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Canela-Pérez I, Azuara-Liceaga E, Cuéllar P, Saucedo-Cárdenas O, Valdés J. Multiple types of nuclear localization signals in Entamoeba histolytica. Biochem Biophys Rep 2024; 39:101770. [PMID: 39055170 PMCID: PMC11269297 DOI: 10.1016/j.bbrep.2024.101770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Entamoeba histolytica is a protozoan parasite that belongs to the Amoebozoa supergroup whose study related to the nucleocytoplasmic transport of proteins through the nucleus is poorly studied. In this work, we have performed in silico predictions of the potential nuclear localization signals (NLS) corresponding to the proteome of 8201 proteins from Entamoeba histolytica annotated in the AmoebaDB database. We have found the presence of monopartite nuclear localization signals (MNLSs), bipartite nuclear localization signals (BNLSs), and non-canonical monopartite NLSs with lengths exceeding 20 amino acid residues. Additionally, we detected a new type of NLS consisting of multiple juxtaposed bipartite NLSs (JNLSs) that have not been described in any eukaryotic organism. Also, we have generated consensus sequences for the nuclear import of proteins with the NLSs obtained. Docking experiments between EhImportin α and an MNLS, BNLS, and JNLS outlined the interacting residues between the Importin and cargo proteins, emphasizing their putative roles in nuclear import. By transfecting HA-tagged protein constructs, we assessed the nuclear localization of MNLS (U1A and U2AF1), JMNLS (U2AF2), and non-canonical NLS (N-terminus of Pol ll) in vivo. Our data provide the basis for understanding the nuclear transport process in E. histolytica.
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Affiliation(s)
- Israel Canela-Pérez
- Departamento de Bioquímica, CINVESTAV-México, Av. IPN 2508 colonia San Pedro Zacatenco, GAM, CDMX, 07360, Mexico
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, 03100, Mexico
| | - Patricia Cuéllar
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, 03100, Mexico
| | - Odila Saucedo-Cárdenas
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, 67700, Mexico
| | - Jesús Valdés
- Departamento de Bioquímica, CINVESTAV-México, Av. IPN 2508 colonia San Pedro Zacatenco, GAM, CDMX, 07360, Mexico
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2
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Mooney R, Richardson K, Rodgers K, Giammarini E, Williams R, Kelly S, Amaeze N, Inkster T, Henriquez FL, Mackay W. Acanthamoeba as a protective reservoir for Pseudomonas aeruginosa in a clinical environment. J Hosp Infect 2024:S0195-6701(24)00291-3. [PMID: 39218354 DOI: 10.1016/j.jhin.2024.08.010] [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: 05/09/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Pseudomonas aeruginosa is a growing concern in healthcare associated infections and poses significant risk to those with serious underlying health conditions. The antimicrobial resistance traits of the pathogen and ability to form biofilms make effective mitigation and disinfection strategies difficult. Added to this challenge is the role that free-living amoebae such as Acanthamoeba play in the detection, disinfection, and transmission of P. aeruginosa. P. aeruginosa can survive intracellularly within amoebae, which has the potential to limit detectability and permit transmission into high-risk areas. Herein, we have screened for the presence of Acanthamoeba species and P. aeruginosa within a functioning general hospital in Scotland using a culture and molecular approach, noting their presence at several sites over a 4-month period, particularly within floor drains connecting patient rooms. In addition, microbiome analysis revealed amoebae harbour a unique microbial community comprised primarily of Pseudomonas species that were not readily detected using microbiome sequencing techniques on environmental swabs. Having demonstrated that both organisms were consistently present in hospital settings, we investigated the relationship between Acanthamoeba and P. aeruginosa in the laboratory, showing that i) Acanthamoeba growth rate is increased in the presence of Pseudomonas biofilms and viable Pseudomonas persist within the amoebae and ii) hydrogen peroxide-based disinfectants are significantly less effective against an isolate of P. aeruginosa in the presence of Acanthamoeba than when the bacteria are incubated alone. These findings suggest that amoebae, and other protists, can influence the detection and persistence of P. aeruginosa in high-risk areas and should be considered when implementing mitigation strategies.
