to some characteristic peroxisomal systems such as pathways of lipid metabolism. A considerable amount of research has been performed on glycosomes of trypanosomes since their discovery four decades ago. Not only the role of the glycosomal enzyme systems in the overall cell metabolism appeared to be unique, but the organelles display also remarkable features regarding their biogenesis and structural properties. These features are similar to those of the well-studied peroxisomes of mammalian and plant cells and yeasts yet exhibit also differences reflecting the large evolutionary distance between these protists and the representatives of other major eukaryotic lineages. Despite all research performed, many questions remain about various properties and the biological roles of glycosomes and peroxisomes. Here we review the current knowledge about glycosomes, often comparing it with information about peroxisomes. Furthermore, we highlight particularly many questions that remain about the biogenesis, and the heterogeneity in structure and content of these enigmatic organelles, and the properties of their boundary membrane.
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Affiliation(s)
- Paul A M Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Melisa Gualdrón-López
- Instituto Salud Global, Hospital Clinic-Universitat de Barcelona, and Institute for Health Sciences Trias i Pujol, Barcelona, Spain
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Glycosome heterogeneity in kinetoplastids. Biochem Soc Trans 2021; 49:29-39. [PMID: 33439256 PMCID: PMC7925000 DOI: 10.1042/bst20190517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/18/2020] [Accepted: 11/26/2020] [Indexed: 01/05/2023]
Abstract
Kinetoplastid parasites have essential organelles called glycosomes that are analogous to peroxisomes present in other eukaryotes. While many of the processes that regulate glycosomes are conserved, there are several unique aspects of their biology that are divergent from other systems and may be leveraged as therapeutic targets for the treatment of kinetoplastid diseases. Glycosomes are heterogeneous organelles that likely exist as sub-populations with different protein composition and function in a given cell, between individual cells, and between species. However, the limitations posed by the small size of these organelles makes the study of this heterogeneity difficult. Recent advances in the analysis of small vesicles by flow-cytometry provide an opportunity to overcome these limitations. In this review, we describe studies that document the diverse nature of glycosomes and propose an approach to using flow cytometry and organelle sorting to study the diverse composition and function of these organelles. Because the cellular machinery that regulates glycosome protein import and biogenesis is likely to contribute, at least in part, to glycosome heterogeneity we highlight some ways in which the glycosome protein import machinery differs from that of peroxisomes in other eukaryotes.
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Host and Bacterial Glycolysis during Chlamydia trachomatis Infection. Infect Immun 2020; 88:IAI.00545-20. [PMID: 32900818 DOI: 10.1128/iai.00545-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022] Open
Abstract
The obligate intracellular pathogen Chlamydia trachomatis is the leading cause of noncongenital blindness and causative agent of the most common sexually transmitted infection of bacterial origin. With a reduced genome, C. trachomatis is dependent on its host for survival, in part due to a need for the host cell to compensate for incomplete bacterial metabolic pathways. However, relatively little is known regarding how C. trachomatis is able to hijack host cell metabolism. In this study, we show that two host glycolytic enzymes, aldolase A and pyruvate kinase, as well as lactate dehydrogenase, are enriched at the C. trachomatis inclusion membrane during infection. Inclusion localization was not species specific, since a similar phenotype was observed with C. muridarum Time course experiments showed that the number of positive inclusions increased throughout the developmental cycle. In addition, these host enzymes colocalized to the same inclusion, and their localization did not appear to be dependent on sustained bacterial protein synthesis or on intact host actin, vesicular trafficking, or microtubules. Depletion of the host glycolytic enzyme aldolase A resulted in decreased inclusion size and infectious progeny production, indicating a role for host glycolysis in bacterial growth. Finally, quantitative PCR analysis showed that expression of C. trachomatis glycolytic enzymes inversely correlated with host enzyme localization at the inclusion. We discuss potential mechanisms leading to inclusion localization of host glycolytic enzymes and how it could benefit the bacteria. Altogether, our findings provide further insight into the intricate relationship between host and bacterial metabolism during Chlamydia infection.
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