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Huang Q, Hu W, Meng X, Chen J, Pan G. Nosema bombycis: A remarkable unicellular parasite infecting insects. J Eukaryot Microbiol 2024:e13045. [PMID: 39095558 DOI: 10.1111/jeu.13045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 08/04/2024]
Abstract
Microsporidia are opportunistic fungal-like pathogens that cause microsporidiosis, which results in significant economic losses and threatens public health. Infection of domesticated silkworms by the microsporidium Nosema bombycis causes pébrine disease, for which this species of microsporidia has received much attention. Research has been conducted extensively on this microsporidium over the past few decades to better understand its infection, transmission, host-parasite interaction, and detection. Several tools exist to study this species including the complete genome sequence of N. bombycis. In addition to the understanding of N. bombycis being important for the silkworm industry, this species has become a model organism for studying microsporidia. Research on biology of N. bombycis will contribute to the development of knowledge regarding microsporidia and potential antimicrosporidia drugs. Furthermore, this will provide insight into the molecular evolution and functioning of other fungal pathogens.
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Affiliation(s)
- Qingyuan Huang
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Wanying Hu
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Xianzhi Meng
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jie Chen
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
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Berasategui A, Salem H, Moller AG, Christopher Y, Vidaurre Montoya Q, Conn C, Read TD, Rodrigues A, Ziemert N, Gerardo N. Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants. mSystems 2024; 9:e0057624. [PMID: 38904377 PMCID: PMC11265373 DOI: 10.1128/msystems.00576-24] [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: 04/24/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of Escovopsis and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative Escovopsis strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated Sordariomycetes, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in Escovopsis and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.IMPORTANCEMicrobial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of Escovopsis species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts' potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.
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Affiliation(s)
- Aileen Berasategui
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Cluster of Excellence-Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen, Germany
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hassan Salem
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen, Germany
| | - Abraham G. Moller
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yuliana Christopher
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Panamá City, Panama
| | - Quimi Vidaurre Montoya
- Department of General and Applied Biology, São Paulo State University (UNESP), Institute of Biosciences, Rio Claro, São Paulo, Brazil
| | - Caitlin Conn
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Department of Biology, Berry College, Mount Berry, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Institute of Biosciences, Rio Claro, São Paulo, Brazil
| | - Nadine Ziemert
- Cluster of Excellence-Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Nicole Gerardo
- Department of Biology, Emory University, Atlanta, Georgia, USA
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Usmani M, Coudray N, Riggi M, Raghu R, Ramchandani H, Bobe D, Kopylov M, Zhong ED, Iwasa JH, Ekiert DC, Bhabha G. Cryo-ET reveals the in situ architecture of the polar tube invasion apparatus from microsporidian parasites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603322. [PMID: 39026755 PMCID: PMC11257570 DOI: 10.1101/2024.07.13.603322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Microsporidia are divergent fungal pathogens that employ a harpoon-like apparatus called the polar tube (PT) to invade host cells. The PT architecture and its association with neighboring organelles remain poorly understood. Here, we use cryo-electron tomography to investigate the structural cell biology of the PT in dormant spores from the human-infecting microsporidian species, Encephalitozoon intestinalis . Segmentation and subtomogram averaging of the PT reveal at least four layers: two protein-based layers surrounded by a membrane, and filled with a dense core. Regularly spaced protein filaments form the structural skeleton of the PT. Combining cryo-electron tomography with cellular modeling, we propose a model for the 3-dimensional organization of the polaroplast, an organelle that is continuous with the membrane layer that envelops the PT. Our results reveal the ultrastructure of the microsporidian invasion apparatus in situ , laying the foundation for understanding infection mechanisms.
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Olthof AM, Schwoerer CF, Girardini KN, Weber AL, Doggett K, Mieruszynski S, Heath JK, Moore TE, Biran J, Kanadia RN. Taxonomy of introns and the evolution of minor introns. Nucleic Acids Res 2024:gkae550. [PMID: 38943346 DOI: 10.1093/nar/gkae550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
Classification of introns, which is crucial to understanding their evolution and splicing, has historically been binary and has resulted in the naming of major and minor introns that are spliced by their namesake spliceosome. However, a broad range of intron consensus sequences exist, leading us to here reclassify introns as minor, minor-like, hybrid, major-like, major and non-canonical introns in 263 species across six eukaryotic supergroups. Through intron orthology analysis, we discovered that minor-like introns are a transitory node for intron conversion across evolution. Despite close resemblance of their consensus sequences to minor introns, these introns possess an AG dinucleotide at the -1 and -2 position of the 5' splice site, a salient feature of major introns. Through combined analysis of CoLa-seq, CLIP-seq for major and minor spliceosome components, and RNAseq from samples in which the minor spliceosome is inhibited we found that minor-like introns are also an intermediate class from a splicing mechanism perspective. Importantly, this analysis has provided insight into the sequence elements that have evolved to make minor-like introns amenable to recognition by both minor and major spliceosome components. We hope that this revised intron classification provides a new framework to study intron evolution and splicing.
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Affiliation(s)
- Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Charles F Schwoerer
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Kaitlin N Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Audrey L Weber
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Karen Doggett
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Stephen Mieruszynski
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Joan K Heath
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Timothy E Moore
- Statistical Consulting Services, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT, USA
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon, Israel
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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Peyretaillade E, Akossi RF, Tournayre J, Delbac F, Wawrzyniak I. How to overcome constraints imposed by microsporidian genome features to ensure gene prediction? J Eukaryot Microbiol 2024:e13038. [PMID: 38934348 DOI: 10.1111/jeu.13038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
Since the advent of sequencing techniques and due to their continuous evolution, it has become easier and less expensive to obtain the complete genome sequence of any organism. Nevertheless, to elucidate all biological processes governing organism development, quality annotation is essential. In genome annotation, predicting gene structure is one of the most important and captivating challenges for computational biology. This aspect of annotation requires continual optimization, particularly for genomes as unusual as those of microsporidia. Indeed, this group of fungal-related parasites exhibits specific features (highly reduced gene sizes, sequences with high rate of evolution) linked to their evolution as intracellular parasites, requiring the implementation of specific annotation approaches to consider all these features. This review aimed to outline these characteristics and to assess the increasingly efficient approaches and tools that have enhanced the accuracy of gene prediction for microsporidia, both in terms of sensitivity and specificity. Subsequently, a final part will be dedicated to postgenomic approaches aimed at reinforcing the annotation data generated by prediction software. These approaches include the characterization of other understudied genes, such as those encoding regulatory noncoding RNAs or very small proteins, which also play crucial roles in the life cycle of these microorganisms.
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Affiliation(s)
| | - Reginal F Akossi
- LMGE, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jérémy Tournayre
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, Saint-Genès-Champanelle, France
| | - Frédéric Delbac
- LMGE, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ivan Wawrzyniak
- LMGE, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
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Fang W, Zhou L, Deng B, Guo B, Chen X, Chen P, Lu C, Dong Z, Pan M. Establishment of a Secretory Protein-Inducible CRISPR/Cas9 System for Nosema bombycis in Insect Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:13175-13185. [PMID: 38817125 DOI: 10.1021/acs.jafc.3c08647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Gene editing techniques are widely and effectively used for the control of pathogens, but it is difficult to directly edit the genes of Microsporidia due to its unique spore wall structure. Innovative technologies and methods are urgently needed to break through this limitation of microsporidia therapies. Here, we establish a microsporidia-inducible gene editing system through core components of microsporidia secreted proteins, which could edit target genes after infection with microsporidia. We identified that Nosema bombycis NB29 is a secretory protein and found to interact with itself. The NB29-N3, which lacked the nuclear localization signal, was localized in the cytoplasm, and could be tracked into the nucleus after interacting with NB29-B. Furthermore, the gene editing system was constructed with the Cas9 protein expressed in fusion with the NB29-N3. The system could edit the exogenous gene EGFP and the endogenous gene BmRpn3 after overexpression of NB29 or infection with N. bombycis.
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Affiliation(s)
- Wenxuan Fang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
| | - Liang Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Boyuan Deng
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
| | - Binyu Guo
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
| | - Xue Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
| | - Peng Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Cheng Lu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400716, China
| | - Zhanqi Dong
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400716, China
| | - Minhui Pan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400716, China
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Khalaf A, Francis O, Blaxter ML. Genome evolution in intracellular parasites: Microsporidia and Apicomplexa. J Eukaryot Microbiol 2024:e13033. [PMID: 38785208 DOI: 10.1111/jeu.13033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/29/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Microsporidia and Apicomplexa are eukaryotic, single-celled, intracellular parasites with huge public health and economic importance. Typically, these parasites are studied separately, emphasizing their uniqueness and diversity. In this review, we explore the huge amount of genomic data that has recently become available for the two groups. We compare and contrast their genome evolution and discuss how their transitions to intracellular life may have shaped it. In particular, we explore genome reduction and compaction, genome expansion and ploidy, gene shuffling and rearrangements, and the evolution of centromeres and telomeres.
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Affiliation(s)
- Amjad Khalaf
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Ore Francis
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
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Hiltunen Thorén M, Onuț-Brännström I, Alfjorden A, Pecková H, Swords F, Hooper C, Holzer AS, Bass D, Burki F. Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria. BMC Biol 2024; 22:103. [PMID: 38702750 PMCID: PMC11069148 DOI: 10.1186/s12915-024-01898-x] [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: 12/21/2023] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea. RESULTS Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12-36 Mb) and gene-sparse (~ 2300-5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70-90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group. CONCLUSIONS We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.
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Affiliation(s)
- Markus Hiltunen Thorén
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden.
- Present Address: Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius V. 20 A, Stockholm, SE-114 18, Sweden.
- Present Address: The Royal Swedish Academy of Sciences, Stockholm, SE-114 18, Sweden.
| | - Ioana Onuț-Brännström
- Present Address: Department of Ecology and Genetics, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden
- Present Address: Natural History Museum, Oslo University, Oslo, 0562, Norway
| | - Anders Alfjorden
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden
| | - Hana Pecková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, 370 05, Czech Republic
| | - Fiona Swords
- Marine Institute, Rinville, Oranmore, H91R673, Ireland
| | - Chantelle Hooper
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK
- Sustainable Aquaculture Futures, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Astrid S Holzer
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, 370 05, Czech Republic
- Division of Fish Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna, 1210, Austria
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK
- Sustainable Aquaculture Futures, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Natural History Museum (NHM), Science, London, SW7 5BD, UK
| | - Fabien Burki
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden.