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Affiliation(s)
- Ronnie Mooney
- School of Health and Life Sciences, University of the West of Scotland, Lanarkshire Campus, South Lanarkshire, United Kingdom
| | - Kenny Richardson
- School of Health and Life Sciences, University of the West of Scotland, Lanarkshire Campus, South Lanarkshire, United Kingdom
| | - Kiri Rodgers
- School of Health and Life Sciences, University of the West of Scotland, Lanarkshire Campus, South Lanarkshire, United Kingdom
| | - Elisa Giammarini
- School of Health and Life Sciences, University of the West of Scotland, Lanarkshire Campus, South Lanarkshire, United Kingdom
| | - Roderick Williams
- School of Health and Life Sciences, University of the West of Scotland, Lanarkshire Campus, South Lanarkshire, United Kingdom
| | - Steven Kelly
- School of Health and Life Sciences, University of the West of Scotland, Lanarkshire Campus, South Lanarkshire, United Kingdom
| | - Ngozi Amaeze
- School of Health and Life Sciences, University of the West of Scotland, Lanarkshire Campus, South Lanarkshire, United Kingdom
| | - Teresa Inkster
- Antimicrobial Resistance & Healthcare Associated Infection (ARHAI) Scotland, Delta House, 48 West Nile Street, Glasgow, United Kingdom
| | - Fiona L Henriquez
- School of Health and Life Sciences, University of the West of Scotland, Lanarkshire Campus, South Lanarkshire, United Kingdom
| | - William Mackay
- School of Health and Life Sciences, University of the West of Scotland, Lanarkshire Campus, South Lanarkshire, United Kingdom.
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Iwamoto Y, Nakayama T. Nannostelium ampullaceum gen. et sp. nov., a tiny new member of the protosteloid amoeba of the Cavosteliida (Variosea, Amoebozoa). Protist 2024; 175:126046. [PMID: 38810418 DOI: 10.1016/j.protis.2024.126046] [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: 12/29/2023] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024]
Abstract
Protosteloid amoebae are slime molds characterized by simple sporocarp comprised only of a stalk and typically single spore. Recent molecular phylogenetic studies showed that protosteloid amoebae are scattered among the Amoebozoa, but most of them belongs to the Variosea. The Cavosteliida is one of the largest protosteloid group of the Variosea. We have established novel protosteloid amoeba strain YIP-63 from the fruiting body of jelly fugus Auricularia sp. The strain YIP-63 is unique to have a tiny sporocarp and amoeba comparing to the other protosteloid species, and trophic amoebae forming both round and branched shape. The molecular phylogenetic analyses based on 18S rRNA gene suggest that YIP-63 represents a novel lineage in the Cavosteliida. Therefore, we propose the new genus and new species for the strain YIP-63 as Nannostelium ampullaceum gen. et sp. nov. We provide morphological and molecular data on this novel protosteloid amoeba.
