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Singh PP, Reeves GA, Contrepois K, Papsdorf K, Miklas JW, Ellenberger M, Hu CK, Snyder MP, Brunet A. Evolution of diapause in the African turquoise killifish by remodeling the ancient gene regulatory landscape. Cell 2024; 187:3338-3356.e30. [PMID: 38810644 DOI: 10.1016/j.cell.2024.04.048] [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: 11/24/2021] [Revised: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species.
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Affiliation(s)
| | - G Adam Reeves
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | | | - Jason W Miklas
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA; Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
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2
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de Azevedo BL, Queiroz VF, de Aquino ILM, Machado TB, de Assis FL, Reis E, Araújo Júnior JP, Ullmann LS, Colson P, Greub G, Aylward F, Rodrigues RAL, Abrahão JS. The genomic and phylogenetic analysis of Marseillevirus cajuinensis raises questions about the evolution of Marseilleviridae lineages and their taxonomical organization. J Virol 2024; 98:e0051324. [PMID: 38752754 DOI: 10.1128/jvi.00513-24] [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: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 06/14/2024] Open
Abstract
Marseilleviruses (MsV) are a group of viruses that compose the Marseilleviridae family within the Nucleocytoviricota phylum. They have been found in different samples, mainly in freshwater. MsV are classically organized into five phylogenetic lineages (A/B/C/D/E), but the current taxonomy does not fully represent all the diversity of the MsV lineages. Here, we describe a novel strain isolated from a Brazilian saltwater sample named Marseillevirus cajuinensis. Based on genomics and phylogenetic analyses, M. cajuinensis exhibits a 380,653-bp genome that encodes 515 open reading frames. Additionally, M. cajuinensis encodes a transfer RNA, a feature that is rarely described for Marseilleviridae. Phylogeny suggests that M. cajuinensis forms a divergent branch within the MsV lineage A. Furthermore, our analysis suggests that the common ancestor for the five classical lineages of MsV diversified into three major groups. The organization of MsV into three main groups is reinforced by a comprehensive analysis of clusters of orthologous groups, sequence identities, and evolutionary distances considering several MsV isolates. Taken together, our results highlight the importance of discovering new viruses to expand the knowledge about known viruses that belong to the same lineages or families. This work proposes a new perspective on the Marseilleviridae lineages organization that could be helpful to a future update in the taxonomy of the Marseilleviridae family. IMPORTANCE Marseilleviridae is a family of viruses whose members were mostly isolated from freshwater samples. In this work, we describe the first Marseillevirus isolated from saltwater samples, which we called Marseillevirus cajuinensis. Most of M. cajuinensis genomic features are comparable to other Marseilleviridae members, such as its high number of unknown proteins. On the other hand, M. cajuinensis encodes a transfer RNA, which is a gene category involved in protein translation that is rarely described in this viral family. Additionally, our phylogenetic analyses suggested the existence of, at least, three major Marseilleviridae groups. These observations provide a new perspective on Marseilleviridae lineages organization, which will be valuable in future updates to the taxonomy of the family since the current official classification does not capture all the Marseilleviridae known diversity.
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Affiliation(s)
- Bruna Luiza de Azevedo
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Victória Fulgêncio Queiroz
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Isabella Luiza Martins de Aquino
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Talita Bastos Machado
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Lopes de Assis
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Erik Reis
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - João Pessoa Araújo Júnior
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Alameda das Tecomarias s/n, Chácara Capão Bonito, Botucatu, Brazil
| | - Leila Sabrina Ullmann
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Alameda das Tecomarias s/n, Chácara Capão Bonito, Botucatu, Brazil
| | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille University, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Gilbert Greub
- Centre for Research on Intracellular Bacteria and Giant Viruses, Institute of Microbiology, University Hospital Centre and University of Lausanne, Lausanne, Switzerland
| | - Frank Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease Virginia Tech, Blacksburg, Virginia, USA
| | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
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3
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Tomasch J, Kopejtka K, Shivaramu S, Mujakić I, Koblížek M. On the evolution of chromosomal regions with high gene strand bias in bacteria. mBio 2024; 15:e0060224. [PMID: 38752745 DOI: 10.1128/mbio.00602-24] [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: 02/27/2024] [Accepted: 04/17/2024] [Indexed: 06/13/2024] Open
Abstract
On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of "hybrid" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell's information content.
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Affiliation(s)
- Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Sahana Shivaramu
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
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Stephens D, Faghihi Z, Moniruzzaman M. Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals. Virus Evol 2024; 10:veae039. [PMID: 38808038 PMCID: PMC11131425 DOI: 10.1093/ve/veae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/29/2024] [Accepted: 05/12/2024] [Indexed: 05/30/2024] Open
Abstract
Stony corals (Order: Scleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene are contributing to the ongoing decline in coral reef health and coverage. While viruses are established modulators of marine microbial dynamics, their interactions within the coral holobiont and impact on coral health and physiology remain unclear. To address this key knowledge gap, we investigated diverse stony coral genomes for 'endogenous' viruses. Our study uncovered a remarkable number of integrated viral elements recognized as 'Polintoviruses' (Class Polintoviricetes) in thirty Scleractinia genomes; with several species harboring hundreds to thousands of polintoviruses. We reveal massive paralogous expansion of polintoviruses in stony coral genomes, alongside the presence of integrated elements closely related to Polinton-like viruses (PLVs), a group of viruses that exist as free virions. These results suggest multiple integrations of polintoviruses and PLV-relatives, along with paralogous expansions, shaped stony coral genomes. Re-analysis of existing gene expression data reveals all polintovirus structural and non-structural hallmark genes are expressed, providing support for free virion production from polintoviruses. Our results, revealing a significant diversity of polintovirus across the Scleractinia order, open a new research avenue into polintovirus and their possible roles in disease, genomic plasticity, and environmental adaptation in this key group of organisms.
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Affiliation(s)
- Danae Stephens
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
| | - Zahra Faghihi
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
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Zhang YF, Peng YL, Xiao YH, Yu B, Cao MY, Zhang ZL, Huang LQ, Li Y. Jeotgalibacillus haloalkalitolerans sp. nov., a novel alkalitolerant and halotolerant bacterium, isolated from the confluence of the Fenhe River and the Yellow River. Antonie Van Leeuwenhoek 2024; 117:74. [PMID: 38691182 DOI: 10.1007/s10482-024-01968-8] [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: 01/20/2024] [Accepted: 04/08/2024] [Indexed: 05/03/2024]
Abstract
A Gram-stain positive, aerobic, alkalitolerant and halotolerant bacterium, designated HH7-29 T, was isolated from the confluence of the Fenhe River and the Yellow River in Shanxi Province, PR China. Growth occurred at pH 6.0-12.0 (optimum, pH 8.0-8.5) and 15-40℃ (optimum, 32℃) with 0.5-24% NaCl (optimum, 2-9%). The predominant fatty acids (> 10.0%) were iso-C15:0 and anteiso-C15:0. The major menaquinones were MK-7 and MK-8. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified phospholipids. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain HH7-29 T was a member of the genus Jeotgalibacillus, exhibiting high sequence similarity to the 16S rRNA gene sequences of Jeotgalibacillus alkaliphilus JC303T (98.4%), Jeotgalibacillus salarius ASL-1 T (98.1%) and Jeotgalibacillus alimentarius YKJ-13 T (98.1%). The genomic DNA G + C content was 43.0%. Gene annotation showed that strain HH7-29 T had lower protein isoelectric points (pIs) and possessed genes related to ion transport and organic osmoprotectant uptake, implying its potential tolerance to salt and alkali. The average nucleotide identity, digital DNA-DNA hybridization values, amino acid identity values, and percentage of conserved proteins values between strain HH7-29 T and its related species were 71.1-83.8%, 19.5-27.4%, 66.5-88.4% and 59.8-76.6%, respectively. Based on the analyses of phenotypic, chemotaxonomic, phylogenetic and genomic features, strain HH7-29 T represents a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus haloalkalitolerans sp. nov. is proposed. The type strain is HH7-29 T (= KCTC 43417 T = MCCC 1K07541T).
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Affiliation(s)
- Ya-Fei Zhang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Jinzhong, People's Republic of China
| | - Yun-Lin Peng
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Jinzhong, People's Republic of China
| | - Yong-Hui Xiao
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Jinzhong, People's Republic of China
| | - Bing Yu
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Jinzhong, People's Republic of China
| | - Ming-Yue Cao
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Jinzhong, People's Republic of China
| | - Zhi-Ling Zhang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Jinzhong, People's Republic of China
| | - Le-Qun Huang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Jinzhong, People's Republic of China
| | - Yi Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Jinzhong, People's Republic of China.
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Xu X, He M, Xue Q, Li X, Liu A. Genome-based taxonomic classification of the genus Sulfitobacter along with the proposal of a new genus Parasulfitobacter gen. nov. and exploring the gene clusters associated with sulfur oxidation. BMC Genomics 2024; 25:389. [PMID: 38649849 PMCID: PMC11034169 DOI: 10.1186/s12864-024-10269-3] [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: 11/08/2023] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The genus Sulfitobacter, a member of the family Roseobacteraceae, is widely distributed in the ocean and is believed to play crucial roles in the global sulfur cycle. However, gene clusters associated with sulfur oxidation in genomes of the type strains of this genus have been poorly studied. Furthermore, taxonomic errors have been identified in this genus, potentially leading to significant confusion in ecological and evolutionary interpretations in subsequent studies of the genus Sulfitobacter. This study aims to investigate the taxonomic status of this genus and explore the metabolism associated with sulfur oxidation. RESULTS This study suggests that Sulfitobacter algicola does not belong to Sulfitobacter and should be reclassified into a novel genus, for which we propose the name Parasulfitobacter gen. nov., with Parasulfitobacter algicola comb. nov. as the type species. Additionally, enzymes involved in the sulfur oxidation process, such as the sulfur oxidization (Sox) system, the disulfide reductase protein family, and the sulfite dehydrogenase (SoeABC), were identified in almost all Sulfitobacter species. This finding implies that the majority of Sulfitobacter species can oxidize reduced sulfur compounds. Differences in the modular organization of sox gene clusters among Sulfitobacter species were identified, along with the presence of five genes with unknown function located in some of the sox gene clusters. Lastly, this study revealed the presence of the demethylation pathway and the cleavage pathway used by many Sulfitobacter species to degrade dimethylsulfoniopropionate (DMSP). These pathways enable these bacteria to utilize DMSP as important source of sulfur and carbon or as a defence strategy. CONCLUSIONS Our findings contribute to interpreting the mechanism by which Sulfitobacter species participate in the global sulfur cycle. The taxonomic rearrangement of S. algicola into the novel genus Parasulfitobacter will prevent confusion in ecological and evolutionary interpretations in future studies of the genus Sulfitobacter.