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Perveen S, Yazdi AK, Hajian T, Li F, Vedadi M. Kinetic characterization of human mRNA guanine-N7 methyltransferase. Sci Rep 2024; 14:4509. [PMID: 38402266 PMCID: PMC10894281 DOI: 10.1038/s41598-024-55184-5] [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: 01/01/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024] Open
Abstract
The 5'-mRNA-cap formation is a conserved process in protection of mRNA in eukaryotic cells, resulting in mRNA stability and efficient translation. In humans, two methyltransferases, RNA cap guanine-N7 methyltransferase (hRNMT) and cap-specific nucleoside-2'-O-methyltransferase 1 (hCMTr1) methylate the mRNA resulting in cap0 (N7mGpppN-RNA) and cap1 (N7mGpppN2'-Om-RNA) formation, respectively. Coronaviruses mimic this process by capping their RNA to evade human immune systems. The coronaviral nonstructural proteins, nsp14 and nsp10-nsp16, catalyze the same reactions as hRNMT and hCMTr1, respectively. These two viral enzymes are important targets for development of inhibitor-based antiviral therapeutics. However, assessing the selectivity of such inhibitors against human corresponding proteins is crucial. Human RNMTs have been implicated in proliferation of cancer cells and are also potential targets for development of anticancer therapeutics. Here, we report the development and optimization of a radiometric assay for hRNMT, full kinetic characterization of its activity, and optimization of the assay for high-throughput screening with a Z-factor of 0.79. This enables selectivity determination for a large number of hits from various screening of coronaviral methyltransferases, and also screening hRNMT for discovery of inhibitors and chemical probes that potentially could be used to further investigate the roles RNMTs play in cancers.
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Affiliation(s)
- Sumera Perveen
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Taraneh Hajian
- Ontario Institute for Cancer Research, 661 University Ave, Toronto, ON, M5G 0A3, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Masoud Vedadi
- Ontario Institute for Cancer Research, 661 University Ave, Toronto, ON, M5G 0A3, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.
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10
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Lv Q, Hong L, Qi L, Chen Y, Xie Z, Liao H, Li C, Li T, Meng X, Chen J, Bao J, Wei J, Han B, Shen Q, Weiss LM, Zhou Z, Long M, Pan G. Microsporidia dressing up: the spore polaroplast transport through the polar tube and transformation into the sporoplasm membrane. mBio 2024; 15:e0274923. [PMID: 38193684 PMCID: PMC10865828 DOI: 10.1128/mbio.02749-23] [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: 10/11/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024] Open
Abstract
Microsporidia are obligate intracellular parasites that infect a wide variety of hosts including humans. Microsporidian spores possess a unique, highly specialized invasion apparatus involving the polar filament, polaroplast, and posterior vacuole. During spore germination, the polar filament is discharged out of the spore forming a hollow polar tube that transports the sporoplasm components including the nucleus into the host cell. Due to the complicated topological changes occurring in this process, the details of sporoplasm formation are not clear. Our data suggest that the limiting membrane of the nascent sporoplasm is formed by the polaroplast after microsporidian germination. Using electron microscopy and 1,1'-dioctadecyl-3,3,3',3' tetramethyl indocarbocyanine perchlorate staining, we describe that a large number of vesicles, nucleus, and other cytoplasm contents were transported out via the polar tube during spore germination, while the posterior vacuole and plasma membrane finally remained in the empty spore coat. Two Nosema bombycis sporoplasm surface proteins (NbTMP1 and NoboABCG1.1) were also found to localize in the region of the polaroplast and posterior vacuole in mature spores and in the discharged polar tube, which suggested that the polaroplast during transport through the polar tube became the limiting membrane of the sporoplasm. The analysis results of Golgi-tracker green and Golgi marker protein syntaxin 6 were also consistent with the model of the transported polaroplast derived from Golgi transformed into the nascent sporoplasm membrane.IMPORTANCEMicrosporidia, which are obligate intracellular pathogenic organisms, cause huge economic losses in agriculture and even threaten human health. The key to successful infection by the microsporidia is their unique invasion apparatus which includes the polar filament, polaroplast, and posterior vacuole. When the mature spore is activated to geminate, the polar filament uncoils and undergoes a rapid transition into the hollow polar tube that transports the sporoplasm components including the microsporidian nucleus into host cells. Details of the structural difference between the polar filament and polar tube, the process of cargo transport in extruded polar tube, and the formation of the sporoplasm membrane are still poorly understood. Herein, we verify that the polar filament evaginates to form the polar tube, which serves as a conduit for transporting the nucleus and other sporoplasm components. Furthermore, our results indicate that the transported polaroplast transforms into the sporoplasm membrane during spore germination. Our study provides new insights into the cargo transportation process of the polar tube and origin of the sporoplasm membrane, which provide important clarification of the microsporidian infection mechanism.
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Affiliation(s)
- Qing Lv
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Liuyi Hong
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Lei Qi
- Biomedical Research Center for Structural Analysis, Shandong University, Jinan, Shandong, China
| | - Yuqing Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Zhengkai Xie
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Hongjie Liao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Chunfeng Li
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Tian Li
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Xianzhi Meng
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Jie Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Jialing Bao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Junhong Wei
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Bing Han
- Department of Pathogenic Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, China
| | - Qingtao Shen
- School of Life Science, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Louis M. Weiss
- Department of Pathology, Albert Einstein College of Medicine, New York, USA
| | - Zeyang Zhou
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Mengxian Long
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
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11
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Khalaf A, Lawniczak MKN, Blaxter ML, Jaron KS. Polyploidy is widespread in Microsporidia. Microbiol Spectr 2024; 12:e0366923. [PMID: 38214524 PMCID: PMC10845963 DOI: 10.1128/spectrum.03669-23] [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: 10/13/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024] Open
Abstract
Microsporidia are obligate intracellular eukaryotic parasites with an extremely broad host range. They have both economic and public health importance. Ploidy in microsporidia is variable, with a few species formally identified as diploid and one as polyploid. Given the increase in the number of studies sequencing microsporidian genomes, it is now possible to assess ploidy levels across all currently explored microsporidian diversity. We estimate ploidy for all microsporidian data sets available on the Sequence Read Archive using k-mer-based analyses, indicating that polyploidy is widespread in Microsporidia and that ploidy change is dynamic in the group. Using genome-wide heterozygosity estimates, we also show that polyploid microsporidian genomes are relatively homozygous, and we discuss the implications of these findings on the timing of polyploidization events and their origin.IMPORTANCEMicrosporidia are single-celled intracellular parasites, distantly related to fungi, that can infect a broad range of hosts, from humans all the way to protozoans. Exploiting the wealth of microsporidian genomic data available, we use k-mer-based analyses to assess ploidy status across the group. Understanding a genome's ploidy is crucial in order to assemble it effectively and may also be relevant for better understanding a parasite's behavior and life cycle. We show that tetraploidy is present in at least six species in Microsporidia and that these polyploidization events are likely to have occurred independently. We discuss why these findings may be paradoxical, given that Microsporidia, like other intracellular parasites, have extremely small, reduced genomes.
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Affiliation(s)
- Amjad Khalaf
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Mark L. Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Kamil S. Jaron
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
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12
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Sharma H, Jespersen N, Ehrenbolger K, Carlson LA, Barandun J. Ultrastructural insights into the microsporidian infection apparatus reveal the kinetics and morphological transitions of polar tube and cargo during host cell invasion. PLoS Biol 2024; 22:e3002533. [PMID: 38422169 DOI: 10.1371/journal.pbio.3002533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 03/12/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
During host cell invasion, microsporidian spores translocate their entire cytoplasmic content through a thin, hollow superstructure known as the polar tube. To achieve this, the polar tube transitions from a compact spring-like state inside the environmental spore to a long needle-like tube capable of long-range sporoplasm delivery. The unique mechanical properties of the building blocks of the polar tube allow for an explosive transition from compact to extended state and support the rapid cargo translocation process. The molecular and structural factors enabling this ultrafast process and the structural changes during cargo delivery are unknown. Here, we employ light microscopy and in situ cryo-electron tomography to visualize multiple ultrastructural states of the Vairimorpha necatrix polar tube, allowing us to evaluate the kinetics of its germination and characterize the underlying morphological transitions. We describe a cargo-filled state with a unique ordered arrangement of microsporidian ribosomes, which cluster along the thin tube wall, and an empty post-translocation state with a reduced diameter but a thicker wall. Together with a proteomic analysis of endogenously affinity-purified polar tubes, our work provides comprehensive data on the infection apparatus of microsporidia and uncovers new aspects of ribosome regulation and transport.
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Affiliation(s)
- Himanshu Sharma
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
- Department of Medical Biochemistry and Biophysics, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Wallenberg Centre for Molecular Medicine, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Nathan Jespersen
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Kai Ehrenbolger
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
- Department of Medical Biochemistry and Biophysics, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Wallenberg Centre for Molecular Medicine, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Wallenberg Centre for Molecular Medicine, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
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13
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Ast T, Itoh Y, Sadre S, McCoy JG, Namkoong G, Wengrod JC, Chicherin I, Joshi PR, Kamenski P, Suess DLM, Amunts A, Mootha VK. METTL17 is an Fe-S cluster checkpoint for mitochondrial translation. Mol Cell 2024; 84:359-374.e8. [PMID: 38199006 PMCID: PMC11046306 DOI: 10.1016/j.molcel.2023.12.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 08/13/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular pathogenesis of FA, we performed quantitative proteomics in FXN-deficient human cells. Nearly every annotated Fe-S cluster-containing protein was depleted, indicating that as a rule, cluster binding confers stability to Fe-S proteins. We also observed depletion of a small mitoribosomal assembly factor METTL17 and evidence of impaired mitochondrial translation. Using comparative sequence analysis, mutagenesis, biochemistry, and cryoelectron microscopy, we show that METTL17 binds to the mitoribosomal small subunit during late assembly and harbors a previously unrecognized [Fe4S4]2+ cluster required for its stability. METTL17 overexpression rescued the mitochondrial translation and bioenergetic defects, but not the cellular growth, of FXN-depleted cells. These findings suggest that METTL17 acts as an Fe-S cluster checkpoint, promoting translation of Fe-S cluster-rich oxidative phosphorylation (OXPHOS) proteins only when Fe-S cofactors are replete.
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Affiliation(s)
- Tslil Ast
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Shayan Sadre
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason G McCoy
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gil Namkoong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jordan C Wengrod
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ivan Chicherin
- Department of Biology, M.V.Lomonosov Moscow State University, Moscow 119234, Russia
| | - Pallavi R Joshi
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Piotr Kamenski
- Department of Biology, M.V.Lomonosov Moscow State University, Moscow 119234, Russia
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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14
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Senderskiy IV, Dolgikh VV, Ismatullaeva DA, Mirzakhodjaev BA, Nikitina AP, Pankratov DL. Treatment of Microsporidium Nosema bombycis Spores with the New Antiseptic M250 Helps to Avoid Bacterial and Fungal Contamination of Infected Cultures without Affecting Parasite Polar Tube Extrusion. Microorganisms 2024; 12:154. [PMID: 38257981 PMCID: PMC10819227 DOI: 10.3390/microorganisms12010154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Microsporidia are a group of widespread eukaryotic spore-forming intracellular parasites of great economic and scientific importance. Since microsporidia cannot be cultured outside of a host cell, the search for new antimicrosporidian drugs requires an effective antiseptic to sterilize microsporidian spores to infect cell lines. Here, we show that a new polyhexamethylene guanidine derivative M250, which is active against fungi and bacteria at a concentration of 0.5-1 mg/L, is more than 1000 times less effective against spores of the microsporidium Nosema bombycis, a highly virulent pathogen of the silkworm Bombyx mori (LC50 is 0.173%). Treatment of N. bombycis spores that were isolated non-sterilely from silkworm caterpillars with 0.1% M250 solution does not reduce the rate of spore polar tube extrusion. However, it completely prevents contamination of the Sf-900 III cell culture medium by microorganisms in the presence of antibiotics. The addition of untreated spores to the medium results in contamination, whether antibiotics are present or not. Since 0.1% M250 does not affect spore discharging, this compound may be promising for preventing bacterial and fungal contamination of microsporidia-infected cell cultures.