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Affiliation(s)
- Yoshiaki Iwamoto
- University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
| | - Takeshi Nakayama
- University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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4
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Mi-ichi F, Tsugawa H, Vo TK, Kurizaki Y, Yoshida H, Arita M. Characterization of Entamoeba fatty acid elongases; validation as targets and provision of promising leads for new drugs against amebiasis. PLoS Pathog 2024; 20:e1012435. [PMID: 39172749 PMCID: PMC11340893 DOI: 10.1371/journal.ppat.1012435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/19/2024] [Indexed: 08/24/2024] Open
Abstract
Entamoeba histolytica is a protozoan parasite belonging to the phylum Amoebozoa that causes amebiasis, a global public health problem. E. histolytica alternates its form between a proliferative trophozoite and a dormant cyst. Trophozoite proliferation is closely associated with amebiasis symptoms and pathogenesis whereas cysts transmit the disease. Drugs are available for clinical use; however, they have issues of adverse effects and dual targeting of disease symptoms and transmission remains to be improved. Development of new drugs is therefore urgently needed. An untargeted lipidomics analysis recently revealed structural uniqueness of the Entamoeba lipidome at different stages of the parasite's life cycle involving very long (26-30 carbons) and/or medium (8-12 carbons) acyl chains linked to glycerophospholipids and sphingolipids. Here, we investigated the physiology of this unique acyl chain diversity in Entamoeba, a non-photosynthetic protist. We characterized E. histolytica fatty acid elongases (EhFAEs), which are typically components of the fatty acid elongation cycle of photosynthetic protists and plants. An approach combining genetics and lipidomics revealed that EhFAEs are involved in the production of medium and very long acyl chains in E. histolytica. This approach also showed that the K3 group herbicides, flufenacet, cafenstrole, and fenoxasulfone, inhibited the production of very long acyl chains, thereby impairing Entamoeba trophozoite proliferation and cyst formation. Importantly, none of these three compounds showed toxicity to a human cell line; therefore, EhFAEs are reasonable targets for developing new anti-amebiasis drugs and these compounds are promising leads for such drugs. Interestingly, in the Amoebazoan lineage, gain and loss of the genes encoding two different types of fatty acid elongase have occurred during evolution, which may be relevant to parasite adaptation. Acyl chain diversity in lipids is therefore a unique and indispensable feature for parasitic adaptation of Entamoeba.
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Affiliation(s)
- Fumika Mi-ichi
- Central Laboratory, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Hiroshi Tsugawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Tam Kha Vo
- Central Laboratory, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuto Kurizaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hiroki Yoshida
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan
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5
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Hooper PM, Bass D, Feil EJ, Vincent WF, Lovejoy C, Owen CJ, Tsola SL, Jungblut AD. Arctic cyanobacterial mat community diversity decreases with latitude across the Canadian Arctic. FEMS Microbiol Ecol 2024; 100:fiae067. [PMID: 38653723 DOI: 10.1093/femsec/fiae067] [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: 12/20/2023] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Cyanobacterial mats are commonly reported as hotspots of microbial diversity across polar environments. These thick, multilayered microbial communities provide a refuge from extreme environmental conditions, with many species able to grow and coexist despite the low allochthonous nutrient inputs. The visibly dominant phototrophic biomass is dependent on internal nutrient recycling by heterotrophic organisms within the mats; however, the specific contribution of heterotrophic protists remains little explored. In this study, mat community diversity was examined along a latitudinal gradient (55-83°N), spanning subarctic taiga, tundra, polar desert, and the High Arctic ice shelves. The prokaryotic and eukaryotic communities were targeted, respectively, by V4 16S ribosomal RNA (rRNA) and V9 18S rRNA gene amplicon high-throughput sequencing. Prokaryotic and eukaryotic richness decreased, in tandem with decreasing temperatures and shorter seasons of light availability, from the subarctic to the High Arctic. Taxonomy-based annotation of the protist community revealed diverse phototrophic, mixotrophic, and heterotrophic genera in all mat communities, with fewer parasitic taxa in High Arctic communities. Co-occurrence network analysis identified greater heterogeneity in eukaryotic than prokaryotic community structure among cyanobacterial mats across the Canadian Arctic. Our findings highlight the sensitivity of microbial eukaryotes to environmental gradients across northern high latitudes.