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Affiliation(s)
- Xiaokun Xu
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Mengdan He
- School of Basic Medical Sciences, Shandong Second Medical University, 261042, Weifang, Shandong, P. R. China
| | - Qingjie Xue
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Xiuzhen Li
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Ang Liu
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China.
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Sulaiman JE, Thompson J, Qian Y, Vivas EI, Diener C, Gibbons SM, Safdar N, Venturelli OS. Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.13.589383. [PMID: 38659900 PMCID: PMC11042340 DOI: 10.1101/2024.04.13.589383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The human gut pathogen Clostridioides difficile displays extreme genetic variability and confronts a changeable nutrient landscape in the gut. We mapped gut microbiota inter-species interactions impacting the growth and toxin production of diverse C. difficile strains in different nutrient environments. Although negative interactions impacting C. difficile are prevalent in environments promoting resource competition, they are sparse in an environment containing C. difficile-preferred carbohydrates. C. difficile strains display differences in interactions with Clostridium scindens and the ability to compete for proline. C. difficile toxin production displays substantial community-context dependent variation and does not trend with growth-mediated inter-species interactions. C. difficile shows substantial differences in transcriptional profiles in the presence of the closely related species C. hiranonis or C. scindens. In co-culture with C. hiranonis, C. difficile exhibits massive alterations in metabolism and other cellular processes, consistent with their high metabolic overlap. Further, Clostridium hiranonis inhibits the growth and toxin production of diverse C. difficile strains across different nutrient environments and ameliorates the disease severity of a C. difficile challenge in a murine model. In sum, strain-level variability and nutrient environments are major variables shaping gut microbiota interactions with C. difficile.
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Affiliation(s)
- Jordy Evan Sulaiman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jaron Thompson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Yili Qian
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Eugenio I. Vivas
- Gnotobiotic Animal Core Facility, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Sean M. Gibbons
- Institute for Systems Biology, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- eScience Institute, University of Washington, Seattle, WA, USA
| | - Nasia Safdar
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, William S. Middleton Veterans Hospital Madison, Madison, WI, USA
| | - Ophelia S. Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
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Cheng X, Jiang W, Wang Q, Liu K, Dai W, Liu Y, Shao C, Li Q. Unveiling Gene Expression Dynamics during Early Embryogenesis in Cynoglossus semilaevis: A Transcriptomic Perspective. Life (Basel) 2024; 14:505. [PMID: 38672775 PMCID: PMC11050975 DOI: 10.3390/life14040505] [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: 03/24/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Commencing with sperm-egg fusion, the early stages of metazoan development include the cleavage and formation of blastula and gastrula. These early embryonic events play a crucial role in ontogeny and are accompanied by a dramatic remodeling of the gene network, particularly encompassing the maternal-to-zygotic transition. Nonetheless, the gene expression dynamics governing early embryogenesis remain unclear in most metazoan lineages. We conducted transcriptomic profiling on two types of gametes (oocytes and sperms) and early embryos (ranging from the four-cell to the gastrula stage) of an economically valuable flatfish-the Chinese tongue sole Cynoglossus semilaevis (Pleuronectiformes: Cynoglossidae). Comparative transcriptome analysis revealed that large-scale zygotic genome activation (ZGA) occurs in the blastula stage, aligning with previous findings in zebrafish. Through the comparison of the most abundant transcripts identified in each sample and the functional analysis of co-expression modules, we unveiled distinct functional enrichments across different gametes/developmental stages: actin- and immune-related functions in sperms; mitosis, transcription inhibition, and mitochondrial function in oocytes and in pre-ZGA embryos (four- to 1000-cell stage); and organ development in post-ZGA embryos (blastula and gastrula). These results provide insights into the intricate transcriptional regulation of early embryonic development in Cynoglossidae fish and expand our knowledge of developmental constraints in vertebrates.
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Affiliation(s)
- Xinyi Cheng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China;
- BGI Research, Wuhan 430074, China;
| | - Wei Jiang
- BGI Research, Shenzhen 518083, China;
| | - Qian Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.W.); (K.L.); (Y.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Kaiqiang Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.W.); (K.L.); (Y.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Wei Dai
- BGI Research, Wuhan 430074, China;
| | - Yuyan Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.W.); (K.L.); (Y.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.W.); (K.L.); (Y.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qiye Li
- BGI Research, Wuhan 430074, China;
- BGI Research, Shenzhen 518083, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Fricke LC, Lindsey ARI. Identification of Parthenogenesis-Inducing Effector Proteins in Wolbachia. Genome Biol Evol 2024; 16:evae036. [PMID: 38530785 PMCID: PMC11019157 DOI: 10.1093/gbe/evae036] [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: 12/13/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 03/28/2024] Open
Abstract
Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called "parthenogenesis induction" phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 yr ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing Wolbachia and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex determining factor Transformer, and a eukaryotic-like serine-threonine kinase with leucine-rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model Saccharomyces cerevisiae. We suggest that these proteins are parthenogenesis-inducing factors and our results indicate that this would be made possible by a novel mechanism of bacterial-host interaction.
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Affiliation(s)
- Laura C Fricke
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
| | - Amelia R I Lindsey
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
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10
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Shao X, Wang YN, Zhang YF, Meng D, Su JY, Yu B, Sun ML, Li Y. Marinobacter qingdaonensis sp. nov., a moderately halotolerant bacterium isolated from intertidal sediment. Int J Syst Evol Microbiol 2024; 74. [PMID: 38591775 DOI: 10.1099/ijsem.0.006327] [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: 04/10/2024] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped and halotolerant bacterium, designated as strain ASW11-75T, was isolated from intertidal sediments in Qingdao, PR China, and identified using a polyphasic taxonomic approach. Growth of strain ASW11-75T occurred at 10-45 °C (optimum, 37 °C), pH 6.5-9.0 (optimum, pH 8.0) and 0.5-18.0 % NaCl concentrations (optimum, 2.5 %). Phylogenetic analyses based on 16S rRNA gene sequences and 1179 single-copy orthologous clusters indicated that strain ASW11-75T is affiliated with the genus Marinobacter. Strain ASW11-75T showed highest 16S rRNA gene sequence similarity to 'Marinobacter arenosus' CAU 1620T (98.5 %). The digital DNA-DNA hybridization and average nucleotide identity values between strain ASW11-75T and its closely related strains (Marinobacter salarius R9SW1T, Marinobacter similis A3d10T, 'Marinobacter arenosus' CAU 1620T, Marinobacter sediminum R65T, Marinobacter salinus Hb8T, Marinobacter alexandrii LZ-8T and Marinobacter nauticus ATCC 49840T) were 19.8-24.5 % and 76.6-80.7 %, respectively. The predominant cellular fatty acids were C16 : 0, C18 : 1 ω9c and C16 : 0 N alcohol. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid and two unidentified lipids. The major isoprenoid quinone was ubiquinone-9. The genomic DNA G+C content was 62.2 mol%. Based on genomic and gene function analysis, strain ASW11-75T had lower protein isoelectric points with higher ratios of acidic residues to basic residues and possessed genes related to ion transport and organic osmoprotectant uptake, implying its potential tolerance to salt. The results of polyphasic characterization indicated strain ASW11-75T represents a novel Marinobacter species, for which the name Marinobacter qingdaonensis sp. nov. with the type strain ASW11-75T is proposed. The type strain is ASW11-75T (=KCTC 82497T=MCCC 1K05587T).
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Affiliation(s)
- Xuan Shao
- Henan Provincial Engineering Research Center for Development and Application of Characteristic Microorganism Resources, Engineering Technology Research Center of Biomass Degradation and Gasification, Key Laboratory on Agricultural Microorganism Resources Development of Shangqiu, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Ya-Nan Wang
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Ya-Fei Zhang
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Di Meng
- Henan Provincial Engineering Research Center for Development and Application of Characteristic Microorganism Resources, Engineering Technology Research Center of Biomass Degradation and Gasification, Key Laboratory on Agricultural Microorganism Resources Development of Shangqiu, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Jing-Yun Su
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Bing Yu
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Mei-Ling Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266000, PR China
| | - Yi Li
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
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11
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Schutz K, Melie T, Smith SD, Quandt CA. Patterns recovered in phylogenomic analysis of Candida auris and close relatives implicate broad environmental flexibility in Candida/Clavispora clade yeasts. Microb Genom 2024; 10. [PMID: 38630608 DOI: 10.1099/mgen.0.001233] [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: 04/19/2024] Open
Abstract
Fungal pathogens commonly originate from benign or non-pathogenic strains living in the natural environment. The recently emerged human pathogen, Candida auris, is one example of a fungus believed to have originated in the environment and recently transitioned into a clinical setting. To date, however, there is limited evidence about the origins of this species in the natural environment and when it began associating with humans. One approach to overcome this gap is to reconstruct phylogenetic relationships between (1) strains isolated from clinical and non-clinical environments and (2) between species known to cause disease in humans and benign environmental saprobes. C. auris belongs to the Candida/Clavispora clade, a diverse group of 45 yeast species including human pathogens and environmental saprobes. We present a phylogenomic analysis of the Candida/Clavispora clade aimed at understanding the ecological breadth and evolutionary relationships between an expanded sample of environmentally and clinically isolated yeasts. To build a robust framework for investigating these relationships, we developed a whole-genome sequence dataset of 108 isolates representing 18 species, including four newly sequenced species and 18 environmentally isolated strains. Our phylogeny, based on 619 orthologous genes, shows environmentally isolated species and strains interspersed with clinically isolated counterparts, suggesting that there have been many transitions between humans and the natural environment in this clade. Our findings highlight the breadth of environments these yeasts inhabit and imply that many clinically isolated yeasts in this clade could just as easily live outside the human body in diverse natural environments and vice versa.
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Affiliation(s)
- Kyle Schutz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Tina Melie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
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12
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Moraïs S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, Lamed E, Artan-Furman A, Bolam DN, Yadav MP, Bayer EA, Martin WF, Mizrahi I. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science 2024; 383:eadj9223. [PMID: 38484069 PMCID: PMC7615765 DOI: 10.1126/science.adj9223] [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: 07/25/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multienzymatic cellulosome structures capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut, potentially during domestication where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations but are rare in populations from industrialized societies thus indicating potential disappearance in response to the westernized lifestyle.