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Affiliation(s)
- Igor V. Senderskiy
- All-Russian Institute of Plant Protection, Podbelsky Chausse 3, 196608 Saint-Petersburg, Russia;
| | - Viacheslav V. Dolgikh
- All-Russian Institute of Plant Protection, Podbelsky Chausse 3, 196608 Saint-Petersburg, Russia;
| | - Diloram A. Ismatullaeva
- Scientific Research Institute of Sericulture, Ipakchi Str. 1, Tashkent 100069, Uzbekistan; (D.A.I.); (B.A.M.)
| | - Bakhtiyar A. Mirzakhodjaev
- Scientific Research Institute of Sericulture, Ipakchi Str. 1, Tashkent 100069, Uzbekistan; (D.A.I.); (B.A.M.)
| | - Anastasiia P. Nikitina
- Department of Microbiology and Virology, Pavlov First Saint-Petersburg State Medical University, L’vaTolstogo Str. 6-8, 197022 Saint-Petersburg, Russia; (A.P.N.); (D.L.P.)
| | - Danil L. Pankratov
- Department of Microbiology and Virology, Pavlov First Saint-Petersburg State Medical University, L’vaTolstogo Str. 6-8, 197022 Saint-Petersburg, Russia; (A.P.N.); (D.L.P.)
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15
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Tournayre J, Polonais V, Wawrzyniak I, Akossi RF, Parisot N, Lerat E, Delbac F, Souvignet P, Reichstadt M, Peyretaillade E. MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation. Int J Mol Sci 2024; 25:880. [PMID: 38255958 PMCID: PMC10815200 DOI: 10.3390/ijms25020880] [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: 10/27/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
With nearly 1700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help understand the biological functions of these microorganisms, complete genome sequencing is routinely used. Nevertheless, the proper prediction of their gene catalogue is challenging due to their taxon-specific evolutionary features. As innovative genome annotation strategies are needed to obtain a representative snapshot of the overall lifestyle of these parasites, the MicroAnnot tool, a dedicated workflow for microsporidian sequence annotation using data from curated databases of accurately annotated microsporidian genes, has been developed. Furthermore, specific modules have been implemented to perform small gene (<300 bp) and transposable element identification. Finally, functional annotation was performed using the signature-based InterProScan software. MicroAnnot's accuracy has been verified by the re-annotation of four microsporidian genomes for which structural annotation had previously been validated. With its comparative approach and transcriptional signal identification method, MicroAnnot provides an accurate prediction of translation initiation sites, an efficient identification of transposable elements, as well as high specificity and sensitivity for microsporidian genes, including those under 300 bp.
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Affiliation(s)
- Jérémy Tournayre
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (J.T.); (P.S.); (M.R.)
| | - Valérie Polonais
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Ivan Wawrzyniak
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Reginald Florian Akossi
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Nicolas Parisot
- UMR 203, BF2I, INRAE, INSA Lyon, Université de Lyon, 69621 Villeurbanne, France
| | - Emmanuelle Lerat
- VAS, CNRS, UMR5558, LBBE, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France;
| | - Frédéric Delbac
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Pierre Souvignet
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (J.T.); (P.S.); (M.R.)
| | - Matthieu Reichstadt
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (J.T.); (P.S.); (M.R.)
| | - Eric Peyretaillade
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
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16
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Williams TA, Davin AA, Szánthó LL, Stamatakis A, Wahl NA, Woodcroft BJ, Soo RM, Eme L, Sheridan PO, Gubry-Rangin C, Spang A, Hugenholtz P, Szöllősi GJ. Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. THE ISME JOURNAL 2024; 18:wrae129. [PMID: 39001714 PMCID: PMC11293204 DOI: 10.1093/ismejo/wrae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024]
Abstract
In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.
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Affiliation(s)
- Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol BS81TQ, United Kingdom
| | - Adrian A Davin
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 113-0033 Tokyo, Japan
| | - Lénárd L Szánthó
- MTA-ELTE “Lendület” Evolutionary Genomics Research Group, Eötvös University, 1117 Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495 Okinawa, Japan
| | - Alexandros Stamatakis
- Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, 70013 Heraklion, Greece
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Noah A Wahl
- Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, 70013 Heraklion, Greece
| | - Ben J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Rochelle M Soo
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Laura Eme
- Unité d’Ecologie, Systématique et Evolution, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Paul O Sheridan
- School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Cecile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, United Kingdom
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, The Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gergely J Szöllősi
- MTA-ELTE “Lendület” Evolutionary Genomics Research Group, Eötvös University, 1117 Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495 Okinawa, Japan
- Institute of Evolution, HUN REN Centre for Ecological Research, 1121 Budapest, Hungary
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17
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Svedberg D, Winiger RR, Berg A, Sharma H, Tellgren-Roth C, Debrunner-Vossbrinck BA, Vossbrinck CR, Barandun J. Functional annotation of a divergent genome using sequence and structure-based similarity. BMC Genomics 2024; 25:6. [PMID: 38166563 PMCID: PMC10759460 DOI: 10.1186/s12864-023-09924-y] [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: 08/27/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Microsporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence similarity. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes. RESULTS In this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin named ANNOTEX (Annotation Extension for ChimeraX), allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome of Vairimorpha necatrix. First, the 3080 predicted protein-coding DNA sequences, of which 89% were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of the V. necatrix genome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterized Encephalitozoon cuniculi genes. CONCLUSION We provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.
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Affiliation(s)
- Dennis Svedberg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Rahel R Winiger
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
| | - Alexandra Berg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Himanshu Sharma
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Christian Tellgren-Roth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Charles R Vossbrinck
- Department of Environmental Science, Connecticut Agricultural Experiment Station, New Haven, CT, 06504, USA
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden.
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18
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Hacker C, Sendra K, Keisham P, Filipescu T, Lucocq J, Salimi F, Ferguson S, Bhella D, MacNeill SA, Embley M, Lucocq J. Biogenesis, inheritance, and 3D ultrastructure of the microsporidian mitosome. Life Sci Alliance 2024; 7:e202201635. [PMID: 37903625 PMCID: PMC10618108 DOI: 10.26508/lsa.202201635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 11/01/2023] Open
Abstract
During the reductive evolution of obligate intracellular parasites called microsporidia, a tiny remnant mitochondrion (mitosome) lost its typical cristae, organellar genome, and most canonical functions. Here, we combine electron tomography, stereology, immunofluorescence microscopy, and bioinformatics to characterise mechanisms of growth, division, and inheritance of this minimal mitochondrion in two microsporidia species (grown within a mammalian RK13 culture-cell host). Mitosomes of Encephalitozoon cuniculi (2-12/cell) and Trachipleistophora hominis (14-18/nucleus) displayed incremental/non-phasic growth and division and were closely associated with an organelle identified as equivalent to the fungal microtubule-organising centre (microsporidian spindle pole body; mSPB). The mitosome-mSPB association was resistant to treatment with microtubule-depolymerising drugs nocodazole and albendazole. Dynamin inhibitors (dynasore and Mdivi-1) arrested mitosome division but not growth, whereas bioinformatics revealed putative dynamins Drp-1 and Vps-1, of which, Vps-1 rescued mitochondrial constriction in dynamin-deficient yeast (Schizosaccharomyces pombe). Thus, microsporidian mitosomes undergo incremental growth and dynamin-mediated division and are maintained through ordered inheritance, likely mediated via binding to the microsporidian centrosome (mSPB).
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Affiliation(s)
- Christian Hacker
- https://ror.org/02wn5qz54 School of Medicine, University of St Andrews, St Andrews, UK
| | - Kacper Sendra
- Biosciences Institute, The Medical School, Catherine Cookson Building, Newcastle University, Newcastle upon Tyne, UK
| | - Priyanka Keisham
- https://ror.org/02wn5qz54 School of Medicine, University of St Andrews, St Andrews, UK
| | - Teodora Filipescu
- https://ror.org/02wn5qz54 School of Medicine, University of St Andrews, St Andrews, UK
| | - James Lucocq
- Department of Surgery, Dundee Medical School Ninewells Hospital, Dundee, UK
| | - Fatemeh Salimi
- https://ror.org/02wn5qz54 School of Medicine, University of St Andrews, St Andrews, UK
| | - Sophie Ferguson
- https://ror.org/02wn5qz54 School of Medicine, University of St Andrews, St Andrews, UK
| | - David Bhella
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Stuart A MacNeill
- https://ror.org/02wn5qz54 School of Biology, University of St Andrews, St Andrews, UK
| | - Martin Embley
- Biosciences Institute, Centre for Bacterial Cell Biology, Baddiley-Clark Building, Newcastle University, Newcastle upon Tyne, UK
| | - John Lucocq
- https://ror.org/02wn5qz54 School of Medicine, University of St Andrews, St Andrews, UK
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19
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Ma M, Ling M, Huang Q, Xu Y, Yang X, Kyei B, Wang Q, Tang X, Shen Z, Zhang Y, Zhao G. Functional characterization of Nosema bombycis (microsporidia) trehalase 3. Parasitol Res 2023; 123:59. [PMID: 38112902 DOI: 10.1007/s00436-023-08082-0] [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: 09/20/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023]
Abstract
Nosema bombycis, an obligate intracellular parasite, is a single-celled eukaryote known to infect various tissues of silkworms, leading to the manifestation of pebrine. Trehalase, a glycosidase responsible for catalyzing the hydrolysis of trehalose into two glucose molecules, assumes a crucial role in thermal stress tolerance, dehydration, desiccation stress, and asexual development. Despite its recognized importance in these processes, the specific role of trehalase in N. bombycis remains uncertain. This investigation focused on exploring the functions of trehalase 3 in N. bombycis (NbTre3). Immunofluorescence analysis of mature (dormant) spores indicated that NbTre3 primarily localizes to the spore membrane or spore wall, suggesting a potential involvement in spore germination. Reverse transcription-quantitative polymerase chain reaction results indicated that the transcriptional level of NbTre3 peaked at 6 h post N. bombycis infection, potentially contributing to energy storage for proliferation. Throughout the life cycle of N. bombycis within the host cell, NbTre3 was detected in sporoplasm during the proliferative stage rather than the sporulation stage. RNA interference experiments revealed a substantial decrease in the relative transcriptional level of NbTre3, accompanied by a certain reduction in the relative transcriptional level of Nb16S rRNA. These outcomes suggest that NbTre3 may play a role in the proliferation of N. bombycis. The application of the His pull-down technique identified 28 proteins interacting with NbTre3, predominantly originating from the host silkworm. This finding implies that NbTre3 may participate in the metabolism of the host cell, potentially utilizing the host cell's energy resources.