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Affiliation(s)
- Patrick M Hooper
- Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - David Bass
- Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Barrack Road, Weymouth, DT4 8UB, United Kingdom
- Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Edward J Feil
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Warwick F Vincent
- Département de Biologie, Takuvik International Research Laboratory and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Connie Lovejoy
- Département de Biologie, Takuvik International Research Laboratory and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, G1V 0A6, Canada
- Québec Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Christopher J Owen
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Stephania L Tsola
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Anne D Jungblut
- Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
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6
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Tekle YI, Tefera H. A Small Genome amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba. Genome Biol Evol 2024; 16:evae058. [PMID: 38504610 PMCID: PMC10980511 DOI: 10.1093/gbe/evae058] [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: 12/04/2023] [Revised: 01/22/2024] [Accepted: 03/14/2024] [Indexed: 03/21/2024] Open
Abstract
This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. Additionally, our investigation into noncoding and repetitive elements sheds light on the evolution of genome size in amoebae, with E. silvestris distinguished by low percentage of repetitive elements. Furthermore, the analysis reveals that E. silvestris has the lowest mean number of introns per gene among the species studied, providing further support for its observed compact genome. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic data sets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.
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Affiliation(s)
- Yonas I Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Hanna Tefera
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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7
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Záhonová K, Füssy Z, Stairs CW, Leger MM, Tachezy J, Čepička I, Roger AJ, Hampl V. Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans. Microb Genom 2023; 9. [PMID: 37994879 DOI: 10.1099/mgen.0.001143] [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] [Indexed: 11/24/2023] Open
Abstract
Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles (MROs) adapted to function anaerobically. We compared in silico reconstructed MRO proteomes of eight species (six genera) and found that the common ancestor of Archamoebae possessed very few typical components of the protein translocation machinery, electron transport chain and tricarboxylic acid cycle. On the other hand, it contained a sulphate activation pathway and bacterial iron-sulphur (Fe-S) assembly system of MIS-type. The metabolic capacity of the MROs, however, varies markedly within this clade. The glycine cleavage system is widely conserved among Archamoebae, except in Entamoeba, probably owing to its role in catabolic function or one-carbon metabolism. MRO-based pyruvate metabolism was dispensed within subgroups Entamoebidae and Rhizomastixidae, whereas sulphate activation could have been lost in isolated cases of Rhizomastix libera, Mastigamoeba abducta and Endolimax sp. The MIS (Fe-S) assembly system was duplicated in the common ancestor of Mastigamoebidae and Pelomyxidae, and one of the copies took over Fe-S assembly in their MRO. In Entamoebidae and Rhizomastixidae, we hypothesize that Fe-S cluster assembly in both compartments may be facilitated by dual localization of the single system. We could not find evidence for changes in metabolic functions of the MRO in response to changes in habitat; it appears that such environmental drivers do not strongly affect MRO reduction in this group of eukaryotes.
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Affiliation(s)
- Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Courtney W Stairs
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Microbiology Research Group, Department of Biology, Lund University, Lund, Sweden
| | - Michelle M Leger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
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Chistyakova LV, Yu Kostygov A, Goodkov AV, Radaev AV, Frolov AO. Phylogenetic position of the pelobiont Mastigamoeba aspera and revision of the family Mastigamoebidae (Archamoebae, Pelobiontida). Eur J Protistol 2023; 91:126029. [PMID: 37918183 DOI: 10.1016/j.ejop.2023.126029] [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: 07/31/2023] [Revised: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
In this study, we presented the results of our molecular phylogenetic analysis of Archamoebae using a newly obtained sequence of the 18S rRNA gene of Mastigamoeba aspera, the type species of the genus. In addition, we characterized the general organization of the tubulin cytoskeleton of M. aspera by immunofluorescent microscopy and TEM. Our findings allowed us to revise the family Mastigamoebidae and establish within it two subfamilies: Mastigamoebinae for the genus Mastigamoeba and Seraviniinae subfam. nov. for the genera Seravinia gen. nov., Paramastigamoeba gen. nov., Iodamoeba and Endolimax. The type genera Mastigamoeba and Seravinia are clearly distinguished by the structure of the basal apparatus of flagella. In addition, the tubulin cytoskeleton of several Mastigamoeba spp. contains a rim of microtubules around the nuclei.