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Affiliation(s)
- Sarah Moraïs
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sarah Winkler
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Falk S. P. Nagies
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Nils Kapust
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Eva Lamed
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - Avital Artan-Furman
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - David N. Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Madhav P. Yadav
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Edward A. Bayer
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - William F. Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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13
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Tavis S, Hettich RL. Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome. BMC Genomics 2024; 25:267. [PMID: 38468234 PMCID: PMC10926591 DOI: 10.1186/s12864-024-10082-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: 11/13/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024] Open
Abstract
In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence of predicting protein function across all organisms, function prediction tools generally fail to use all of the types of data available for any specific organism, including protein and transcript expression information. Additionally, the release of Alphafold predictions for all Uniprot proteins provides a novel opportunity for leveraging structural information. We constructed a bespoke machine learning model to predict the function of recalcitrant proteins of unknown function in Pseudomonas putida based on these sources of data, which annotated 1079 terms to 213 proteins. Among the predicted functions supplied by the model, we found evidence for a significant overrepresentation of nitrogen metabolism and macromolecule processing proteins. These findings were corroborated by manual analyses of selected proteins which identified, among others, a functionally unannotated operon that likely encodes a branch of the shikimate pathway.
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Affiliation(s)
- Steven Tavis
- Genome Science and Technology Graduate Program, University of Tennessee Knoxville, Knoxville, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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14
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Majander K, Pla-Díaz M, du Plessis L, Arora N, Filippini J, Pezo-Lanfranco L, Eggers S, González-Candelas F, Schuenemann VJ. Redefining the treponemal history through pre-Columbian genomes from Brazil. Nature 2024; 627:182-188. [PMID: 38267579 PMCID: PMC10917687 DOI: 10.1038/s41586-023-06965-x] [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] [Received: 05/25/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions1,2. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico3-6. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses.
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Affiliation(s)
- Kerttu Majander
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Marta Pla-Díaz
- Unidad Mixta Infección y Salud Pública, FISABIO/Universidad de Valencia-I2SysBio, Valencia, Spain
- CIBER in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, Spain
| | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, Switzerland
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Jose Filippini
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Luis Pezo-Lanfranco
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
- Institute of Environmental Science and Technology (ICTA) and Prehistory Department, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sabine Eggers
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública, FISABIO/Universidad de Valencia-I2SysBio, Valencia, Spain.
- CIBER in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, Spain.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
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15
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Luo Z, McTaggart A, Schwessinger B. Genome biology and evolution of mating-type loci in four cereal rust fungi. PLoS Genet 2024; 20:e1011207. [PMID: 38498573 PMCID: PMC10977897 DOI: 10.1371/journal.pgen.1011207] [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: 08/28/2023] [Revised: 03/28/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Permanent heterozygous loci, such as sex- or mating-compatibility regions, often display suppression of recombination and signals of genomic degeneration. In Basidiomycota, two distinct loci confer mating compatibility. These loci encode homeodomain (HD) transcription factors and pheromone receptor (Pra)-ligand allele pairs. To date, an analysis of genome level mating-type (MAT) loci is lacking for obligate biotrophic basidiomycetes in the Pucciniales, an order containing serious agricultural plant pathogens. Here, we focus on four species of Puccinia that infect oat and wheat, including P. coronata f. sp. avenae, P. graminis f. sp. tritici, P. triticina and P. striiformis f. sp. tritici. MAT loci are located on two separate chromosomes supporting previous hypotheses of a tetrapolar mating compatibility system in the Pucciniales. The HD genes are multiallelic in all four species while the PR locus appears biallelic, except for P. graminis f. sp. tritici, which potentially has multiple alleles. HD loci are largely conserved in their macrosynteny, both within and between species, without strong signals of recombination suppression. Regions proximal to the PR locus, however, displayed signs of recombination suppression and genomic degeneration in the three species with a biallelic PR locus. Our observations support a link between recombination suppression, genomic degeneration, and allele diversity of MAT loci that is consistent with recent mathematical modelling and simulations. Finally, we confirm that MAT genes are expressed during the asexual infection cycle, and we propose that this may support regulating nuclear maintenance and pairing during infection and spore formation. Our study provides insights into the evolution of MAT loci of key pathogenic Puccinia species. Understanding mating compatibility can help predict possible combinations of nuclear pairs, generated by sexual reproduction or somatic recombination, and the potential evolution of new virulent isolates of these important plant pathogens.
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Affiliation(s)
- Zhenyan Luo
- Research Biology School, Australian National University, Canberra, ACT, Australia
| | - Alistair McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, Queensland, Australia
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16
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Taujale R, Gravel N, Zhou Z, Yeung W, Kochut K, Kannan N. Informatic challenges and advances in illuminating the druggable proteome. Drug Discov Today 2024; 29:103894. [PMID: 38266979 DOI: 10.1016/j.drudis.2024.103894] [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: 10/15/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
The understudied members of the druggable proteomes offer promising prospects for drug discovery efforts. While large-scale initiatives have generated valuable functional information on understudied members of the druggable gene families, translating this information into actionable knowledge for drug discovery requires specialized informatics tools and resources. Here, we review the unique informatics challenges and advances in annotating understudied members of the druggable proteome. We demonstrate the application of statistical evolutionary inference tools, knowledge graph mining approaches, and protein language models in illuminating understudied protein kinases, pseudokinases, and ion channels.
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Affiliation(s)
- Rahil Taujale
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Nathan Gravel
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | | | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Krystof Kochut
- School of Computing, University of Georgia, Athens, GA, USA
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
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17
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Camacho J, Mesén-Porras E, Rojas-Gätjens D, Pérez-Pantoja D, Puente-Sánchez F, Chavarría M. Draft genome sequence of three hydrocarbon-degrading Pseudomonadota strains isolated from an abandoned century-old oil exploration well. Microbiol Resour Announc 2024; 13:e0107623. [PMID: 38289048 PMCID: PMC10868222 DOI: 10.1128/mra.01076-23] [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: 11/10/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024] Open
Abstract
We present genome sequences of three Pseudomonadota strains isolated from an abandoned century-old oil exploration well. A Pseudomonas sp. genome showed a size of 5,378,420 bp, while Acinetobacter genomes sized 3,522,593 and 3,864,311 bp. Genomes included catabolic genes for benzoate, 4-hydroxybenzoate, salicylate, vanillate, indoleacetate, anthranilate, n-alkanes, 4-hydroxyphenylacetate, phenylacetate, among others.
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Affiliation(s)
- Jefferson Camacho
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Esteve Mesén-Porras
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Danilo Pérez-Pantoja
- Instituto Universitario de Investigación y Desarrollo Tecnológico, Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Fernando Puente-Sánchez
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms väg, Uppsala, Sweden
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
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18
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Uddin S, Munir MZ, Larriba E, Pérez-Pérez JM, Gull S, Pervaiz T, Mahmood U, Mahmood Z, Sun Y, Li Y. Temporal profiling of physiological, histological, and transcriptomic dissection during auxin-induced adventitious root formation in tetraploid Robinia pseudoacacia micro-cuttings. PLANTA 2024; 259:66. [PMID: 38332379 DOI: 10.1007/s00425-024-04341-1] [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: 10/10/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
MAIN CONCLUSION Optimal levels of indole-3-butyric acid (IBA) applied at the stem base promote adventitious root (AR) initiation and primordia formation, thus promoting the rooting of leafy micro-cuttings of tetraploid Robinia pseudoacacia. Tetraploid Robinia pseudoacacia L. is a widely cultivated tree in most regions of China that has a hard-rooting capability, propagated by stem cuttings. This study utilizes histological, physiological, and transcriptomic approaches to explore how root primordia are induced after indole butyric acid (IBA) treatment of micro-cuttings. IBA application promoted cell divisions in some cells within the vasculature, showing subcellular features associated with adventitious root (AR) founder cells. The anatomical structure explicitly showed that AR initiated from the cambium layer and instigate the inducible development of AR primordia. Meanwhile, the hormone data showed that similar to that of indole-3-acetic acid, the contents of trans-zeatin and abscisic acid peaked at early stages of AR formation and increased gradually in primordia formation across the subsequent stages, suggesting their indispensable roles in AR induction. On the contrary, 24-epibrassinolide roughly maintained at extremely high levels during primordium initiation thoroughly, indicating its presence was involved in cell-specific reorganization during AR development. Furthermore, antioxidant activities transiently increased in the basal region of micro-cuttings and may serve as biochemical indicators for distinct rooting phases, potentially aiding in AR formation. Transcriptomic analysis during the early stages of root formation shows significant downregulation of the abscisic acid and jasmonate signaling pathways, while ethylene and cytokinin signaling seems upregulated. Network analysis of genes involved in carbon metabolism and photosynthesis indicates that the basal region of the micro-cuttings undergoes rapid reprogramming, which results in the breakdown of sugars into pyruvate. This pyruvate is then utilized to fuel the tricarboxylic acid cycle, thereby sustaining growth through aerobic respiration. Collectively, our findings provide a time-course morphophysiological dissection and also suggest the regulatory role of a conserved auxin module in AR development in these species.
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Affiliation(s)
- Saleem Uddin
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Muhammad Zeeshan Munir
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Eduardo Larriba
- Instituto de Bioingeniería, Universidad Miguel Hernández de Elche, Alicante, Spain
| | | | - Sadia Gull
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Tariq Pervaiz
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 22963, USA
| | - Umer Mahmood
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Zahid Mahmood
- Crop Sciences Institute, National Agricultural Research Centre, Islamabad, 44000, Pakistan
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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19
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Benson CW, Sheltra MR, Huff DR. The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss. G3 (BETHESDA, MD.) 2024; 14:jkad238. [PMID: 37847611 PMCID: PMC10849329 DOI: 10.1093/g3journal/jkad238] [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: 05/28/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
To complete its parasitic lifecycle, Salmacisia buchloëana, a biotrophic fungus, manipulates reproductive organ development, meristem determinacy, and resource allocation in its dioecious plant host, buffalograss (Bouteloua dactyloides; Poaceae). To gain insight into S. buchloëana's ability to manipulate its host, we sequenced and assembled the 20.1 Mb genome of S. buchloëana into 22 chromosome-level pseudomolecules. Phylogenetic analysis suggests that S. buchloëana is nested within the genus Tilletia and diverged from Tilletia caries and Tilletia walkeri ∼40 MYA. We find that S. buchloëana contains a novel chromosome arm with no syntenic relationship to other publicly available Tilletia genomes, and that genes on the novel arm are upregulated upon infection, suggesting that this unique chromosomal segment may have played a critical role in S. buchloëana's evolution and host specificity. Salmacisia buchloëana has one of the largest fractions of serine peptidases (1.53% of the proteome) and one of the highest GC contents (62.3%) in all classified fungi. Analysis of codon base composition indicated that GC content is controlled more by selective constraints than directional mutation, and that S. buchloëana has a unique bias for the serine codon UCG. Finally, we identify 3 inteins within the S. buchloëana genome, 2 of which are located in a gene often used in fungal taxonomy. The genomic and transcriptomic resources generated here will aid plant pathologists and breeders by providing insight into the extracellular components contributing to sex determination in dioecious grasses.