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Affiliation(s)
- Mingzhen Ma
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Min Ling
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Qilong Huang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Yijie Xu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Xu Yang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Bismark Kyei
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Qiang Wang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China
- The Key Laboratory of Genetic Improvement of Silkworm and Mulberry of Agricultural Ministry, Zhenjiang, Jiangsu Province, China
| | - Xudong Tang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China
- The Key Laboratory of Genetic Improvement of Silkworm and Mulberry of Agricultural Ministry, Zhenjiang, Jiangsu Province, China
| | - Zhongyuan Shen
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China
- The Key Laboratory of Genetic Improvement of Silkworm and Mulberry of Agricultural Ministry, Zhenjiang, Jiangsu Province, China
| | - Yiling Zhang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China.
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China.
- The Key Laboratory of Genetic Improvement of Silkworm and Mulberry of Agricultural Ministry, Zhenjiang, Jiangsu Province, China.
| | - Guodong Zhao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China
- The Key Laboratory of Genetic Improvement of Silkworm and Mulberry of Agricultural Ministry, Zhenjiang, Jiangsu Province, China
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20
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Antao NV, Lam C, Davydov A, Riggi M, Sall J, Petzold C, Liang FX, Iwasa JH, Ekiert DC, Bhabha G. 3D reconstructions of parasite development and the intracellular niche of the microsporidian pathogen Encephalitozoon intestinalis. Nat Commun 2023; 14:7662. [PMID: 37996434 PMCID: PMC10667486 DOI: 10.1038/s41467-023-43215-0] [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: 06/30/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023] Open
Abstract
Microsporidia are an early-diverging group of fungal pathogens with a wide host range. Several microsporidian species cause opportunistic infections in humans that can be fatal. As obligate intracellular parasites with highly reduced genomes, microsporidia are dependent on host metabolites for successful replication and development. Our knowledge of microsporidian intracellular development remains rudimentary, and our understanding of the intracellular niche occupied by microsporidia has relied on 2D TEM images and light microscopy. Here, we use serial block-face scanning electron microscopy (SBF-SEM) to capture 3D snapshots of the human-infecting species, Encephalitozoon intestinalis, within host cells. We track E. intestinalis development through its life cycle, which allows us to propose a model for how its infection organelle, the polar tube, is assembled de novo in developing spores. 3D reconstructions of parasite-infected cells provide insights into the physical interactions between host cell organelles and parasitophorous vacuoles, which contain the developing parasites. The host cell mitochondrial network is substantially remodeled during E. intestinalis infection, leading to mitochondrial fragmentation. SBF-SEM analysis shows changes in mitochondrial morphology in infected cells, and live-cell imaging provides insights into mitochondrial dynamics during infection. Our data provide insights into parasite development, polar tube assembly, and microsporidia-induced host mitochondria remodeling.
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Affiliation(s)
- Noelle V Antao
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Cherry Lam
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Ari Davydov
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Margot Riggi
- Department of Biochemistry, University of Utah, Salt Lake City, USA
| | - Joseph Sall
- Office of Science and Research Microscopy Laboratory, New York University School of Medicine, New York, NY, USA
| | - Christopher Petzold
- Office of Science and Research Microscopy Laboratory, New York University School of Medicine, New York, NY, USA
| | - Feng-Xia Liang
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
- Office of Science and Research Microscopy Laboratory, New York University School of Medicine, New York, NY, USA
| | - Janet H Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, USA
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
- Department of Microbiology, New York University School of Medicine, New York, NY, USA.
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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21
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Hidifira AM, Alvares-Saraiva AM, Perez EC, Spadacci-Morena DD, de Araujo RS, Lallo MA. Increased susceptibility to encephalitozoonosis associated with mixed Th1/Th2 profile and M1/M2 profile in mice immunosuppressed with cyclophosphamide. Exp Parasitol 2023; 254:108606. [PMID: 37666408 DOI: 10.1016/j.exppara.2023.108606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Encephalitozoon cuniculi is a unicellular, spore-forming, obligate intracellular eukaryote belonging to the phylum Microsporidia. It is known to infect mainly immunocompromised and immunocompetent mammals, including humans. The parasite-host relationship has been evaluated using both in vitro cell culturing and animal models. For example, Balb/c and C57BL/6 mouse strains have been used interchangeably, although the latter has been considered more susceptible due to the higher fungal load observed after infection. In the present study, we identified the characteristics of the immune response of C57BL/6 mice treated or not with the immunosuppressant cyclophosphamide (Cy) and challenged with E. cuniculi by intraperitoneal route. After 14 days of infection, serum was collected to analyze Th1, Th2, and Th17 cytokine levels. In addition, peritoneal washes were performed, and the spleen sample was collected for immune cell phenotyping, whereas liver, spleen, kidney, lung, intestine, and central nervous system (CNS) samples were collected for histopathological analysis. Although infected mice displayed a reduced absolute number of macrophages, they showed an M1 profile, an elevated number of CD4+T, CD8+T, B-1, and B-2 lymphocytes, with a predominance of Th1 inflammatory cytokines (interferon [IFN]-γ, tumor necrosis factor [TNF]-α, and interleukin [IL]-2) and Th17. Furthermore, Cy-Infected mice showed a reduced absolute number of macrophages with an M1 profile but a reduced number of CD4+T, CD8+T, B-1, and B-2 lymphocytes, with a predominance of Th1 inflammatory cytokines (IFN-γ, TNF-α, and IL-2) and Th2 (IL-4). This group displayed a higher fungal burden as well and developed more severe encephalitozoonosis, which was associated with a reduced number of T and B lymphocytes and a mixed profile of Th1 and Th2 cytokines.
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Affiliation(s)
- Amanda Miyuki Hidifira
- Programa de Patologia Ambiental e Experimental, Universidade Paulista (UNIP), São Paulo, Brazil
| | | | | | | | | | - Maria Anete Lallo
- Programa de Patologia Ambiental e Experimental, Universidade Paulista (UNIP), São Paulo, Brazil.
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22
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Milner DS, Galindo LJ, Irwin NAT, Richards TA. Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes. Annu Rev Microbiol 2023; 77:45-66. [PMID: 36944262 DOI: 10.1146/annurev-micro-032421-115538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.
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Affiliation(s)
- David S Milner
- Department of Biology, University of Oxford, Oxford, United Kingdom;
| | | | - Nicholas A T Irwin
- Department of Biology, University of Oxford, Oxford, United Kingdom;
- Merton College, University of Oxford, Oxford, United Kingdom
| | - Thomas A Richards
- Department of Biology, University of Oxford, Oxford, United Kingdom;
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23
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Wadi L, El Jarkass HT, Tran TD, Islah N, Luallen RJ, Reinke AW. Genomic and phenotypic evolution of nematode-infecting microsporidia. PLoS Pathog 2023; 19:e1011510. [PMID: 37471459 PMCID: PMC10393165 DOI: 10.1371/journal.ppat.1011510] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 06/24/2023] [Indexed: 07/22/2023] Open
Abstract
Microsporidia are a large phylum of intracellular parasites that can infect most types of animals. Species in the Nematocida genus can infect nematodes including Caenorhabditis elegans, which has become an important model to study mechanisms of microsporidia infection. To understand the genomic properties and evolution of nematode-infecting microsporidia, we sequenced the genomes of nine species of microsporidia, including two genera, Enteropsectra and Pancytospora, without any previously sequenced genomes. Core cellular processes, including metabolic pathways, are mostly conserved across genera of nematode-infecting microsporidia. Each species encodes unique proteins belonging to large gene families that are likely used to interact with host cells. Most strikingly, we observed one such family, NemLGF1, is present in both Nematocida and Pancytospora species, but not any other microsporidia. To understand how Nematocida phenotypic traits evolved, we measured the host range, tissue specificity, spore size, and polar tube length of several species in the genus. Our phylogenetic analysis shows that Nematocida is composed of two groups of species with distinct traits and that species with longer polar tubes infect multiple tissues. Together, our work details both genomic and trait evolution between related microsporidia species and provides a useful resource for further understanding microsporidia evolution and infection mechanisms.
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Affiliation(s)
- Lina Wadi
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | | | - Tuan D Tran
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Nizar Islah
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Robert J Luallen
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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24
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Antao NV, Lam C, Davydov A, Riggi M, Sall J, Petzold C, Liang FX, Iwasa J, Ekiert DC, Bhabha G. 3D reconstructions of parasite development and the intracellular niche of the microsporidian pathogen E. intestinalis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.02.547383. [PMID: 37425741 PMCID: PMC10327200 DOI: 10.1101/2023.07.02.547383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Microsporidia are an early-diverging group of fungal pathogens that infect a wide range of hosts. Several microsporidian species infect humans, and infections can lead to fatal disease in immunocompromised individuals. As obligate intracellular parasites with highly reduced genomes, microsporidia are dependent on metabolites from their hosts for successful replication and development. Our knowledge of how microsporidian parasites develop inside the host remains rudimentary, and our understanding of the intracellular niche occupied by microsporidia has thus far relied largely on 2D TEM images and light microscopy. Here, we use serial block face scanning electron microscopy (SBF-SEM) to capture 3D snapshots of the human-infecting microsporidian, Encephalitozoon intestinalis , within host cells. We track the development of E. intestinalis through its life cycle, which allows us to propose a model for how its infection organelle, the polar tube, is assembled de novo in each developing spore. 3D reconstructions of parasite-infected cells provide insights into the physical interactions between host cell organelles and parasitophorous vacuoles, which contain the developing parasites. The host cell mitochondrial network is substantially remodeled during E. intestinalis infection, leading to mitochondrial fragmentation. SBF-SEM analysis shows changes in mitochondrial morphology in infected cells, and live-cell imaging provides insights into mitochondrial dynamics during infection. Together, our data provide insights into parasite development, polar tube assembly, and microsporidia-induced mitochondrial remodeling in the host cell.
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25
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Žárský V, Karnkowska A, Boscaro V, Trznadel M, Whelan TA, Hiltunen-Thorén M, Onut-Brännström I, Abbott CL, Fast NM, Burki F, Keeling PJ. Contrasting outcomes of genome reduction in mikrocytids and microsporidians. BMC Biol 2023; 21:137. [PMID: 37280585 DOI: 10.1186/s12915-023-01635-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Intracellular symbionts often undergo genome reduction, losing both coding and non-coding DNA in a process that ultimately produces small, gene-dense genomes with few genes. Among eukaryotes, an extreme example is found in microsporidians, which are anaerobic, obligate intracellular parasites related to fungi that have the smallest nuclear genomes known (except for the relic nucleomorphs of some secondary plastids). Mikrocytids are superficially similar to microsporidians: they are also small, reduced, obligate parasites; however, as they belong to a very different branch of the tree of eukaryotes, the rhizarians, such similarities must have evolved in parallel. Since little genomic data are available from mikrocytids, we assembled a draft genome of the type species, Mikrocytos mackini, and compared the genomic architecture and content of microsporidians and mikrocytids to identify common characteristics of reduction and possible convergent evolution. RESULTS At the coarsest level, the genome of M. mackini does not exhibit signs of extreme genome reduction; at 49.7 Mbp with 14,372 genes, the assembly is much larger and gene-rich than those of microsporidians. However, much of the genomic sequence and most (8075) of the protein-coding genes code for transposons, and may not contribute much of functional relevance to the parasite. Indeed, the energy and carbon metabolism of M. mackini share several similarities with those of microsporidians. Overall, the predicted proteome involved in cellular functions is quite reduced and gene sequences are extremely divergent. Microsporidians and mikrocytids also share highly reduced spliceosomes that have retained a strikingly similar subset of proteins despite having reduced independently. In contrast, the spliceosomal introns in mikrocytids are very different from those of microsporidians in that they are numerous, conserved in sequence, and constrained to an exceptionally narrow size range (all 16 or 17 nucleotides long) at the shortest extreme of known intron lengths. CONCLUSIONS Nuclear genome reduction has taken place many times and has proceeded along different routes in different lineages. Mikrocytids show a mix of similarities and differences with other extreme cases, including uncoupling the actual size of a genome with its functional reduction.
