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Ojeda-Martinez D, Diaz I, Santamaria ME, Ortego F. Comparative genomics reveals carbohydrate enzymatic fluctuations and herbivorous adaptations in arthropods. Comput Struct Biotechnol J 2024; 23:3744-3758. [PMID: 39525084 PMCID: PMC11543626 DOI: 10.1016/j.csbj.2024.10.027] [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: 07/08/2024] [Revised: 10/16/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024] Open
Abstract
Background Arthropods represent the largest and most diverse phylum on Earth, playing a pivotal role in the biosphere. One key to their evolutionary success is their ability to feed on plant material. However, their endogenous enzymatic repertoire, which contributes to plant digestion, remains largely unexplored and poorly understood. Results We analyzed 815 arthropod proteomes and identified a total of 268,171 carbohydrate-active modules. Our findings revealed a strong correlation between enzymatic content and feeding habits, with herbivorous species possessing significantly higher enzyme levels. We identified widespread carbohydrate-active families across the AA, CBM, GH, and GT classes, and observed a progressive increase in taxa-exclusive families in more recent arthropod lineages. Notably, we highlighted the impact of the transition from ametabolous to holometabolous development on carbohydrate metabolism, as well as the ecological adaptations of different species groups. By reconstructing the ancestral enzymatic profiles of arthropods, we identified significant fluctuations in 10 carbohydrate-active families over time. Conclusions Our analysis advances the understanding of the evolutionary mechanisms utilized by the megadiverse phylum Arthropoda. We emphasize the critical role of herbivory as a selective force shaping enzymatic strategies, particularly those involved in carbohydrate metabolism. The distribution and exclusivity of carbohydrate-active families across different arthropod groups provide insights into their evolutionary trajectories and offer a clearer picture of the metabolic pathways that led their ancestors to their present forms.
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Affiliation(s)
- Dairon Ojeda-Martinez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - M. Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Félix Ortego
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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Granados-Casas AO, Fernández-Bravo A, Stchigel AM, Cano-Lira JF. Genomic Sequencing and Functional Analysis of the Ex-Type Strain of Malbranchea zuffiana. J Fungi (Basel) 2024; 10:600. [PMID: 39330360 PMCID: PMC11433161 DOI: 10.3390/jof10090600] [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: 07/03/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 09/28/2024] Open
Abstract
Malbranchea is a genus within the order Onygenales (phylum Ascomycota) that includes predominantly saprobic cosmopolitan species. Despite its ability to produce diverse secondary metabolites, no genomic data for Malbranchea spp. are currently available in databases. Therefore, in this study, we obtained, assembled, and annotated the genomic sequence of the ex-type strain of Malbranchea zuffiana (CBS 219.58). For the genomic sequencing, we employed both the Illumina and PacBio platforms, followed by hybrid assembly using MaSuRCA. Quality assessment of the assembly was performed using QUAST and BUSCO tools. Annotation was conducted using BRAKER2, and functional annotation was completed with InterProScan. The resulting genome was of high quality, with a size of 26.46 Mbp distributed across 38 contigs and a BUSCO completion rate of 95.7%, indicating excellent contiguity and assembly completeness. A total of 8248 protein-encoding genes were predicted, with functional annotations assigned to 73.9% of them. Moreover, 82 genes displayed homology with entries in the Pathogen Host Interactions (PHI) database, while 494 genes exhibited similarity to entries in the Carbohydrate-Active Enzymes (CAZymes) database. Furthermore, 30 biosynthetic gene clusters (BGCs) were identified, suggesting significant potential for the biosynthesis of diverse secondary metabolites. Comparative functional analysis with closely related species unveiled a considerable abundance of domains linked to enzymes involved in keratin degradation, alongside a restricted number of domains associated with enzymes engaged in plant cell wall degradation in all studied species of the Onygenales. This genome-based elucidation not only enhances our comprehension of the biological characteristics of M. zuffiana but also furnishes valuable insights for subsequent investigations concerning Malbranchea species and the order Onygenales.