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Affiliation(s)
- Christopher W Benson
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - Matthew R Sheltra
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - David R Huff
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
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Luo B, Su JY, Zhang YF, Xiao YH, Peng YL, Sun ML, Li Y. Alteromonas arenosi sp. nov., a novel bioflocculant-producing bacterium, isolated from intertidal sand. Antonie Van Leeuwenhoek 2024; 117:28. [PMID: 38280034 DOI: 10.1007/s10482-023-01926-w] [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: 09/03/2023] [Accepted: 12/30/2023] [Indexed: 01/29/2024]
Abstract
A novel Gram-stain-negative, strictly aerobic and bioflocculant-producing bacterium, designated as ASW11-36T, was isolated from an intertidal sand collected from coastal areas of Qingdao, PR China. Growth occurred at 15-40 °C (optimum, 30 °C), pH 7.0-9.0 (optimum, pH 7.5) and with 1.5-7.0% (w/v) NaCl (optimum, 2.5-3.0%). In the whole-cell fatty acid pattern prevailed C16:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The major isoprenoid quinone was determined to be Q-8 and the major polar lipids were phosphatidylethanolamine (PE) and phosphatidylglycerol (PG), one unidentified aminolipid (AL), one unidentified glycolipid (GL), and two lipids (L1, L2). Based on the phylogenetic analyses of 16S rRNA gene sequences and 618 single-copy orthologous clusters, strain ASW11-36T could represent a novel member of the genus Alteromonas and was closely related to Alteromonas flava P0211T (98.4%) and Alteromonas facilis P0213T (98.3%). The pairwise average nucleotide identity and digital DNA-DNA hybridization values of the ASW11-36T genome assembly against the closely related species genomes were 71.8% and 21.7%, respectively, that clearly lower than the proposed thresholds for species. Based on phenotypic, phylogenetic, and chemotaxonomic analyses, strain ASW11-36T is considered to represent a novel species of the genus Alteromonas, for which the name Alteromonas arenosi sp. nov. is proposed. The type strain is ASW11-36T (= KCTC 82496T = MCCC 1K05585T). In addition, the strain yielded 65% of flocculating efficiency in kaolin suspension with CaCl2 addition. The draft genome of ASW11-36T shared abundant putative CAZy family related genes, especially involved in the biosynthesis of exopolysaccharides, implying its potential environmental and biological applications.
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Affiliation(s)
- Bi Luo
- College of Life Sciences, Financial Assets Department, Shanxi Agricultural University, Taigu, 030801, China
| | - Jing-Yun Su
- College of Life Sciences, Financial Assets Department, Shanxi Agricultural University, Taigu, 030801, China
| | - Ya-Fei Zhang
- College of Life Sciences, Financial Assets Department, Shanxi Agricultural University, Taigu, 030801, China
| | - Yong-Hui Xiao
- College of Life Sciences, Financial Assets Department, Shanxi Agricultural University, Taigu, 030801, China
| | - Yun-Lin Peng
- College of Life Sciences, Financial Assets Department, Shanxi Agricultural University, Taigu, 030801, China
| | - Mei-Ling Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266000, China.
| | - Yi Li
- College of Life Sciences, Financial Assets Department, Shanxi Agricultural University, Taigu, 030801, China.
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García-Saldaña EA, Cerqueda-García D, Ibarra-Laclette E, Aluja M. Insights into the differences related to the resistance mechanisms to the highly toxic fruit Hippomane mancinella (Malpighiales: Euphorbiaceae) between the larvae of the sister species Anastrepha acris and Anastrepha ludens (Diptera: Tephritidae) through comparative transcriptomics. Front Physiol 2024; 15:1263475. [PMID: 38304114 PMCID: PMC10830740 DOI: 10.3389/fphys.2024.1263475] [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: 07/19/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
The Manchineel, Hippomane mancinella ("Death Apple Tree") is one of the most toxic fruits worldwide and nevertheless is the host plant of the monophagous fruit fly species Anastrepha acris (Diptera: Tephritidae). Here we aimed at elucidating the detoxification mechanisms in larvae of A. acris reared on a diet enriched with the toxic fruit (6% lyophilizate) through comparative transcriptomics. We compared the performance of A. acris larvae with that of the sister species A. ludens, a highly polyphagous pest species that is unable to infest H. mancinella in nature. The transcriptional alterations in A. ludens were significantly greater than in A. acris. We mainly found two resistance mechanisms in both species: structural, activating cuticle protein biosynthesis (chitin-binding proteins likely reducing permeability to toxic compounds in the intestine), and metabolic, triggering biosynthesis of serine proteases and xenobiotic metabolism activation by glutathione-S-transferases and cytochrome P450 oxidoreductase. Some cuticle proteins and serine proteases were not orthologous between both species, suggesting that in A. acris, a structural resistance mechanism has been selected allowing specialization to the highly toxic host plant. Our results represent a nice example of how two phylogenetically close species diverged over recent evolutionary time related to resistance mechanisms to plant secondary metabolites.
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Affiliation(s)
- Essicka A. García-Saldaña
- Clúster Científico y Tecnológico BioMimic, Red de Manejo Biorracional de Plagas y Vectores, Instituto de Ecología, A C–INECOL, Xalapa, Veracruz, Mexico
| | - Daniel Cerqueda-García
- Clúster Científico y Tecnológico BioMimic, Red de Manejo Biorracional de Plagas y Vectores, Instituto de Ecología, A C–INECOL, Xalapa, Veracruz, Mexico
| | - Enrique Ibarra-Laclette
- Clúster Científico y Tecnológico BioMimic, Red de Estudios Moleculares Avanzados, Instituto de Ecología, A C–INECOL, Xalapa, Veracruz, Mexico
| | - Martín Aluja
- Clúster Científico y Tecnológico BioMimic, Red de Manejo Biorracional de Plagas y Vectores, Instituto de Ecología, A C–INECOL, Xalapa, Veracruz, Mexico
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22
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Flaiz M, Poehlein A, Wilhelm W, Mook A, Daniel R, Dürre P, Bengelsdorf FR. Refining and illuminating acetogenic Eubacterium strains for reclassification and metabolic engineering. Microb Cell Fact 2024; 23:24. [PMID: 38233843 PMCID: PMC10795377 DOI: 10.1186/s12934-024-02301-8] [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: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND The genus Eubacterium is quite diverse and includes several acetogenic strains capable of fermenting C1-substrates into valuable products. Especially, Eubacterium limosum and closely related strains attract attention not only for their capability to ferment C1 gases and liquids, but also due to their ability to produce butyrate. Apart from its well-elucidated metabolism, E. limosum is also genetically accessible, which makes it an interesting candidate to be an industrial biocatalyst. RESULTS In this study, we examined genomic, phylogenetic, and physiologic features of E. limosum and the closest related species E. callanderi as well as E. maltosivorans. We sequenced the genomes of the six Eubacterium strains 'FD' (DSM 3662T), 'Marburg' (DSM 3468), '2A' (DSM 2593), '11A' (DSM 2594), 'G14' (DSM 107592), and '32' (DSM 20517) and subsequently compared these with previously available genomes of the E. limosum type strain (DSM 20543T) as well as the strains 'B2', 'KIST612', 'YI' (DSM 105863T), and 'SA11'. This comparison revealed a close relationship between all eleven Eubacterium strains, forming three distinct clades: E. limosum, E. callanderi, and E. maltosivorans. Moreover, we identified the gene clusters responsible for methanol utilization as well as genes mediating chain elongation in all analyzed strains. Subsequent growth experiments revealed that strains of all three clades can convert methanol and produce acetate, butyrate, and hexanoate via reverse β-oxidation. Additionally, we used a harmonized electroporation protocol and successfully transformed eight of these Eubacterium strains to enable recombinant plasmid-based expression of the gene encoding the fluorescence-activating and absorption shifting tag (FAST). Engineered Eubacterium strains were verified regarding their FAST-mediated fluorescence at a single-cell level using a flow cytometry approach. Eventually, strains 'FD' (DSM 3662T), '2A' (DSM 2593), '11A' (DSM 2594), and '32' (DSM 20517) were genetically engineered for the first time. CONCLUSION Strains of E. limosum, E. callanderi, and E. maltosivorans are outstanding candidates as biocatalysts for anaerobic C1-substrate conversion into valuable biocommodities. A large variety of strains is genetically accessible using a harmonized electroporation protocol, and FAST can serve as a reliable fluorescent reporter protein to characterize genetically engineered cells. In total eleven strains have been assigned to distinct clades, providing a clear and updated classification. Thus, the description of respective Eubacterium species has been emended, improved, aligned, and is requested to be implemented in respective databases.
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Affiliation(s)
- Maximilian Flaiz
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany.
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Wiebke Wilhelm
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Alexander Mook
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Frank R Bengelsdorf
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany.
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23
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Hyde JR, Armond T, Herring JA, Hope S, Grose JH, Breakwell DP, Pickett BE. Diversity and conservation of the genome architecture of phages infecting the Alphaproteobacteria. Microbiol Spectr 2024; 12:e0282723. [PMID: 37991376 PMCID: PMC10783043 DOI: 10.1128/spectrum.02827-23] [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: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE This study reports the results of the largest analysis of genome sequences from phages that infect the Alphaproteobacteria class of bacterial hosts. We analyzed over 100 whole genome sequences of phages to construct dotplots, categorize them into genetically distinct clusters, generate a bootstrapped phylogenetic tree, compute protein orthologs, and predict packaging strategies. We determined that the phage sequences primarily cluster by the bacterial host family, phage morphotype, and genome size. We expect that the findings reported in this seminal study will facilitate future analyses that will improve our knowledge of the phages that infect these hosts.