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Affiliation(s)
- Vojtečh Žárský
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Anna Karnkowska
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, 02-089, Warsaw, Poland
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada.
| | - Morelia Trznadel
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Thomas A Whelan
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Markus Hiltunen-Thorén
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, 752 36, Uppsala, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ioana Onut-Brännström
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, 752 36, Uppsala, Sweden
- Department of Ecology and Genetics, Uppsala University, 752 36, Uppsala, Sweden
- Natural History Museum, University of Oslo, 0562, Oslo, Norway
| | - Cathryn L Abbott
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, V9T 6N7, Canada
| | - Naomi M Fast
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Fabien Burki
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, 752 36, Uppsala, Sweden
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada.
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26
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Thore S, Fribourg S, Mackereth CD. 1H, 15N and 13C resonance assignments of a minimal CPSF73-CPSF100 C-terminal heterodimer. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:43-48. [PMID: 36723825 DOI: 10.1007/s12104-023-10118-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 11/26/2022] [Indexed: 06/02/2023]
Abstract
The initial pre-mRNA transcript in eukaryotes is processed by a large multi-protein complex in order to correctly cleave the 3' end, and to subsequently add the polyadenosine tail. This cleavage and polyadenylation specificity factor (CPSF) is composed of separate subunits, with structural information available for both isolated subunits and also larger assembled complexes. Nevertheless, certain key components of CPSF still lack high-resolution atomic data. One such region is the heterodimer formed between the first and second C-terminal domains of the endonuclease CPSF73, with those from the catalytically inactive CPSF100. Here we report the backbone and sidechain resonance assignments of a minimal C-terminal heterodimer of CPSF73-CPSF100 derived from the parasite Encephalitozoon cuniculi. The assignment process used several amino-acid specific labeling strategies, and the chemical shift values allow for secondary structure prediction.
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Affiliation(s)
- Stéphane Thore
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, F-33000, Bordeaux, France
| | - Sébastien Fribourg
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, F-33000, Bordeaux, France
| | - Cameron D Mackereth
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600, Pessac, France.
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27
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Mascarenhas Dos Santos AC, Julian AT, Liang P, Juárez O, Pombert JF. Telomere-to-Telomere genome assemblies of human-infecting Encephalitozoon species. BMC Genomics 2023; 24:237. [PMID: 37142951 PMCID: PMC10158259 DOI: 10.1186/s12864-023-09331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Microsporidia are diverse spore forming, fungal-related obligate intracellular pathogens infecting a wide range of hosts. This diversity is reflected at the genome level with sizes varying by an order of magnitude, ranging from less than 3 Mb in Encephalitozoon species (the smallest known in eukaryotes) to more than 50 Mb in Edhazardia spp. As a paradigm of genome reduction in eukaryotes, the small Encephalitozoon genomes have attracted much attention with investigations revealing gene dense, repeat- and intron-poor genomes characterized by a thorough pruning of molecular functions no longer relevant to their obligate intracellular lifestyle. However, because no Encephalitozoon genome has been sequenced from telomere-to-telomere and since no methylation data is available for these species, our understanding of their overall genetic and epigenetic architectures is incomplete. METHODS In this study, we sequenced the complete genomes from telomere-to-telomere of three human-infecting Encephalitozoon spp. -E. intestinalis ATCC 50506, E. hellem ATCC 50604 and E. cuniculi ATCC 50602- using short and long read platforms and leveraged the data generated as part of the sequencing process to investigate the presence of epigenetic markers in these genomes. We also used a mixture of sequence- and structure-based computational approaches, including protein structure prediction, to help identify which Encephalitozoon proteins are involved in telomere maintenance, epigenetic regulation, and heterochromatin formation. RESULTS The Encephalitozoon chromosomes were found capped by TTAGG 5-mer telomeric repeats followed by telomere associated repeat elements (TAREs) flanking hypermethylated ribosomal RNA (rRNA) gene loci featuring 5-methylcytosines (5mC) and 5-hemimethylcytosines (5hmC), themselves followed by lesser methylated subtelomeres and hypomethylated chromosome cores. Strong nucleotide biases were identified between the telomeres/subtelomeres and chromosome cores with significant changes in GC/AT, GT/AC and GA/CT contents. The presence of several genes coding for proteins essential to telomere maintenance, epigenetic regulation, and heterochromatin formation was further confirmed in the Encephalitozoon genomes. CONCLUSION Altogether, our results strongly support the subtelomeres as sites of heterochromatin formation in Encephalitozoon genomes and further suggest that these species might shutdown their energy-consuming ribosomal machinery while dormant as spores by silencing of the rRNA genes using both 5mC/5hmC methylation and facultative heterochromatin formation at these loci.
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Affiliation(s)
| | | | - Pingdong Liang
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
| | - Oscar Juárez
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
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28
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Meagher RB, Lewis ZA, Ambati S, Lin X. DectiSomes: C-type lectin receptor-targeted liposomes as pan-antifungal drugs. Adv Drug Deliv Rev 2023; 196:114776. [PMID: 36934519 PMCID: PMC10133202 DOI: 10.1016/j.addr.2023.114776] [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: 01/04/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/19/2023]
Abstract
Combatting the ever-increasing threat from invasive fungal pathogens faces numerous fundamental challenges, including constant human exposure to large reservoirs of species in the environment, the increasing population of immunocompromised or immunosuppressed individuals, the unsatisfactory efficacy of current antifungal drugs and their associated toxicity, and the scientific and economic barriers limiting a new antifungal pipeline. DectiSomes represent a new drug delivery platform that enhances antifungal efficacy for diverse fungal pathogens and reduces host toxicity for current and future antifungals. DectiSomes employ pathogen receptor proteins - C-type lectins - to target drug-loaded liposomes to conserved fungal cognate ligands and away from host cells. DectiSomes represent one leap forward for urgently needed effective pan-antifungal therapy. Herein, we discuss the problems of battling fungal diseases and the state of DectiSome development.
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Affiliation(s)
- Richard B Meagher
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Zachary A Lewis
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Suresh Ambati
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Xiaorong Lin
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
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29
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Wu Y, Yu Y, Sun Q, Yu Y, Chen J, Li T, Meng X, Pan G, Zhou Z. A Putative TRAPα Protein of Microsporidia Nosema bombycis Exhibits Non-Canonical Alternative Polyadenylation in Transcripts. J Fungi (Basel) 2023; 9:jof9040407. [PMID: 37108862 PMCID: PMC10142623 DOI: 10.3390/jof9040407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Microsporidia are obligate intracellular eukaryotic parasites that have significantly reduced genomes and that have lost most of their introns. In the current study, we characterized a gene in microsporidia Nosema bombycis, annotated as TRAPα (HNbTRAPα). The homologous of TRAPα are a functional component of ER translocon and facilitates the initiation of protein translocation in a substrate-specific manner, which is conserved in animals but absent from most fungi. The coding sequence of HNbTRAPα consists of 2226 nucleotides, longer than the majority of homologs in microsporidia. A 3′ RACE analysis indicated that there were two mRNA isoforms resulting from non-canonical alternative polyadenylation (APA), and the polyadenylate tail was synthesized after the C951 or C1167 nucleotide, respectively. Indirect immunofluorescence analysis showed two different localization characteristics of HNbTRAPα, which are mainly located around the nuclear throughout the proliferation stage and co-localized with the nuclear in mature spores. This study demonstrated that the post-transcriptional regulation mechanism exists in Microsporidia and expands the mRNA isoform repertoire.
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Affiliation(s)
- Yujiao Wu
- State Key Laboratory of Resource Insects, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
| | - Ying Yu
- State Key Laboratory of Resource Insects, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
| | - Quan Sun
- State Key Laboratory of Resource Insects, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
| | - Yixiang Yu
- State Key Laboratory of Resource Insects, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
| | - Jie Chen
- State Key Laboratory of Resource Insects, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
| | - Tian Li
- State Key Laboratory of Resource Insects, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
| | - Xianzhi Meng
- State Key Laboratory of Resource Insects, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
- Correspondence: (G.P.); (Z.Z.)
| | - Zeyang Zhou
- State Key Laboratory of Resource Insects, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Beibei, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400715, China
- Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze River (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Chongqing Normal University, Chongqing 400047, China
- Correspondence: (G.P.); (Z.Z.)
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Analysis of Pneumocystis Transcription Factor Evolution and Implications for Biology and Lifestyle. mBio 2023; 14:e0271122. [PMID: 36651897 PMCID: PMC9973273 DOI: 10.1128/mbio.02711-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Pneumocystis jirovecii kills hundreds of thousands of immunocompromised patients each year. Yet many aspects of the biology of this obligate pathogen remain obscure because it is not possible to culture the fungus in vitro independently of its host. Consequently, our understanding of Pneumocystis pathobiology is heavily reliant upon bioinformatic inferences. We have exploited a powerful combination of genomic and phylogenetic approaches to examine the evolution of transcription factors in Pneumocystis species. We selected protein families (Pfam families) that correspond to transcriptional regulators and used bioinformatic approaches to compare these families in the seven Pneumocystis species that have been sequenced to date with those from other yeasts, other human and plant pathogens, and other obligate parasites. Some Pfam families of transcription factors have undergone significant reduction during their evolution in the Pneumocystis genus, and other Pfam families have been lost or appear to be in the process of being lost. Meanwhile, other transcription factor families have been retained in Pneumocystis species, and some even appear to have undergone expansion. On this basis, Pneumocystis species seem to have retained transcriptional regulators that control chromosome maintenance, ribosomal gene regulation, RNA processing and modification, and respiration. Meanwhile, regulators that promote the assimilation of alternative carbon sources, amino acid, lipid, and sterol biosynthesis, and iron sensing and homeostasis appear to have been lost. Our analyses of transcription factor retention, loss, and gain provide important insights into the biology and lifestyle of Pneumocystis. IMPORTANCE Pneumocystis jirovecii is a major fungal pathogen of humans that infects healthy individuals, colonizing the lungs of infants. In immunocompromised and transplant patients, this fungus causes life-threatening pneumonia, and these Pneumocystis infections remain among the most common and serious infections in HIV/AIDS patients. Yet we remain remarkably ignorant about the biology and epidemiology of Pneumocystis due to the inability to culture this fungus in vitro. Our analyses of transcription factor retentions, losses, and gains in sequenced Pneumocystis species provide valuable new views of their specialized biology, suggesting the retention of many metabolic and stress regulators and the loss of others that are essential in free-living fungi. Given the lack of in vitro culture methods for Pneumocystis, this powerful bioinformatic approach has advanced our understanding of the lifestyle of P. jirovecii and the nature of its dependence on the host for survival.