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Affiliation(s)
- Alan Omar Granados-Casas
- Mycology Unit, School of Medicine, Universitat Rovira i Virgili, C/ Sant Llorenç 21, 43201 Reus, Spain
| | - Ana Fernández-Bravo
- Mycology Unit, School of Medicine, Universitat Rovira i Virgili, C/ Sant Llorenç 21, 43201 Reus, Spain
| | - Alberto Miguel Stchigel
- Mycology Unit, School of Medicine, Universitat Rovira i Virgili, C/ Sant Llorenç 21, 43201 Reus, Spain
| | - José Francisco Cano-Lira
- Mycology Unit, School of Medicine, Universitat Rovira i Virgili, C/ Sant Llorenç 21, 43201 Reus, Spain
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Lind AL, McDonald NA, Gerrick ER, Bhatt AS, Pollard KS. Hybrid assemblies of microbiome Blastocystis protists reveal evolutionary diversification reflecting host ecology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567959. [PMID: 38045412 PMCID: PMC10690189 DOI: 10.1101/2023.11.20.567959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The most prevalent microbial eukaryote in the human gut is Blastocystis, an obligate commensal protist also common in many other vertebrates. Blastocystis is descended from free-living stramenopile ancestors; how it has adapted to thrive within humans and a wide range of hosts is unclear. Here, we cultivated six Blastocystis strains spanning the diversity of the genus and generated highly contiguous, annotated genomes with long-read DNA-seq, Hi-C, and RNA-seq. Comparative genomics between these strains and two closely related stramenopiles with different lifestyles, the lizard gut symbiont Proteromonas lacertae and the free-living marine flagellate Cafeteria burkhardae, reveal the evolutionary history of the Blastocystis genus. We find substantial gene content variability between Blastocystis strains. Blastocystis isolated from an herbivorous tortoise has many plant carbohydrate metabolizing enzymes, some horizontally acquired from bacteria, likely reflecting fermentation within the host gut. In contrast, human-isolated Blastocystis have gained many heat shock proteins, and we find numerous subtype-specific expansions of host-interfacing genes, including cell adhesion and cell surface glycan genes. In addition, we observe that human-isolated Blastocystis have substantial changes in gene structure, including shortened introns and intergenic regions, as well as genes lacking canonical termination codons. Finally, our data indicate that the common ancestor of Blastocystis lost nearly all ancestral genes for heterokont flagella morphology, including cilia proteins, microtubule motor proteins, and ion channel proteins. Together, these findings underscore the huge functional variability within the Blastocystis genus and provide candidate genes for the adaptations these lineages have undergone to thrive in the gut microbiomes of diverse vertebrates.
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Affiliation(s)
- Abigail L Lind
- Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA
| | | | - Elias R Gerrick
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, California, USA
| | - Katherine S Pollard
- Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Chan Zuckerberg Biohub SF, San Francisco, CA
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Orłowska M, Barua D, Piłsyk S, Muszewska A. Fucose as a nutrient ligand for Dikarya and a building block of early diverging lineages. IMA Fungus 2023; 14:17. [PMID: 37670396 PMCID: PMC10481521 DOI: 10.1186/s43008-023-00123-8] [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: 02/13/2023] [Accepted: 08/07/2023] [Indexed: 09/07/2023] Open
Abstract
Fucose is a deoxyhexose sugar present and studied in mammals. The process of fucosylation has been the primary focus in studies relating to fucose in animals due to the presence of fucose in Lewis antigens. Very few studies have reported its presence in Fungi, mostly in Mucoromycotina. The constitution of 25% and 12% of this sugar in the carbohydrates of cell wall in the respective Umbelopsis and Mucorales strains boosts the need to bridge the gap of knowledge on fucose metabolism across the fungal tree of life. In the absence of a network map involving fucose proteins, we carried out an in-silico approach to construct the fucose metabolic map in Fungi. We analyzed the taxonomic distribution of 85 protein families in Fungi including diverse early diverging fungal lineages. The expression of fucose-related protein-coding genes proteins was validated with the help of transcriptomic data originating from representatives of early diverging fungi. We found proteins involved in several metabolic activities apart from fucosylation such as synthesis, transport and binding. Most of the identified protein families are shared with Metazoa suggesting an ancestral origin in Opisthokonta. However, the overall complexity of fucose metabolism is greater in Metazoa than in Fungi. Massive gene loss has shaped the evolutionary history of these metabolic pathways, leading to a repeated reduction of these pathways in most yeast-forming lineages. Our results point to a distinctive mode of utilization of fucose among fungi belonging to Dikarya and the early diverging lineages. We speculate that, while Dikarya used fucose as a source of nutrients for metabolism, the early diverging group of fungi depended on fucose as a building block and signaling compound.
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Affiliation(s)
- Małgorzata Orłowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland.
| | - Drishtee Barua
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
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Secrets of the fungus-specific potassium channel TOK family. Trends Microbiol 2022; 31:511-520. [PMID: 36567187 DOI: 10.1016/j.tim.2022.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 12/25/2022]
Abstract
Several families of potassium (K+) channels are found in membranes of all eukaryotes, underlining the importance of K+ uptake and redistribution within and between cells and organs. Among them, TOK (tandem-pore outward-rectifying K+) channels consist of eight transmembrane domains and two pore domains per subunit organized in dimers. These channels were originally studied in yeast, but recent identifications and characterizations in filamentous fungi shed new light on this fungus-specific K+ channel family. Although their actual function in vivo is often puzzling, recent works indicate a role in cellular K+ homeostasis and even suggest a role in plant-fungus symbioses. This review aims at synthesizing the current knowledge on fungal TOK channels and discussing their potential role in yeasts and filamentous fungi.
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