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Affiliation(s)
- Jonathan R. Hyde
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Thomas Armond
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jacob A. Herring
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P. Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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24
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Sepúlveda-Rebolledo P, González-Rosales C, Dopson M, Pérez-Rueda E, Holmes DS, Valdés JH. Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives. Res Microbiol 2024; 175:104135. [PMID: 37678513 DOI: 10.1016/j.resmic.2023.104135] [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] [Received: 05/29/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Extreme acidophiles thrive in acidic environments, confront a multitude of challenges, and demonstrate remarkable adaptability in their metabolism to cope with the ever-changing environmental fluctuations, which encompass variations in temperature, pH levels, and the availability of electron acceptors and donors. The survival and proliferation of members within the Acidithiobacillia class rely on the deployment of transcriptional regulatory systems linked to essential physiological traits. The study of these transcriptional regulatory systems provides valuable insights into critical processes, such as energy metabolism and nutrient assimilation, and how they integrate into major genetic-metabolic circuits. In this study, we examined the transcriptional regulatory repertoires and potential interactions of forty-three Acidithiobacillia complete and draft genomes, encompassing nine species. To investigate the function and diversity of Transcription Factors (TFs) and their DNA Binding Sites (DBSs), we conducted a genome-wide comparative analysis, which allowed us to identify these regulatory elements in representatives of Acidithiobacillia. We classified TFs into gene families and compared their occurrence among all representatives, revealing conservation patterns across the class. The results identified conserved regulators for several pathways, including iron and sulfur oxidation, the main pathways for energy acquisition, providing new evidence for viable regulatory interactions and branch-specific conservation in Acidithiobacillia. The identification of TFs and DBSs not only corroborates existing experimental information for selected species, but also introduces novel candidates for experimental validation. Moreover, these promising candidates have the potential for further extension to new representatives within the class.
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Affiliation(s)
- Pedro Sepúlveda-Rebolledo
- Centro de Genómica y Bioinformática and PhD. Program on Integrative Genomics, Facultad de Ciencias, Universidad Mayor, Santiago (8580745), Chile.
| | - Carolina González-Rosales
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago (8580638), Chile; Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Yucatán, Mexico.
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago (8580638), Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago (7510156), Chile.
| | - Jorge H Valdés
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago (8370146), Chile.
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25
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Hellmuth M, Stadler PF. The Theory of Gene Family Histories. Methods Mol Biol 2024; 2802:1-32. [PMID: 38819554 DOI: 10.1007/978-1-0716-3838-5_1] [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: 06/01/2024]
Abstract
Most genes are part of larger families of evolutionary-related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to phylogenetic tree of the underlying species has remained a challenging topic despite their importance as a basis for detailed investigations into adaptation and functional evolution of individual members of the gene family. The identification of orthologs, moreover, is a particularly important subproblem of the more general setting considered here. In the last few years, an extensive body of mathematical results has appeared that tightly links orthology, a formal notion of best matches among genes, and horizontal gene transfer. The purpose of this chapter is to broadly outline some of the key mathematical insights and to discuss their implication for practical applications. In particular, we focus on tree-free methods, i.e., methods to infer orthology or horizontal gene transfer as well as gene trees, species trees, and reconciliations between them without using a priori knowledge of the underlying trees or statistical models for the inference of phylogenetic trees. Instead, the initial step aims to extract binary relations among genes.
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Affiliation(s)
- Marc Hellmuth
- Department of Mathematics, Faculty of Science, Stockholm University, Stockholm, Sweden
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Leipzig University, Leipzig, Germany.
- Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
- Universidad Nacional de Colombia, Bogotá, Colombia.
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria.
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.
- Santa Fe Institute, Santa Fe, NM, USA.
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26
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Braga MDV, Doerr D, Rubert DP, Stoye J. Family-Free Genome Comparison. Methods Mol Biol 2024; 2802:57-72. [PMID: 38819556 DOI: 10.1007/978-1-0716-3838-5_3] [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: 06/01/2024]
Abstract
The comparison of large-scale genome structures across distinct species offers valuable insights into the species' phylogeny, genome organization, and gene associations. In this chapter, we review the family-free genome comparison tool FFGC that, relying on built-in interfaces with a sequence comparison tool (either BLAST+ or DIAMOND) and with an ILP solver (either CPLEX or Gurobi), provides several methods for analyses that do not require prior classification of genes across the studied genomes. Taking annotated genome sequences as input, FFGC is a complete workflow for genome comparison allowing not only the computation of measures of similarity and dissimilarity but also the inference of gene families, simultaneously based on sequence similarities and large-scale genomic features.
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Affiliation(s)
- Marilia D V Braga
- Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Daniel Doerr
- Department for Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, German Diabetes Center (DDZ), Leibniz Institute for Diabetes Research, and Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Diego P Rubert
- Faculdade de Computacão, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Jens Stoye
- Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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27
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Moraïs S, Mazor M, Tovar-Herrera O, Zehavi T, Zorea A, Ifrach M, Bogumil D, Brandis A, Walter J, Elia N, Gur E, Mizrahi I. Plasmid-encoded toxin defence mediates mutualistic microbial interactions. Nat Microbiol 2024; 9:108-119. [PMID: 38151647 PMCID: PMC10769881 DOI: 10.1038/s41564-023-01521-9] [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: 07/18/2022] [Accepted: 10/11/2023] [Indexed: 12/29/2023]
Abstract
Gut environments harbour dense microbial ecosystems in which plasmids are widely distributed. Plasmids facilitate the exchange of genetic material among microorganisms while enabling the transfer of a diverse array of accessory functions. However, their precise impact on microbial community composition and function remains largely unexplored. Here we identify a prevalent bacterial toxin and a plasmid-encoded resistance mechanism that mediates the interaction between Lactobacilli and Enterococci. This plasmid is widespread across ecosystems, including the rumen and human gut microbiota. Biochemical characterization of the plasmid revealed a defence mechanism against reuterin, a toxin produced by various gut microbes, such as Limosilactobacillus reuteri. Using a targeted metabolomic approach, we find reuterin to be prevalent across rumen ecosystems with impacts on microbial community structure. Enterococcus strains carrying the protective plasmid were isolated and their interactions with L. reuteri, the toxin producer, were studied in vitro. Interestingly, we found that by conferring resistance against reuterin, the plasmid mediates metabolic exchange between the defending and the attacking microbial species, resulting in a beneficial relationship or mutualism. Hence, we reveal here an ecological role for a plasmid-coded defence system in mediating a beneficial interaction.
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Affiliation(s)
- Sarah Moraïs
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Michael Mazor
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Omar Tovar-Herrera
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Tamar Zehavi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Morya Ifrach
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - David Bogumil
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Jens Walter
- Department of Medicine, University College Cork, Cork, Ireland
| | - Natalie Elia
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Eyal Gur
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
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28
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Mejía L, Espinosa-Mata E, Freire AL, Zapata S, González-Candelas F. Listeria monocytogenes, a silent foodborne pathogen in Ecuador. Front Microbiol 2023; 14:1278860. [PMID: 38179446 PMCID: PMC10764610 DOI: 10.3389/fmicb.2023.1278860] [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: 08/17/2023] [Accepted: 11/23/2023] [Indexed: 01/06/2024] Open
Abstract
Listeria monocytogenes is a foodborne pathogen that can produce serious, even fatal, infections. Among other foods, it can be found in unpasteurized dairy and ready-to-eat products. Surveillance of L. monocytogenes is of great interest since sources of infection are difficult to determine due to the long incubation period, and because the symptoms of listeriosis are similar to other diseases. We performed a genomic study of L. monocytogenes isolated from fresh cheeses and clinical samples from Ecuador. Sixty-five isolates were evaluated and sequenced, 14 isolates from cheese samples and 20 from clinical listeriosis cases from the National Institute of National Institute of Public Health Research, and 31 isolates from artisanal cheese samples from 8 provinces. All isolates exhibited heterogeneous patterns of the presence of pathogenicity islands. All isolates exhibited at least 4 genes from LIPI-1, but all references (26 L. monocytogenes closed genomes available in the NCBI database) showed the complete island, which encompasses 5 genes but is present in only two Ecuadorian isolates. Most isolates lacked gene actA. Genes from LIPI-2 were absent in all isolates. LIPI-3 and LIPI-4 were present in only a few references and isolates. With respect to the stress survival islets, our samples either presented SSI-1 or SSI-F2365, except for one isolate that presented SSI-F2365 and also one gene from SSI-1. None of the samples presented SSI-2. The predominant ST (sequence type) was ST2 (84.62% 55/65), and the only ST found in food (93.33% 42/45) and clinical samples (65% 13/20). Isolates were not grouped according to their sampling origin, date, or place in a phylogenetic tree obtained from the core alignment. The presence of ST2 in food and clinical samples, with high genomic similarity, suggests a foodborne infection risk linked to the consumption of fresh cheeses in Ecuador.
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Affiliation(s)
- Lorena Mejía
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Valencia, Spain
| | - Estefanía Espinosa-Mata
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Ana Lucía Freire
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sonia Zapata
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Valencia, Spain
- CIBER (Centro de Investigación Biomédica en Red) in Epidemiology and Public Health, Valencia, Spain
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Klemm P, Stadler PF, Lechner M. Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs. FRONTIERS IN BIOINFORMATICS 2023; 3:1322477. [PMID: 38152702 PMCID: PMC10751348 DOI: 10.3389/fbinf.2023.1322477] [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] [Received: 10/16/2023] [Accepted: 11/06/2023] [Indexed: 12/29/2023] Open
Abstract
Proteinortho is a widely used tool to predict (co)-orthologous groups of genes for any set of species. It finds application in comparative and functional genomics, phylogenomics, and evolutionary reconstructions. With a rapidly increasing number of available genomes, the demand for large-scale predictions is also growing. In this contribution, we evaluate and implement major algorithmic improvements that significantly enhance the speed of the analysis without reducing precision. Graph-based detection of (co-)orthologs is typically based on a reciprocal best alignment heuristic that requires an all vs. all comparison of proteins from all species under study. The initial identification of similar proteins is accelerated by introducing an alternative search tool along with a revised search strategy-the pseudo-reciprocal best alignment heuristic-that reduces the number of required sequence comparisons by one-half. The clustering algorithm was reworked to efficiently decompose very large clusters and accelerate processing. Proteinortho6 reduces the overall processing time by an order of magnitude compared to its predecessor while maintaining its small memory footprint and good predictive quality.
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Affiliation(s)
- Paul Klemm
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Institute of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
- Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria
- Facultad de Ciencias, Universidad National de Colombia, Bogotá, Colombia
- Santa Fe Institute, Santa Fe, NM, United States
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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Martinez-Gutierrez CA, Uyeda JC, Aylward FO. A timeline of bacterial and archaeal diversification in the ocean. eLife 2023; 12:RP88268. [PMID: 38059790 DOI: 10.7554/elife.88268] [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] [Indexed: 12/08/2023] Open
Abstract
Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.
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Affiliation(s)
| | - Josef C Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, United States
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31
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Fricke LC, Lindsey ARI. Identification of parthenogenesis-inducing effector proteins in Wolbachia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569668. [PMID: 38076953 PMCID: PMC10705499 DOI: 10.1101/2023.12.01.569668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called "parthenogenesis-induction" phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 years ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing Wolbachia and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex-determining factor Transformer, and a eukaryotic-like serine-threonine kinase with leucine rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model, Saccharomyces cerevisiae. We suggest these proteins are parthenogenesis-inducing factors and our results indicate this would be made possible by a novel mechanism of bacterial-host interaction.