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Structural and Functional Annotation of Hypothetical Proteins from the Microsporidia Species Vittaforma corneae ATCC 50505 Using in silico Approaches. Int J Mol Sci 2023; 24:ijms24043507. [PMID: 36834914 PMCID: PMC9960886 DOI: 10.3390/ijms24043507] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Microsporidia are spore-forming eukaryotes that are related to fungi but have unique traits that set them apart. They have compact genomes as a result of evolutionary gene loss associated with their complete dependency on hosts for survival. Despite having a relatively small number of genes, a disproportionately high percentage of the genes in microsporidia genomes code for proteins whose functions remain unknown (hypothetical proteins-HPs). Computational annotation of HPs has become a more efficient and cost-effective alternative to experimental investigation. This research developed a robust bioinformatics annotation pipeline of HPs from Vittaforma corneae, a clinically important microsporidian that causes ocular infections in immunocompromised individuals. Here, we describe various steps to retrieve sequences and homologs and to carry out physicochemical characterization, protein family classification, identification of motifs and domains, protein-protein interaction network analysis, and homology modelling using a variety of online resources. Classification of protein families produced consistent findings across platforms, demonstrating the accuracy of annotation utilizing in silico methods. A total of 162 out of 2034 HPs were fully annotated, with the bulk of them categorized as binding proteins, enzymes, or regulatory proteins. The protein functions of several HPs from Vittaforma corneae were accurately inferred. This improved our understanding of microsporidian HPs despite challenges related to the obligate nature of microsporidia, the absence of fully characterized genes, and the lack of homologous genes in other systems.
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Paria P, Tassanakajon A. Identification of Potential Druggable Targets and Structure-Based Virtual Screening for Drug-like Molecules against the Shrimp Pathogen Enterocytozoon hepatopenaei. Int J Mol Sci 2023; 24:ijms24021412. [PMID: 36674953 PMCID: PMC9867128 DOI: 10.3390/ijms24021412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Enterocytozoon hepatopenaei (EHP) causes slow growth syndrome in shrimp, resulting in huge economic losses for the global shrimp industry. Despite worldwide reports, there are no effective therapeutics for controlling EHP infections. In this study, five potential druggable targets of EHP, namely, aquaporin (AQP), cytidine triphosphate (CTP) synthase, thymidine kinase (TK), methionine aminopeptidase2 (MetAP2), and dihydrofolate reductase (DHFR), were identified via functional classification of the whole EHP proteome. The three-dimensional structures of the proteins were constructed using the artificial-intelligence-based program AlphaFold 2. Following the prediction of druggable sites, the ZINC15 and ChEMBL databases were screened against targets using docking-based virtual screening. Molecules with affinity scores ≥ 7.5 and numbers of interactions ≥ 9 were initially selected and subsequently enriched based on their ADMET properties and electrostatic complementarities. Five compounds were finally selected against each target based on their complex stabilities and binding energies. The compounds CHEMBL3703838, CHEMBL2132563, and CHEMBL133039 were selected against AQP; CHEMBL1091856, CHEMBL1162979, and CHEMBL525202 against CTP synthase; CHEMBL4078273, CHEMBL1683320, and CHEMBL3674540 against TK; CHEMBL340488, CHEMBL1966988, and ZINC000828645375 against DHFR; and CHEMBL3913373, ZINC000016682972, and CHEMBL3142997 against MetAP2.The compounds exhibited high stabilities and low binding free energies, indicating their abilities to suppress EHP infections; however, further validation is necessary for determining their efficacy.
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Wong DK, Grisdale CJ, Slat VA, Rader SD, Fast NM. The evolution of pre-mRNA splicing and its machinery revealed by reduced extremophilic red algae. J Eukaryot Microbiol 2023; 70:e12927. [PMID: 35662328 DOI: 10.1111/jeu.12927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The Cyanidiales are a group of mostly thermophilic and acidophilic red algae that thrive near volcanic vents. Despite their phylogenetic relationship, the reduced genomes of Cyanidioschyzon merolae and Galdieria sulphuraria are strikingly different with respect to pre-mRNA splicing, a ubiquitous eukaryotic feature. Introns are rare and spliceosomal machinery is extremely reduced in C. merolae, in contrast to G. sulphuraria. Previous studies also revealed divergent spliceosomes in the mesophilic red alga Porphyridium purpureum and the red algal derived plastid of Guillardia theta (Cryptophyta), along with unusually high levels of unspliced transcripts. To further examine the evolution of splicing in red algae, we compared C. merolae and G. sulphuraria, investigating splicing levels, intron position, intron sequence features, and the composition of the spliceosome. In addition to identifying 11 additional introns in C. merolae, our transcriptomic analysis also revealed typical eukaryotic splicing in G. sulphuraria, whereas most transcripts in C. merolae remain unspliced. The distribution of intron positions within their host genes was examined to provide insight into patterns of intron loss in red algae. We observed increasing variability of 5' splice sites and branch donor regions with increasing intron richness. We also found these relationships to be connected to reductions in and losses of corresponding parts of the spliceosome. Our findings highlight patterns of intron and spliceosome evolution in related red algae under the pressures of genome reduction.
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Affiliation(s)
- Donald K Wong
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Cameron J Grisdale
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Viktor A Slat
- Department of Chemistry, University of Northern British Columbia, Prince George, BC, Canada
| | - Stephen D Rader
- Department of Chemistry, University of Northern British Columbia, Prince George, BC, Canada
| | - Naomi M Fast
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada
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Carriere E, Abdul Hamid AI, Feki I, Dubuffet A, Delbac F, Gueirard P. A mouse ear skin model to study the dynamics of innate immune responses against the microsporidian Encephalitozoon cuniculi. Front Microbiol 2023; 14:1168970. [PMID: 37125152 PMCID: PMC10136781 DOI: 10.3389/fmicb.2023.1168970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 03/29/2023] [Indexed: 05/02/2023] Open
Abstract
Microsporidia are obligate intracellular parasites related to fungi that cause severe infections in immunocompromised individuals. Encephalitozoon cuniculi is a microsporidian species capable of infecting mammals, including human and rodents. In response to microsporidian infection, innate immune system serves as the first line of defense and allows a partial clearance of the parasite via the innate immune cells, namely macrophages, neutrophils, dendritic cells, and Natural Killer cells. According to the literature, microsporidia bypass this response in vitro by modulating the response of macrophages. In order to study host-parasites interactions in vivo, we developed a model using the mouse ear pinna in combination with an intravital imaging approach. Fluorescent E. cuniculi spores were inoculated into the skin tissue to follow for the first time in real time in an in vivo model the recruitment dynamics of EGFP + phagocytic cells in response to the parasite. The results show that parasites induce an important inflammatory recruitment of phagocytes, with alterations of their motility properties (speed, displacement length, straightness). This cellular response persists in the injection zone, with spores detected inside the phagocytes up to 72 h post-infection. Immunostainings performed on ear tissue cryosections evoke the presence of developing infectious foci from 5 days post-infection, in favor of parasite proliferation in this tissue. Overall, the newly set up mice ear pinna model will increase our understanding of the immunobiology of microsporidia and in particular, to know how they can bypass and hijack the host immune system of an immunocompetent or immunosuppressed host.
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Xiong X, Geden CJ, Bergstralh DT, White RL, Werren JH, Wang X. New insights into the genome and transmission of the microsporidian pathogen Nosema muscidifuracis. Front Microbiol 2023; 14:1152586. [PMID: 37125197 PMCID: PMC10133504 DOI: 10.3389/fmicb.2023.1152586] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Nosema is a diverse genus of unicellular microsporidian parasites of insects and other arthropods. Nosema muscidifuracis infects parasitoid wasp species of Muscidifurax zaraptor and M. raptor (Hymenoptera: Pteromalidae), causing ~50% reduction in longevity and ~90% reduction in fecundity. Methods and Results Here, we report the first assembly of the N. muscidifuracis genome (14,397,169 bp in 28 contigs) of high continuity (contig N50 544.3 Kb) and completeness (BUSCO score 97.0%). A total of 2,782 protein-coding genes were annotated, with 66.2% of the genes having two copies and 24.0% of genes having three copies. These duplicated genes are highly similar, with a sequence identity of 99.3%. The complex pattern suggests extensive gene duplications and rearrangements across the genome. We annotated 57 rDNA loci, which are highly GC-rich (37%) in a GC-poor genome (25% genome average). Nosema-specific qPCR primer sets were designed based on 18S rDNA annotation as a diagnostic tool to determine its titer in host samples. We discovered high Nosema titers in Nosema-cured M. raptor and M. zaraptor using heat treatment in 2017 and 2019, suggesting that the remedy did not completely eliminate the Nosema infection. Cytogenetic analyses revealed heavy infections of N. muscidifuracis within the ovaries of M. raptor and M. zaraptor, consistent with the titer determined by qPCR and suggesting a heritable component of infection and per ovum vertical transmission. Discussion The parasitoids-Nosema system is laboratory tractable and, therefore, can serve as a model to inform future genome manipulations of Nosema-host system for investigations of Nosemosis.
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Affiliation(s)
- Xiao Xiong
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital, Shanghai Sunshine Rehabilitation Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Christopher J. Geden
- Center for Medical, Agricultural and Veterinary Entomology, USDA Agricultural Research Service, Gainesville, FL, United States
| | - Dan T. Bergstralh
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Roxie L. White
- Center for Medical, Agricultural and Veterinary Entomology, USDA Agricultural Research Service, Gainesville, FL, United States
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Department of Entomology and Plant Pathology, College of Agriculture, Auburn University, AL, United States
- Alabama Agricultural Experiment Station, Center for Advanced Science, Innovation and Commerce, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
- *Correspondence: Xu Wang,
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Trzebny A, Slodkowicz-Kowalska A, Björkroth J, Dabert M. Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content. MICROBIAL ECOLOGY 2023; 85:247-263. [PMID: 34939130 PMCID: PMC9849180 DOI: 10.1007/s00248-021-01944-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
The animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.
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Affiliation(s)
- Artur Trzebny
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
| | - Anna Slodkowicz-Kowalska
- Department of Biology and Medical Parasitology, Poznan University of Medical Sciences, Poznan, Poland
| | - Johanna Björkroth
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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Juhas M. The World of Microorganisms. BRIEF LESSONS IN MICROBIOLOGY 2023:1-16. [DOI: 10.1007/978-3-031-29544-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Wan YC, Troemel ER, Reinke AW. Conservation of Nematocida microsporidia gene expression and host response in Caenorhabditis nematodes. PLoS One 2022; 17:e0279103. [PMID: 36534656 PMCID: PMC9762603 DOI: 10.1371/journal.pone.0279103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Microsporidia are obligate intracellular parasites that are known to infect most types of animals. Many species of microsporidia can infect multiple related hosts, but it is not known if microsporidia express different genes depending upon which host species is infected or if the host response to infection is specific to each microsporidia species. To address these questions, we took advantage of two species of Nematocida microsporidia, N. parisii and N. ausubeli, that infect two species of Caenorhabditis nematodes, C. elegans and C. briggsae. We performed RNA-seq at several time points for each host infected with either microsporidia species. We observed that Nematocida transcription was largely independent of its host. We also observed that the host transcriptional response was similar when infected with either microsporidia species. Finally, we analyzed if the host response to microsporidia infection was conserved across host species. We observed that although many of the genes upregulated in response to infection are not direct orthologs, the same expanded gene families are upregulated in both Caenorhabditis hosts. Together our results describe the transcriptional interactions of Nematocida infection in Caenorhabditis hosts and demonstrate that these responses are evolutionarily conserved.