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Affiliation(s)
- Ludmila V Chistyakova
- Laboratory of Parasitic Worms and Protists, Zoological Institute RAS, St. Petersburg, Russia.
| | - Alexei Yu Kostygov
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, St. Petersburg, Russia
| | - Andrew V Goodkov
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, St. Petersburg, Russia.
| | | | - Alexander O Frolov
- Laboratory of Parasitic Worms and Protists, Zoological Institute RAS, St. Petersburg, Russia
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9
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Lang BF, Beck N, Prince S, Sarrasin M, Rioux P, Burger G. Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction. FRONTIERS IN PLANT SCIENCE 2023; 14:1222186. [PMID: 37469769 PMCID: PMC10352661 DOI: 10.3389/fpls.2023.1222186] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/15/2023] [Indexed: 07/21/2023]
Abstract
Compared to nuclear genomes, mitochondrial genomes (mitogenomes) are small and usually code for only a few dozen genes. Still, identifying genes and their structure can be challenging and time-consuming. Even automated tools for mitochondrial genome annotation often require manual analysis and curation by skilled experts. The most difficult steps are (i) the structural modelling of intron-containing genes; (ii) the identification and delineation of Group I and II introns; and (iii) the identification of moderately conserved, non-coding RNA (ncRNA) genes specifying 5S rRNAs, tmRNAs and RNase P RNAs. Additional challenges arise through genetic code evolution which can redefine the translational identity of both start and stop codons, thus obscuring protein-coding genes. Further, RNA editing can render gene identification difficult, if not impossible, without additional RNA sequence data. Current automated mito- and plastid-genome annotators are limited as they are typically tailored to specific eukaryotic groups. The MFannot annotator we developed is unique in its applicability to a broad taxonomic scope, its accuracy in gene model inference, and its capabilities in intron identification and classification. The pipeline leverages curated profile Hidden Markov Models (HMMs), covariance (CMs) and ERPIN models to better capture evolutionarily conserved signatures in the primary sequence (HMMs and CMs) as well as secondary structure (CMs and ERPIN). Here we formally describe MFannot, which has been available as a web-accessible service (https://megasun.bch.umontreal.ca/apps/mfannot/) to the research community for nearly 16 years. Further, we report its performance on particularly intron-rich mitogenomes and describe ongoing and future developments.
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10
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Tekle YI, Tran H, Wang F, Singla M, Udu I. Omics of an Enigmatic Marine Amoeba Uncovers Unprecedented Gene Trafficking from Giant Viruses and Provides Insights into Its Complex Life Cycle. MICROBIOLOGY RESEARCH 2023; 14:656-672. [PMID: 37752971 PMCID: PMC10521059 DOI: 10.3390/microbiolres14020047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Amoebozoa include lineages of diverse ecology, behavior, and morphology. They are assumed to encompass members with the largest genome sizes of all living things, yet genomic studies in the group are limited. Trichosphaerium, a polymorphic, multinucleate, marine amoeba with a complicated life cycle, has puzzled experts for over a century. In an effort to explore the genomic diversity and investigate extraordinary behavior observed among the Amoebozoa, we used integrated omics approaches to study this enigmatic marine amoeba. Omics data, including single-cell transcriptomics and cytological data, demonstrate that Trichosphaerium sp. possesses the complete meiosis toolkit genes. These genes are expressed in life stages of the amoeba including medium and large cells. The life cycle of Trichosphaerium sp. involves asexual processes via binary fission and multiple fragmentation of giant cells, as well as sexual-like processes involving genes implicated in sexual reproduction and polyploidization. These findings are in stark contrast to a life cycle previously reported for this amoeba. Despite the extreme morphological plasticity observed in Trichosphaerium, our genomic data showed that populations maintain a species-level intragenomic variation. A draft genome of Trichosphaerium indicates elevated lateral gene transfer (LGT) from bacteria and giant viruses. Gene trafficking in Trichosphaerium is the highest within Amoebozoa and among the highest in microbial eukaryotes.