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Affiliation(s)
- Laura C Fricke
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Amelia RI Lindsey
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, 55108
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Wang W, Dong Z, Du Z, Wu P. Genome-scale approach to reconstructing the phylogenetic tree of psyllids (superfamily Psylloidea) with account of systematic bias. Mol Phylogenet Evol 2023; 189:107924. [PMID: 37699449 DOI: 10.1016/j.ympev.2023.107924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 09/14/2023]
Abstract
Psyllids (class Insecta: order Hemiptera: superfamily Psylloidea) are a taxonomically and phylogenetically challenging clade. Recent studies have largely advanced the phylogeny of this group, yet the family-level relationships among Aphalaridae, Carsidaridae, and others remain unresolved. Genome-scale phylogenetic analysis is known to provide a finer resolution for problems like that. However, such phylogenomics also introduces new problems: incorrect trees with high confidence yielded due to systematic error (bias). Here we addressed these issues using hundreds of single-copy orthologous (SCO) genes in psyllid transcriptomes and genomes. Our analyses revealed conflicts between the nucleotide-based and amino-acid-based phylogenetic trees. While the nucleotide-based phylogeny strongly supported the (Aphalaridae + Carsidaridae) + Others relationship, the amino-acid-based one recovered Aphalaridae + (Carsidaridae + Others) with 100% support. Further inspection revealed significant compositional heterogeneity in nucleotide sequences for 67% of SCO genes, but not in the corresponding translated amino acid sequences. We then used different strategies to combat this compositional bias, and found that using the RY-coding strategy (coding the standard nucleotides as purines and pyrimidines) the nucleotide-based phylogeny became consistent with the amino-acid-based one. We further applied RY-coding to a published concatenated nucleotide dataset and recovered the Aphalaridae monophyly (which is refuted by the original literature on non-recoded sequences) at the base of psyllid tree. Moreover, it was found that variations in evolutionary rate could lead to errors in nucleotide-based phylogeny. The fast-evolving Heteropsylla cubana (Psyllidae: Ciriacreminae) was incorrectly placed within the subfamily Psyllinae. This bias can be avoided by using data removal or RY-coding strategies. Together, our results strongly support the family relationship of Aphalaridae + (Carsidaridae + Others), and show that the amino-acid-based concatenation analysis is more robust than nucleotide-based one. Future phylogenomic analysis of psyllid nucleotide sequences should take into account methods such as the RY-coding scheme to address potential systematic biases arising from composition and rate heterogeneities.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zequn Dong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengxiang Wu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Jensen MG, Svraka L, Baez E, Lund M, Poehlein A, Brüggemann H. Species- and strain-level diversity of Corynebacteria isolated from human facial skin. BMC Microbiol 2023; 23:366. [PMID: 38017392 PMCID: PMC10683109 DOI: 10.1186/s12866-023-03129-9] [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: 07/09/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Sequencing of the human skin microbiome revealed that Corynebacterium is an ubiquitous and abundant bacterial genus on human skin. Shotgun sequencing further highlighted the microbial "dark matter" of the skin microbiome, consisting of microorganisms, including corynebacterial species that were not cultivated and genome-sequenced so far. In this pilot project, facial human skin swabs of 13 persons were cultivated to selectively obtain corynebacteria. 54 isolates were collected and 15 of these were genome-sequenced and the pan-genome was determined. The strains were biochemically characterized and antibiotic susceptibility testing (AST) was performed. RESULTS Among the 15 sequenced strains, nine different corynebacterial species were found, including two so far undescribed species, tentatively named "Corynebacterium vikingii" and "Corynebacterium borealis", for which closed genome sequences were obtained. Strain variability beyond the species level was determined in biochemical tests, such as the variable presence of urease activity and the capacity to ferment different sugars. The ability to grow under anaerobic conditions on solid agar was found to be species-specific. AST revealed resistances to clindamycin in seven strains. A Corynebacterium pseudokroppenstedtii strain showed additional resistance towards beta-lactam and fluoroquinolone antibiotics; a chromosomally located 17 kb gene cluster with five antibiotic resistance genes was found in the closed genome of this strain. CONCLUSIONS Taken together, this pilot study identified an astonishing diversity of cutaneous corynebacterial species in a relatively small cohort and determined species- and strain-specific individualities regarding biochemical and resistance profiles. This further emphasizes the need for cultivation-based studies to be able to study these microorganisms in more detail, in particular regarding their host-interacting and, potentially, -beneficial and/or -detrimental properties.
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Affiliation(s)
| | - Lejla Svraka
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Elena Baez
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Michael Lund
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Holger Brüggemann
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus, Denmark.
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Brunetti AE, Lyra ML, Bauermeister A, Bunk B, Boedeker C, Müsken M, Neto FC, Mendonça JN, Caraballo-Rodríguez AM, Melo WG, Pupo MT, Haddad CF, Cabrera GM, Overmann J, Lopes NP. Host macrocyclic acylcarnitines mediate symbiotic interactions between frogs and their skin microbiome. iScience 2023; 26:108109. [PMID: 37867936 PMCID: PMC10587524 DOI: 10.1016/j.isci.2023.108109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/23/2023] [Accepted: 09/28/2023] [Indexed: 10/24/2023] Open
Abstract
The host-microbiome associations occurring on the skin of vertebrates significantly influence hosts' health. However, the factors mediating their interactions remain largely unknown. Herein, we used integrated technical and ecological frameworks to investigate the skin metabolites sustaining a beneficial symbiosis between tree frogs and bacteria. We characterize macrocyclic acylcarnitines as the major metabolites secreted by the frogs' skin and trace their origin to an enzymatic unbalance of carnitine palmitoyltransferases. We found that these compounds colocalize with bacteria on the skin surface and are mostly represented by members of the Pseudomonas community. We showed that Pseudomonas sp. MPFS isolated from frogs' skin can exploit acylcarnitines as its sole carbon and nitrogen source, and this metabolic capability is widespread in Pseudomonas. We summarize frogs' multiple mechanisms to filter environmental bacteria and highlight that acylcarnitines likely evolved for another function but were co-opted to provide nutritional benefits to the symbionts.
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Affiliation(s)
- Andrés E. Brunetti
- Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones N3300LQH, Argentina
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Straße 8, 07745 Jena, Germany
| | - Mariana L. Lyra
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi 129188, United Arab Emirates
| | - Anelize Bauermeister
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Christian Boedeker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Niedersachsen, Germany
| | - Fausto Carnevale Neto
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Jacqueline Nakau Mendonça
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Weilan G.P. Melo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Mônica T. Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Célio F.B. Haddad
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
| | - Gabriela M. Cabrera
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad de Microanálisis y Métodos Físicos aplicados a la Química Orgánica (UMYMFOR), Buenos Aires C1428EGA, Argentina
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Norberto P. Lopes
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
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R N, Kh M, Hegde SN, Begum N, Kukkupuni SK, Gowda M, Narendran P. De novo genome assembly and annotation of the medicinal plant Tinospora cordifolia (Willd.) Miers ex Hook. f. & Thom's. Funct Integr Genomics 2023; 23:330. [PMID: 37935874 DOI: 10.1007/s10142-023-01262-2] [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] [Received: 07/04/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023]
Abstract
Indian natural climbing shrub Tinospora cordifolia, often known as "Guduchi" and "Amrita," is a highly esteemed medicinal plant in the Indian system of medicine (ISM). It is a member of the Menispermaceae family which consists of a rich source of protein, micronutrients, and rich source of bioactive components which are used in treating various systemic diseases. The current study was designed to know the biological characterization of the plant genome and biosynthesis of plant metabolites essential for its medicinal applications. Tinospora cordifolia's complete genome was sequenced using Illumina HiSeq2500 sequencing technology. The draft genome was assembled through a de novo method. An integrative genome annotation approach was used to perform functional gene prediction. The pathway analysis was carried out using the KEGG database. The total genome size obtained after genome assembly was 894 Mb with an N50 of 9148 bp. The integrative annotation approach resulted in 35,111 protein-coding genes. In addition, genes responsible for the synthesis of syringin, a secondary metabolite found in plants, were identified. In comparison to the standard drug (dopamine, rasagiline, and selegiline), syringin's molecular docking exhibited a greater binding affinity from the range of - 4.3 to - 6.6 kcal/mol for all the targets of Parkinson's disease and for Alzheimer's targets; it has shown the maximum potency from the range of - 6.5 to - 7.4 kcal/mol with respect to the standard drug (donepezil, galantamine, and rivastigmine). This study provides the genomic information of Tinospora cordifolia which is helpful in understanding genomic insights and metabolic pathways connected to the corresponding plant genome and predicts the possible useful effect for the molecular characterization of therapeutic drugs.
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Affiliation(s)
- Namitha R
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Manasa Kh
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Santhosh N Hegde
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Noorunnisa Begum
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Subrahmanya Kumar Kukkupuni
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Malali Gowda
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India.
| | - Pavithra Narendran
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India.
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Choquet M, Lenner F, Cocco A, Toullec G, Corre E, Toullec JY, Wallberg A. Comparative Population Transcriptomics Provide New Insight into the Evolutionary History and Adaptive Potential of World Ocean Krill. Mol Biol Evol 2023; 40:msad225. [PMID: 37816123 PMCID: PMC10642690 DOI: 10.1093/molbev/msad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change.
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Affiliation(s)
- Marvin Choquet
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Felix Lenner
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Arianna Cocco
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gaëlle Toullec
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Erwan Corre
- CNRS, Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff, Roscoff, France
| | - Jean-Yves Toullec
- CNRS, UMR 7144, AD2M, Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Lin HC, de Ulzurrun GVD, Chen SA, Yang CT, Tay RJ, Iizuka T, Huang TY, Kuo CY, Gonçalves AP, Lin SY, Chang YC, Stajich JE, Schwarz EM, Hsueh YP. Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus. PLoS Biol 2023; 21:e3002400. [PMID: 37988381 PMCID: PMC10662756 DOI: 10.1371/journal.pbio.3002400] [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: 05/30/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
Nutritional deprivation triggers a switch from a saprotrophic to predatory lifestyle in soil-dwelling nematode-trapping fungi (NTF). In particular, the NTF Arthrobotrys oligospora secretes food and sex cues to lure nematodes to its mycelium and is triggered to develop specialized trapping devices. Captured nematodes are then invaded and digested by the fungus, thus serving as a food source. In this study, we examined the transcriptomic response of A. oligospora across the stages of sensing, trap development, and digestion upon exposure to the model nematode Caenorhabditis elegans. A. oligospora enacts a dynamic transcriptomic response, especially of protein secretion-related genes, in the presence of prey. Two-thirds of the predicted secretome of A. oligospora was up-regulated in the presence of C. elegans at all time points examined, and among these secreted proteins, 38.5% are predicted to be effector proteins. Furthermore, functional studies disrupting the t-SNARE protein Sso2 resulted in impaired ability to capture nematodes. Additionally, genes of the DUF3129 family, which are expanded in the genomes of several NTF, were highly up-regulated upon nematode exposure. We observed the accumulation of highly expressed DUF3129 proteins in trap cells, leading us to name members of this gene family as Trap Enriched Proteins (TEPs). Gene deletion of the most highly expressed TEP gene, TEP1, impairs the function of traps and prevents the fungus from capturing prey efficiently. In late stages of predation, we observed up-regulation of a variety of proteases, including metalloproteases. Following penetration of nematodes, these metalloproteases facilitate hyphal growth required for colonization of prey. These findings provide insights into the biology of the predatory lifestyle switch in a carnivorous fungus and provide frameworks for other fungal-nematode predator-prey systems.