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Affiliation(s)
- Yin Chen Wan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Emily R. Troemel
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Aaron W. Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada,* E-mail:
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Sendra KM, Watson AK, Kozhevnikova E, Moore AL, Embley TM, Hirt RP. Inhibition of mitosomal alternative oxidase causes lifecycle arrest of early-stage Trachipleistophora hominis meronts during intracellular infection of mammalian cells. PLoS Pathog 2022; 18:e1011024. [PMID: 36538568 PMCID: PMC9767352 DOI: 10.1371/journal.ppat.1011024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022] Open
Abstract
Mitosomes are highly reduced forms of mitochondria which have lost two of the 'defining' features of the canonical organelle, the mitochondrial genome, and the capacity to generate energy in the form of ATP. Mitosomes are found in anaerobic protists and obligate parasites and, in most of the studied organisms, have a conserved function in the biosynthesis of iron-sulfur clusters (ISC) that are indispensable cofactors of many essential proteins. The genomes of some mitosome-bearing human pathogenic Microsporidia encode homologues of an alternative oxidase (AOX). This mitochondrial terminal respiratory oxidase is absent from the human host, and hence is a potential target for the development of new antimicrobial agents. Here we present experimental evidence for the mitosomal localization of AOX in the microsporidian Trachipleistophora hominis and demonstrate that it has an important role during the parasite's life cycle progression. Using a recently published methodology for synchronising T. hominis infection of mammalian cell lines, we demonstrated specific inhibition of T. hominis early meront growth and replication by an AOX inhibitor colletochlorin B. Treatment of T. hominis-infected host cells with the drug also inhibited re-infection by newly formed dispersive spores. Addition of the drug during the later stages of the parasite life cycle, when our methods suggest that AOX is not actively produced and T. hominis mitosomes are mainly active in Fe/S cluster biosynthesis, had no inhibitory effects on the parasites. Control experiments with the AOX-deficient microsporidian species Encephalitozoon cuniculi, further demonstrated the specificity of inhibition by the drug. Using the same methodology, we demonstrate effects of two clinically used anti-microsporidian drugs albendazole and fumagillin on the cell biology and life cycle progression of T. hominis infecting mammalian host cells. In summary, our results reveal that T. hominis mitosomes have an active role to play in the progression of the parasite life cycle as well as an important role in the biosynthesis of essential Fe/S clusters. Our work also demonstrates that T. hominis is a useful model for testing the efficacy of therapeutic agents and for studying the physiology and cell biology of microsporidian parasites growing inside infected mammalian cells.
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Affiliation(s)
- Kacper M. Sendra
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew K. Watson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Anthony L. Moore
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - T. Martin Embley
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Robert P. Hirt
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores. Nat Commun 2022; 13:6962. [PMID: 36379934 PMCID: PMC9666519 DOI: 10.1038/s41467-022-34691-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/02/2022] [Indexed: 11/17/2022] Open
Abstract
Proteasomes play an essential role in the life cycle of intracellular pathogens with extracellular stages by ensuring proteostasis in environments with limited resources. In microsporidia, divergent parasites with extraordinarily streamlined genomes, the proteasome complexity and structure are unknown, which limits our understanding of how these unique pathogens adapt and compact essential eukaryotic complexes. We present cryo-electron microscopy structures of the microsporidian 20S and 26S proteasome isolated from dormant or germinated Vairimorpha necatrix spores. The discovery of PI31-like peptides, known to inhibit proteasome activity, bound simultaneously to all six active sites within the central cavity of the dormant spore proteasome, suggests reduced activity in the environmental stage. In contrast, the absence of the PI31-like peptides and the existence of 26S particles post-germination in the presence of ATP indicates that proteasomes are reactivated in nutrient-rich conditions. Structural and phylogenetic analyses reveal that microsporidian proteasomes have undergone extensive reductive evolution, lost at least two regulatory proteins, and compacted nearly every subunit. The highly derived structure of the microsporidian proteasome, and the minimized version of PI31 presented here, reinforce the feasibility of the development of specific inhibitors and provide insight into the unique evolution and biology of these medically and economically important pathogens.
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Depotter JRL, Ökmen B, Ebert MK, Beckers J, Kruse J, Thines M, Doehlemann G. High Nucleotide Substitution Rates Associated with Retrotransposon Proliferation Drive Dynamic Secretome Evolution in Smut Pathogens. Microbiol Spectr 2022; 10:e0034922. [PMID: 35972267 PMCID: PMC9603552 DOI: 10.1128/spectrum.00349-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest in U. hordei and are positively correlated with the mating-type locus sizes, which is up to ~560 kb in U. hordei. Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these occur in specific genome regions of smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more accessory nature results in substitutions that often lead to amino acid alterations. IMPORTANCE Genomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. They also impact genome evolution as their repetitive nature facilitates nonhomologous recombination. Furthermore, TEs have been linked to specific epigenetic genome organizations. We report a recent TE proliferation in the genome of the barley covered smut fungus, Ustilago hordei. This proliferation is associated with a distinct nucleotide substitution regime that has a higher rate and a higher fraction of CG substitutions. This different regime shapes the evolution of genes in subjected genome regions. We hypothesize that TEs may influence the error-rate of DNA polymerase in a hitherto unknown fashion.
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Affiliation(s)
- J. R. L. Depotter
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - B. Ökmen
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - M. K. Ebert
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - J. Beckers
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - J. Kruse
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany
| | - G. Doehlemann
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
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Zhang R, Zheng S, Huang H, Sun X, Huang Y, Wei J, Pan G, Li C, Zhou Z. Expression of anti-NbHK single-chain antibody in fusion with NSlmb enhances the resistance to Nosema bombycis in Sf9-III cells. BULLETIN OF ENTOMOLOGICAL RESEARCH 2022; 112:502-508. [PMID: 35382911 DOI: 10.1017/s0007485321001036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nosema bombycis is a destructive and specific intracellular parasite of silkworm, which is extremely harmful to the silkworm industry. N. bombycis is considered as a quarantine pathogen of sericulture because of its long incubation period and horizontal and vertical transmission. Herein, two single-chain antibodies targeting N. bombycis hexokinase (NbHK) were cloned and expressed in fusion with the N-terminal of Slmb (a Drosophila melanogaster FBP), which contains the F-box domain. Western blotting demonstrated that Sf9-III cells expressed NSlmb-scFv-7A and NSlmb-scFv-6H, which recognized native NbHK. Subsequently, the NbHK was degraded by host ubiquitination system. When challenged with N. bombycis, the transfected Sf9-III cells exhibited better resistance relative to the controls, demonstrating that NbHK is a prospective target for parasite controls and this approach represents a potential solution for constructing N. bombycis-resistant Bombyx mori.
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Affiliation(s)
- Renze Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Shiyi Zheng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Affiliated Jinhua Hospital, Zhejiang University of Medicine, Jinhua Municipal Central Hospital, Jinhua, Zhejiang 321000, China
| | - Hongyun Huang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Xi Sun
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Yukang Huang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Junhong Wei
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Guoqing Pan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Chunfeng Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Zeyang Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
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Heterologous Expressed NbSWP12 from Microsporidia Nosema bombycis Can Bind with Phosphatidylinositol 3-phosphate and Affect Vesicle Genesis. J Fungi (Basel) 2022; 8:jof8080764. [PMID: 35893133 PMCID: PMC9332396 DOI: 10.3390/jof8080764] [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: 06/10/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 02/01/2023] Open
Abstract
Microsporidia are a big group of single-celled obligate intracellular organisms infecting most animals and some protozoans. These minimalist eukaryotes lack numerous genes in metabolism and vesicle trafficking. Here, we demonstrated that the spore wall protein NbSWP12 of microsporidium Nosema bombycis belongs to Bin/Amphiphysin/Rvs (BAR) protein family and can specifically bind with phosphatidylinositol 3-phosphate [Ptdlns(3)P]. Since Ptdlns(3)P is involved in endosomal vesicle biogenesis and trafficking, we heterologous expressed NbSWP12 in yeast Saccharomyces cerevisiae and proved that NbSWP12 can target the cell membrane and endocytic vesicles. Nbswp12 transformed into Gvp36 (a BAR protein of S. cerevisiae) deletion mutant rescued the defect phenotype of vesicular traffic. This study identified a BAR protein function in vesicle genesis and sorting and provided clues for further understanding of how microsporidia internalize nutrients and metabolites during proliferation.
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Luo J, Xu J, Xie C, Zhao Z, Guo J, Wen Y, Li T, Zhou Z. Microsporidia Promote Host Mitochondrial Fragmentation by Modulating DRP1 Phosphorylation. Int J Mol Sci 2022; 23:ijms23147746. [PMID: 35887094 PMCID: PMC9321008 DOI: 10.3390/ijms23147746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Microsporidia are obligate intracellular parasites that infect a wide variety of hosts ranging from invertebrates to vertebrates. These parasites have evolved strategies to directly hijack host mitochondria for manipulating host metabolism and immunity. However, the mechanism of microsporidia interacting with host mitochondria is unclear. In the present study, we show that microsporidian Encephalitozoon greatly induce host mitochondrial fragmentation (HMF) in multiple cells. We then reveal that the parasites promote the phosphorylation of dynamin 1-like protein (DRP1) at the 616th serine (Ser616), and dephosphorylation of the 637th serine (Ser637) by highly activating mitochondrial phosphoglycerate mutase 5 (PGAM5). These phosphorylation modifications result in the translocation of DRP1 from cytosol to the mitochondrial outer membrane, and finally lead to HMF. Furthermore, treatment with mitochondrial division inhibitor 1 (Mdivi1) significantly reduced microsporidian proliferation, indicating that the HMF are crucial for microsporidian replication. In summary, our findings reveal the mechanism that microsporidia manipulate HMF and provide references for further understanding the interactions between these ubiquitous pathogens with host mitochondria.
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Affiliation(s)
- Jian Luo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.L.); (J.X.); (C.X.); (Z.Z.); (J.G.); (Y.W.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Jinzhi Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.L.); (J.X.); (C.X.); (Z.Z.); (J.G.); (Y.W.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Chaolu Xie
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.L.); (J.X.); (C.X.); (Z.Z.); (J.G.); (Y.W.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Zuoming Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.L.); (J.X.); (C.X.); (Z.Z.); (J.G.); (Y.W.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Junrui Guo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.L.); (J.X.); (C.X.); (Z.Z.); (J.G.); (Y.W.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Yuan Wen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.L.); (J.X.); (C.X.); (Z.Z.); (J.G.); (Y.W.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.L.); (J.X.); (C.X.); (Z.Z.); (J.G.); (Y.W.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
- Correspondence: (T.L.); (Z.Z.)
| | - Zeyang Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.L.); (J.X.); (C.X.); (Z.Z.); (J.G.); (Y.W.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
- College of Life Science, Chongqing Normal University, Chongqing 400047, China
- Correspondence: (T.L.); (Z.Z.)