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Affiliation(s)
- Yonas I. Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Hanh Tran
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Fang Wang
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Mandakini Singla
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Isimeme Udu
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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11
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Tice AK, Spiegel FW, Brown MW. Phylogenetic placement of the protosteloid amoeba Microglomus paxillus identifies another case of sporocarpic fruiting in Discosea (Amoebozoa). J Eukaryot Microbiol 2023:e12971. [PMID: 36825799 DOI: 10.1111/jeu.12971] [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: 09/29/2022] [Revised: 01/31/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023]
Abstract
Protosteloid amoebae are a paraphyletic assemblage of amoeboid protists found exclusively in the eukaryotic assemblage Amoebozoa. These amoebae can facultatively form a dispersal structure known as a fruiting body, or more specifically, a sporocarp, from a single amoeboid cell. Sporocarps consist of one to a few spores atop a noncellular stalk. Protosteloid amoebae are known in two out of three well-established major assemblages of Amoebozoa. Amoebae with a protosteloid life cycle are known in the major Amoebozoa lineages Discosea and Evosea but not in Tubulinea. To date, only one genus, which is monotypic, lacks sequence data and, therefore, remains phylogenetically homeless. To further clarify the evolutionary milieu of sporocarpic fruiting we used single-cell transcriptomics to obtain data from individual sporocarps of isolates of the protosteloid amoeba Microglomus paxillus. Our phylogenomic analyses using 229 protein coding markers suggest that M. paxillus is a member of the Discosea lineage of Amoebozoa most closely related to Mycamoeba gemmipara. Due to the hypervariable nature of the SSU rRNA sequence we were unable to further resolve the phylogenetic position of M. paxillus in taxon rich datasets using only this marker. Regardless, our results widen the known distribution of sporocarpy in Discosea and stimulate the debate between a single or multiple origins of sporocarpic fruiting in Amoebozoa.
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Affiliation(s)
- Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Frederick W Spiegel
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
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Wang F, Tekle YI. Variation of natural selection in the Amoebozoa reveals heterogeneity across the phylogeny and adaptive evolution in diverse lineages. Front Ecol Evol 2022; 10:851816. [PMID: 36874909 PMCID: PMC9980437 DOI: 10.3389/fevo.2022.851816] [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: 11/13/2022] Open
Abstract
The evolution and diversity of the supergroup Amoebozoa is complex and poorly understood. The supergroup encompasses predominantly amoeboid lineages characterized by extreme diversity in phenotype, behavior and genetics. The study of natural selection, a driving force of diversification, within and among species of Amoebozoa will play a crucial role in understanding the evolution of the supergroup. In this study, we searched for traces of natural selection based on a set of highly conserved protein-coding genes in a phylogenetic framework from a broad sampling of amoebozoans. Using these genes, we estimated substitution rates and inferred patterns of selective pressure in lineages and sites with various models. We also examined the effect of selective pressure on codon usage bias and potential correlations with observed biological traits and habitat. Results showed large heterogeneity of selection across lineages of Amoebozoa, indicating potential species-specific optimization of adaptation to their diverse ecological environment. Overall, lineages in Tubulinea had undergone stronger purifying selection with higher average substitution rates compared to Discosea and Evosea. Evidence of adaptive evolution was observed in some representative lineages and in a gene (Rpl7a) within Evosea, suggesting potential innovation and beneficial mutations in these lineages. Our results revealed that members of the fast-evolving lineages, Entamoeba and Cutosea, all underwent strong purifying selection but had distinct patterns of codon usage bias. For the first time, this study revealed an overall pattern of natural selection across the phylogeny of Amoebozoa and provided significant implications on their distinctive evolutionary processes.
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Affiliation(s)
- Fang Wang
- Department of Biology, Spelman College, Atlanta, GA, United States
| | - Yonas I Tekle
- Department of Biology, Spelman College, Atlanta, GA, United States
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