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Affiliation(s)
- Hung-Che Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | | | - Sheng-An Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Ching-Ting Yang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Rebecca J. Tay
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tomoyo Iizuka
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tsung-Yu Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Yen Kuo
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - A. Pedro Gonçalves
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Siou-Ying Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yu-Chu Chang
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Erich M. Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Yen-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
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Blasweiler A, Megens HJ, Goldman MRG, Tadmor-Levi R, Lighten J, Groenen MAM, Dirks RP, Jansen HJ, Spaink HP, David L, Boudinot P, Wiegertjes GF. Symmetric expression of ohnologs encoding conserved antiviral responses in tetraploid common carp suggest absence of subgenome dominance after whole genome duplication. Genomics 2023; 115:110723. [PMID: 37804957 DOI: 10.1016/j.ygeno.2023.110723] [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: 06/13/2023] [Revised: 08/22/2023] [Accepted: 09/25/2023] [Indexed: 10/09/2023]
Abstract
Allopolyploids often experience subgenome dominance, with one subgenome showing higher levels of gene expression and greater gene retention. Here, we address the functionality of both subgenomes of allotetraploid common carp (Cyprinus carpio) by analysing a functional network of interferon-stimulated genes (ISGs) crucial in anti-viral immune defence. As an indicator of subgenome dominance we investigated retainment of a core set of ohnologous ISGs. To facilitate our functional genomic analysis a high quality genome was assembled (WagV4.0). Transcriptome data from an in vitro experiment mimicking a viral infection was used to infer ISG expression. Transcriptome analysis confirmed induction of 88 ISG ohnologs on both subgenomes. In both control and infected states, average expression of ISG ohnologs was comparable between the two subgenomes. Also, the highest expressing and most inducible gene copies of an ohnolog pair could be derived from either subgenome. We found no strong evidence of subgenome dominance for common carp.
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Affiliation(s)
- A Blasweiler
- Aquaculture and Fisheries, Wageningen University, the Netherlands; Animal Breeding and Genomics, Wageningen University, the Netherlands.
| | - H-J Megens
- Animal Breeding and Genomics, Wageningen University, the Netherlands
| | - M R G Goldman
- Aquaculture and Fisheries, Wageningen University, the Netherlands
| | - R Tadmor-Levi
- Dept. of Animal Sciences, RH Smith Faculty of Agriculture Food and Environment, The Hebrew University of Jerusalem, Israel
| | - J Lighten
- Biosciences, University of Exeter, United Kingdom
| | - M A M Groenen
- Animal Breeding and Genomics, Wageningen University, the Netherlands
| | - R P Dirks
- Future Genomics Technologies B.V., the Netherlands
| | - H J Jansen
- Future Genomics Technologies B.V., the Netherlands
| | - H P Spaink
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - L David
- Dept. of Animal Sciences, RH Smith Faculty of Agriculture Food and Environment, The Hebrew University of Jerusalem, Israel
| | - P Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, 78350, France
| | - G F Wiegertjes
- Aquaculture and Fisheries, Wageningen University, the Netherlands
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Šimková K, Naraine R, Vintr J, Soukup V, Šindelka R. RNA localization during early development of the axolotl. Front Cell Dev Biol 2023; 11:1260795. [PMID: 37928901 PMCID: PMC10620976 DOI: 10.3389/fcell.2023.1260795] [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: 07/18/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023] Open
Abstract
The asymmetric localization of biomolecules is critical for body plan development. One of the most popular model organisms for early embryogenesis studies is Xenopus laevis but there is a lack of information in other animal species. Here, we compared the early development of two amphibian species-the frog X. laevis and the axolotl Ambystoma mexicanum. This study aimed to identify asymmetrically localized RNAs along the animal-vegetal axis during the early development of A. mexicanum. For that purpose, we performed spatial transcriptome-wide analysis at low resolution, which revealed dynamic changes along the animal-vegetal axis classified into the following categories: profile alteration, de novo synthesis and degradation. Surprisingly, our results showed that many of the vegetally localized genes, which are important for germ cell development, are degraded during early development. Furthermore, we assessed the motif presence in UTRs of degraded mRNAs and revealed the enrichment of several motifs in RNAs of germ cell markers. Our results suggest novel reorganization of the transcriptome during embryogenesis of A. mexicanum to converge to the similar developmental pattern as the X. laevis.
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Affiliation(s)
- Kateřina Šimková
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Ravindra Naraine
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Jan Vintr
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Vladimír Soukup
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Radek Šindelka
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
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40
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Wong EB, Kamaruddin N, Mokhtar M, Yusof N, Khairuddin RFR. Assessing sequence heterogeneity in Chlorellaceae DNA barcode markers for phylogenetic inference. J Genet Eng Biotechnol 2023; 21:104. [PMID: 37851281 PMCID: PMC10584744 DOI: 10.1186/s43141-023-00550-5] [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: 04/19/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
Phylogenetic inference is an important approach that allows the recovery of the evolutionary history and the origin of the Chlorellaceae species. Despite the species' potential for biofuel feedstock production, their high phenotypic plasticity and similar morphological structures among the species have muddled the taxonomy and identification of the Chlorellaceae species. This study aimed to decipher Chlorellaceae DNA barcode marker heterogeneity by examining the sequence divergence and genomic properties of 18S rRNA, ITS (ITS1-5.8S rRNA-ITS2-28S rRNA), and rbcL from 655 orthologous sequences of 64 species across 31 genera in the Chlorellaceae family. The study assessed the distinct evolutionary properties of the DNA markers that may have caused the discordance between individual trees in the phylogenetic inference using the Robinson-Foulds distance and the Shimodaira-Hasegawa test. Our findings suggest that using the supermatrix approach improves the congruency between trees by reducing stochastic error and increasing the confidence of the inferred Chlorellaceae phylogenetic tree. This study also found that the phylogenies inferred through the supermatrix approach might not always be well supported by all markers. The study highlights that assessing sequence heterogeneity prior to the phylogenetic inference could allow the approach to accommodate sequence evolutionary properties and support species identification from the most congruent phylogeny, which can better represent the evolution of Chlorellaceae species.
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Affiliation(s)
- Ee Bhei Wong
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia
| | - Nurhaida Kamaruddin
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia
| | - Marina Mokhtar
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia
| | - Norjan Yusof
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia
| | - Raja Farhana R Khairuddin
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia.
- Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture, and Healthcare (CRYSTAL), Universiti Malaya, Kuala Lumpur, Malaysia.
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Dong H, Han RZ, Zhang Y, Xamxidin M, Zhou P, Sun C, Qu W, Xu L. Parerythrobacter aestuarii sp. nov., Isolated from Seawater in the Tidal Region of Taizhou. Curr Microbiol 2023; 80:369. [PMID: 37838639 DOI: 10.1007/s00284-023-03483-x] [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: 06/01/2023] [Accepted: 09/08/2023] [Indexed: 10/16/2023]
Abstract
A yellow, Gram-stain-negative, aerobic, and rod-shaped strain, designated as C18T, was isolated from seawater in the tidal region of Taizhou. Growth of strain C18T occurs at 20-45 °C, at pH 5.5-8.0 and with 1.0-8.0% (w/v) NaCl. The 16S rRNA gene sequence analysis showed that strain C18T shared sequence identities with the genera Erythrobacter (< 98.4%), Qipengyuania (< 98.0%), Altererythrobacter (< 96.4%), Parerythrobacter (< 96.2%), Aurantiacibacter (< 96.2%), Tsuneonella (< 96.0%), Pelagerythrobacter (< 96.0%), Alteriqipengyuania (< 95.9%), and Parapontixanthobacter (< 95.7%) type strains. While the phylogenomic tree based on single-copy orthologous clusters revealed that strain C18T was stably clustered into the genus Parerythrobacter. Average nucleotide identity and digital DNA-DNA hybridization values of strain C18T and Parerythrobacter type strains were 73.5-75.2% and 18.5-19.4%, respectively, which were lower than the species delineation thresholds. The sole respiratory quinones were identified as ubiquinone-10. The major fatty acids (> 10%) were C17:1ω6c and summed feature 8 (C18:1ω7c and/or C18:1ω6c). Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unidentified phospholipid, and an unidentified aminophospholipid. Based on the genetic, chemotaxonomic and phenotypic results, strain C18T is concluded to represent a novel species in the genus Parerythrobacter, for which the name Parerythrobacter aestuarii sp. nov. is proposed. The type strain is C18T (= KCTC 82594T = MCCC 1K05109T).
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Affiliation(s)
- Han Dong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Ren-Zhuang Han
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Yu Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing, 312075, People's Republic of China
| | - Maripat Xamxidin
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing, 312075, People's Republic of China
| | - Wu Qu
- Zhejiang Ocean University, Marine Science and Technology College, Zhoushan, 316000, People's Republic of China.
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
- Zhejiang Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing, 312075, People's Republic of China.