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Targeting the alternative oxidase (AOX) for human health and food security, a pharmaceutical and agrochemical target or a rescue mechanism? Biochem J 2022; 479:1337-1359. [PMID: 35748702 PMCID: PMC9246349 DOI: 10.1042/bcj20180192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 11/25/2022]
Abstract
Some of the most threatening human diseases are due to a blockage of the mitochondrial electron transport chain (ETC). In a variety of plants, fungi, and prokaryotes, there is a naturally evolved mechanism for such threats to viability, namely a bypassing of the blocked portion of the ETC by alternative enzymes of the respiratory chain. One such enzyme is the alternative oxidase (AOX). When AOX is expressed, it enables its host to survive life-threatening conditions or, as in parasites, to evade host defenses. In vertebrates, this mechanism has been lost during evolution. However, we and others have shown that transfer of AOX into the genome of the fruit fly and mouse results in a catalytically engaged AOX. This implies that not only is the AOX a promising target for combating human or agricultural pathogens but also a novel approach to elucidate disease mechanisms or, in several cases, potentially a therapeutic cure for human diseases. In this review, we highlight the varying functions of AOX in their natural hosts and upon xenotopic expression, and discuss the resulting need to develop species-specific AOX inhibitors.
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Meng X, Ye H, Shang Z, Sun L, Guo Y, Li N, Xiao L, Feng Y. Identification and Characterization of Three Spore Wall Proteins of Enterocytozoon Bieneusi. Front Cell Infect Microbiol 2022; 12:808986. [PMID: 35795186 PMCID: PMC9251001 DOI: 10.3389/fcimb.2022.808986] [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: 11/04/2021] [Accepted: 05/25/2022] [Indexed: 11/30/2022] Open
Abstract
Enterocytozoon bieneusi is the most common microsporidian pathogen in farm animals and humans. Although several spore wall proteins (SWPs) of other human-pathogenic microsporidia have been identified, SWPs of E. bieneusi remain poorly characterized. In the present study, we identified the sequences of three E. bieneusi SWPs from whole genome sequence data, expressed them in Escherichia coli, generated a monoclonal antibody (mAb) against one of them (EbSWP1), and used the mAb in direct immunofluorescence detection of E. bieneusi spores in fecal samples. The amino acid sequence of EbSWP1 shares some identity to EbSWP2 with a BAR2 domain, while the sequence of EbSWP3 contains a MICSWaP domain. No cross-reactivity among the EbSWPs was demonstrated using the polyclonal antibodies generated against them. The mAb against EbSWP1 was shown to react with E. bieneusi spores in fecal samples. Using chromotrope 2R staining-based microscopy as the gold standard, the sensitivity and specificity of the direct immunofluorescence for the detection of E. bieneusi were 91.4 and 73.7%. Data generated from the study could be useful in the characterization of E. bieneusi and immunological detection of the pathogen.
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Affiliation(s)
- Xinan Meng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Haojie Ye
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ziyu Shang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lianjing Sun
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Na Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Lihua Xiao, ; Yaoyu Feng,
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Lihua Xiao, ; Yaoyu Feng,
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Seatamanoch N, Kongdachalert S, Sunantaraporn S, Siriyasatien P, Brownell N. Microsporidia, a Highly Adaptive Organism and Its Host Expansion to Humans. Front Cell Infect Microbiol 2022; 12:924007. [PMID: 35782144 PMCID: PMC9245026 DOI: 10.3389/fcimb.2022.924007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/23/2022] [Indexed: 12/05/2022] Open
Abstract
Emerging infectious disease has become the center of attention since the outbreak of COVID-19. For the coronavirus, bats are suspected to be the origin of the pandemic. Consequently, the spotlight has fallen on zoonotic diseases, and the focus now expands to organisms other than viruses. Microsporidia is a single-cell organism that can infect a wide range of hosts such as insects, mammals, and humans. Its pathogenicity differs among species, and host immunological status plays an important role in infectivity and disease severity. Disseminated disease from microsporidiosis can be fatal, especially among patients with a defective immune system. Recently, there were two Trachipleistophora hominis, a microsporidia species which can survive in insects, case reports in Thailand, one patient had disseminated microsporidiosis. This review gathered data of disseminated microsporidiosis and T. hominis infections in humans covering the biological and clinical aspects. There was a total of 22 cases of disseminated microsporidiosis reports worldwide. Ten microsporidia species were identified. Maximum likelihood tree results showed some possible correlations with zoonotic transmissions. For T. hominis, there are currently eight case reports in humans, seven of which had Human Immunodeficiency Virus (HIV) infection. It is observed that risks are higher for the immunocompromised to acquire such infections, however, future studies should look into the entire life cycle, to identify the route of transmission and establish preventive measures, especially among the high-risk groups.
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Affiliation(s)
- Nirin Seatamanoch
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Switt Kongdachalert
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sakone Sunantaraporn
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Padet Siriyasatien
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Narisa Brownell
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Vector Biology and Vector Borne Disease Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- *Correspondence: Narisa Brownell,
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Xu J, Luo J, Chen J, Vossbrinck CR, Li T, Zhou Z. Characterization of the Largest Secretory Protein Family, Ricin B Lectin-like Protein, in Nosema bombycis: Insights into Microsporidian Adaptation to Host. J Fungi (Basel) 2022; 8:jof8060551. [PMID: 35736035 PMCID: PMC9224602 DOI: 10.3390/jof8060551] [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: 05/03/2022] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 12/28/2022] Open
Abstract
Microsporidia are a group of obligate intracellular pathogens infecting nearly all animal phyla. The microsporidian Nosema bombycis has been isolated from several lepidopteran species, including the economy-important silkworms as well as several crop pests. Proteins secreted by parasites can be important virulent factors in modulating host pathways. Ricin is a two-chain lectin best known for its extreme vertebrate toxicity. Ricin B lectin-like proteins are widely distributed in microsporidia, especially in N. bombycis. In this study, we identify 52 Ricin B lectin-like proteins (RBLs) in N. bombycis. We show that the N. bombycis RBLs (NbRBLs) are classified into four subfamilies. The subfamily 1 was the most conserved, with all members having a Ricin B lectin domain and most members containing a signal peptide. The other three subfamilies were less conserved, and even lost the Ricin B lectin domain, suggesting that NbRBLs might be a multi-functional family. Our study here indicated that the NbRBL family had evolved by producing tandem duplications firstly and then expanded by segmental duplications, resulting in concentrated localizations mainly in three genomic regions. Moreover, based on RNA-seq data, we found that several Nbrbls were highly expressed during infection. Further, the results show that the NbRBL28 was secreted into host nucleus, where it promotes the expressions of genes involved in cell cycle progression. In summary, the great copy number, high divergence, and concentrated genome distribution of the NbRBLs demonstrated that these proteins might be adaptively evolved and played a vital role in the multi-host N. bombycis.
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Affiliation(s)
- Jinzhi Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.X.); (J.L.); (J.C.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Jian Luo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.X.); (J.L.); (J.C.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Jiajing Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.X.); (J.L.); (J.C.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Charles R. Vossbrinck
- Department of Environmental Science, The Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT 06511, USA;
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.X.); (J.L.); (J.C.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
- Correspondence: (T.L.); (Z.Z.)
| | - Zeyang Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (J.X.); (J.L.); (J.C.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
- College of Life Science, Chongqing Normal University, Chongqing 400047, China
- Correspondence: (T.L.); (Z.Z.)
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49
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Caravello G, Franchet A, Niehus S, Ferrandon D. Phagocytosis Is the Sole Arm of Drosophila melanogaster Known Host Defenses That Provides Some Protection Against Microsporidia Infection. Front Immunol 2022; 13:858360. [PMID: 35493511 PMCID: PMC9043853 DOI: 10.3389/fimmu.2022.858360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microsporidia are obligate intracellular parasites able to infest specifically a large range of species, including insects. The knowledge about the biology of microsporidial infections remains confined to mostly descriptive studies, including molecular approaches such as transcriptomics or proteomics. Thus, functional data to understand insect host defenses are currently lacking. Here, we have undertaken a genetic analysis of known host defenses of the Drosophila melanogaster using an infection model whereby Tubulinosema ratisbonensis spores are directly injected in this insect. We find that phagocytosis does confer some protection in this infection model. In contrast, the systemic immune response, extracellular reactive oxygen species, thioester proteins, xenophagy, and intracellular antiviral response pathways do not appear to be involved in the resistance against this parasite. Unexpectedly, several genes such as PGRP-LE seem to promote this infection. The prophenol oxidases that mediate melanization have different functions; PPO1 presents a phenotype similar to that of PGRP-LE whereas that of PPO2 suggests a function in the resilience to infection. Similarly, eiger and Unpaired3, which encode two cytokines secreted by hemocytes display a resilience phenotype with a strong susceptibility to T. ratisbonensis.
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Affiliation(s)
| | | | | | - Dominique Ferrandon
- UPR9022, University of Strasbourg, Institut de Biologie Moléculaire et Cellulaire (IBMC), Modèles Insectes D’Immunité Innée (M3I) Unité Propre Recherche (UPR) 9022 du Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
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50
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Nicholson D, Salamina M, Panek J, Helena-Bueno K, Brown CR, Hirt RP, Ranson NA, Melnikov SV. Adaptation to genome decay in the structure of the smallest eukaryotic ribosome. Nat Commun 2022; 13:591. [PMID: 35105900 PMCID: PMC8807834 DOI: 10.1038/s41467-022-28281-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/14/2022] [Indexed: 12/18/2022] Open
Abstract
The evolution of microbial parasites involves the counterplay between natural selection forcing parasites to improve and genetic drifts forcing parasites to lose genes and accumulate deleterious mutations. Here, to understand how this counterplay occurs at the scale of individual macromolecules, we describe cryo-EM structure of ribosomes from Encephalitozoon cuniculi, a eukaryote with one of the smallest genomes in nature. The extreme rRNA reduction in E. cuniculi ribosomes is accompanied with unparalleled structural changes, such as the evolution of previously unknown molten rRNA linkers and bulgeless rRNA. Furthermore, E. cuniculi ribosomes withstand the loss of rRNA and protein segments by evolving an ability to use small molecules as structural mimics of degenerated rRNA and protein segments. Overall, we show that the molecular structures long viewed as reduced, degenerated, and suffering from debilitating mutations possess an array of compensatory mechanisms that allow them to remain active despite the extreme molecular reduction. Many parasitic organisms contain molecular structures that are drastically smaller than analogous structures in non-parasitic organisms. Here the authors describe a cryo-EM structure of the ribosome from E. cuniculi that reveals that it compensated rRNA truncations by evolving the ability to use small molecules as ribosomal building blocks.
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Affiliation(s)
- David Nicholson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Marco Salamina
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Johan Panek
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Karla Helena-Bueno
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Charlotte R Brown
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert P Hirt
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sergey V Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK. .,Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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