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Böer T, Bengelsdorf FR, Bömeke M, Daniel R, Poehlein A. Genome-based metabolic and phylogenomic analysis of three Terrisporobacter species. PLoS One 2023; 18:e0290128. [PMID: 37816002 PMCID: PMC10564238 DOI: 10.1371/journal.pone.0290128] [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: 06/26/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023] Open
Abstract
Acetogenic bacteria are of high interest for biotechnological applications as industrial platform organisms, however, acetogenic strains from the genus Terrisporobacter have hitherto been neglected. To date, three published type strains of the genus Terrisporobacter are only covered by draft genome sequences, and the genes and pathway responsible for acetogenesis have not been analyzed. Here, we report complete genome sequences of the bacterial type strains Terrisporobacter petrolearius JCM 19845T, Terrisporobacter mayombei DSM 6539T and Terrisporobacter glycolicus DSM 1288T. Functional annotation, KEGG pathway module reconstructions and screening for virulence factors were performed. Various species-specific vitamin, cofactor and amino acid auxotrophies were identified and a model for acetogenesis of Terrisporobacter was constructed. The complete genomes harbored a gene cluster for the reductive proline-dependent branch of the Stickland reaction located on an approximately 21 kb plasmid, which is exclusively found in the Terrisporobacter genus. Phylogenomic analysis of available Terrisporobacter genomes suggested a reclassification of most isolates as T. glycolicus into T. petrolearius.
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Affiliation(s)
- Tim Böer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Frank R. Bengelsdorf
- Institute for Molecular Biology and Biotechnology of Prokaryotes, University Ulm, Ulm, Germany
| | - Mechthild Bömeke
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
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Ceron-Noriega A, Schoonenberg VAC, Butter F, Levin M. AlexandrusPS: A User-Friendly Pipeline for the Automated Detection of Orthologous Gene Clusters and Subsequent Positive Selection Analysis. Genome Biol Evol 2023; 15:evad187. [PMID: 37831426 PMCID: PMC10612477 DOI: 10.1093/gbe/evad187] [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: 07/03/2023] [Revised: 09/26/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023] Open
Abstract
The detection of adaptive selection in a system approach considering all protein-coding genes allows for the identification of mechanisms and pathways that enabled adaptation to different environments. Currently, available programs for the estimation of positive selection signals can be divided into two groups. They are either easy to apply but can analyze only one gene family at a time, restricting system analysis; or they can handle larger cohorts of gene families, but require considerable prerequisite data such as orthology associations, codon alignments, phylogenetic trees, and proper configuration files. All these steps require extensive computational expertise, restricting this endeavor to specialists. Here, we introduce AlexandrusPS, a high-throughput pipeline that overcomes technical challenges when conducting transcriptome-wide positive selection analyses on large sets of nucleotide and protein sequences. The pipeline streamlines 1) the execution of an accurate orthology prediction as a precondition for positive selection analysis, 2) preparing and organizing configuration files for CodeML, 3) performing positive selection analysis using CodeML, and 4) generating an output that is easy to interpret, including all maximum likelihood and log-likelihood test results. The only input needed from the user is the CDS and peptide FASTA files of proteins of interest. The pipeline is provided in a Docker image, requiring no program or module installation, enabling the application of the pipeline in any computing environment. AlexandrusPS and its documentation are available via GitHub (https://github.com/alejocn5/AlexandrusPS).
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Affiliation(s)
- Alejandro Ceron-Noriega
- Institute of Molecular Biology (IMB), Quantitative Proteomics, Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Department of Human Genetics, Mainz, Germany
| | - Vivien A C Schoonenberg
- Institute of Molecular Biology (IMB), Quantitative Proteomics, Mainz, Germany
- Present address: Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
- Present address: Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.
| | - Falk Butter
- Institute of Molecular Biology (IMB), Quantitative Proteomics, Mainz, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, Greifswald, Germany
| | - Michal Levin
- Institute of Molecular Biology (IMB), Quantitative Proteomics, Mainz, Germany
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Tan KY, Deng S, Tan TK, Hari R, Sitam FT, Othman RY, Wong KT, Mohidin TBM, Choo SW. Genome sequence analysis of Malayan pangolin ( Manis javanica) forensic samples reveals the presence of Paraburkholderia fungorum sequences. PeerJ 2023; 11:e16002. [PMID: 37810781 PMCID: PMC10559893 DOI: 10.7717/peerj.16002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/09/2023] [Indexed: 10/10/2023] Open
Abstract
Background The Malayan pangolin (Manis javanica) is a placental mammal and is listed as Critically Endangered on the IUCN Red List of Threatened Species. Most previous attempts to breed pangolins in captivity have met with little success because of dietary issues, infections, and other complications, although a previous study reported breeding pangolins in captivity to the third generation. In our previous pangolin genome sequencing data analysis, we obtained a considerable amount of bacterial DNA from a pregnant female Malayan pangolin (named "UM3"), which was likely infected by Paraburkholderia fungorum-an agent of biodegradation and bioremediation in agriculture. Methodology Here, we further confirmed and characterized this bacterial species using PCR, histological staining, whole-genome sequencing, and bioinformatics approaches. PCR assays with in-house designed primer sets and 16S universal primers showed clear positive bands in the cerebrum, cerebellum, lung, and blood of UM3 suggesting that UM3 might have developed septicaemia. Histological staining showed the presence of Gram-negative rod-shaped bacteria in the pangolin brain and lungs, indicating the colonization of the bacteria in these two organs. In addition, PCR screening of UM3's fetal tissues revealed the presence of P. fungorum in the gastrocnemius muscle, but not in other tissues that we examined. We also sequenced and reconstructed the genome of pangolin P. fungorum, which has a genome size of 7.7 Mbps. Conclusion Our study is the first to present detailed evidence of the presence of P. fungorum in a pangolin and her fetus (although preliminary results were presented in our previous article). Here, we raise the concern that P. fungorum may potentially infect humans, especially YOPI (young, old, pregnant, and immunocompromised) people. Therefore, caution should be exercised when using this bacterial species as biodegradation or bioremediation agents in agriculture.
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Affiliation(s)
- Ka Yun Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Siwei Deng
- College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang, China
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ranjeev Hari
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Kuala Lumpur, Malaysia
| | - Rofina Yasmin Othman
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Kum Thong Wong
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Siew Woh Choo
- College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang, China
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45
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Wang Q, Hu XY, Sun LP, Niu HJ, Pei CX, Li Y, Xia CQ. Alteromonas Aquimaris sp. nov., Isolated from Surface Seawater. Curr Microbiol 2023; 80:343. [PMID: 37725183 DOI: 10.1007/s00284-023-03472-0] [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: 01/16/2023] [Accepted: 09/02/2023] [Indexed: 09/21/2023]
Abstract
A Gram-negative, aerobic, motile by flagellum, and rod-shaped bacterium, designated ASW11-7T, was isolated from coastal surface seawater sample collected from the Yellow Sea, PR China. Strain ASW11-7T grew optimally at 37℃, 4.0% (w/v) NaCl and pH 7.0. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain ASW11-7T belongs to the genus Alteromonas and most closely related to Alteromonas ponticola MYP5T (99.6% similarity), followed by Alteromonas confluentis DSSK2-12T (98.2%), Alteromonas lipolytica JW12T (98.2%), and Alteromonas hispanica F-32T (98.0%). The draft genome of strain ASW11-7T had a length of 3,530,922 bp with a G + C content of 44.9%, predicting 3108 coding sequences, 5 rRNA, 4 ncRNAs, 49 tRNAs genes, and 18 pseudogenes. The average nucleotide identity and digital DNA-DNA hybridization values between genomic sequences of strain ASW11-7T and closely related species of Alteromonas were in ranges of 66.9-77.8% and 18.3-27.5%, respectively. The major fatty acids of strain ASW11-7T were C16:0, summed feature 3 (C16:1ω7c/C16:1ω6c), and summed feature 8 (C18:1ω7c/C18:1ω6c). The predominant respiratory quinone was Q-8 and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Based on the phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain ASW11-7T is considered to represent a novel Alteromonas species, for which the name Alteromonas aquimaris sp. nov. is proposed. The type strain is ASW11-7T (= KCTC 92853T = MCCC 1K07240T).
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Affiliation(s)
- Qin Wang
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Xin-Yuan Hu
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Li-Ping Sun
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Hui-Jing Niu
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Cai-Xia Pei
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Yi Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| | - Cheng-Qiang Xia
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
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Escalante V, Nayak RR, Noecker C, Babdor J, Spitzer M, Deutschbauer AM, Turnbaugh PJ. Simvastatin induces human gut bacterial cell surface genes. Mol Microbiol 2023:10.1111/mmi.15151. [PMID: 37712143 PMCID: PMC10940213 DOI: 10.1111/mmi.15151] [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] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/16/2023]
Abstract
Drugs intended to target mammalian cells can have broad off-target effects on the human gut microbiota with potential downstream consequences for drug efficacy and side effect profiles. Yet, despite a rich literature on antibiotic resistance, we still know very little about the mechanisms through which commensal bacteria evade non-antibiotic drugs. Here, we focus on statins, one of the most prescribed drug types in the world and an essential tool in the prevention and treatment of high circulating cholesterol levels. Prior work in humans, mice, and cell culture support an off-target effect of statins on human gut bacteria; however, the genetic determinants of statin sensitivity remain unknown. We confirmed that simvastatin inhibits the growth of diverse human gut bacterial strains grown in communities and in pure cultures. Drug sensitivity varied between phyla and was dose-dependent. We selected two representative simvastatin-sensitive species for more in-depth analysis: Eggerthella lenta (phylum: Actinobacteriota) and Bacteroides thetaiotaomicron (phylum: Bacteroidota). Transcriptomics revealed that both bacterial species upregulate genes in response to simvastatin that alter the cell membrane, including fatty acid biogenesis (E. lenta) and drug efflux systems (B. thetaiotaomicron). Transposon mutagenesis identified a key efflux system in B. thetaiotaomicron that enables growth in the presence of statins. Taken together, these results emphasize the importance of the bacterial cell membrane in countering the off-target effects of host-targeted drugs. Continued mechanistic dissection of the various mechanisms through which the human gut microbiota evades drugs will be essential to understand and predict the effects of drug administration in human cohorts and the potential downstream consequences for health and disease.
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Affiliation(s)
- Veronica Escalante
- Department of Microbiology & Immunology, University of California, San Francisco, CA 94143
| | - Renuka R. Nayak
- Department of Medicine, San Francisco Veterans Affairs, San Francisco, CA 94121
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143
| | - Cecilia Noecker
- Department of Microbiology & Immunology, University of California, San Francisco, CA 94143
| | - Joel Babdor
- Department of Microbiology & Immunology, University of California, San Francisco, CA 94143
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew Spitzer
- Department of Microbiology & Immunology, University of California, San Francisco, CA 94143
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Peter J. Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, CA 94143
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158
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Leal-Dutra CA, Yuen LM, Guedes BAM, Contreras-Serrano M, Marques PE, Shik JZ. Evidence that the domesticated fungus Leucoagaricus gongylophorus recycles its cytoplasmic contents as nutritional rewards to feed its leafcutter ant farmers. IMA Fungus 2023; 14:19. [PMID: 37715276 PMCID: PMC10503033 DOI: 10.1186/s43008-023-00126-5] [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: 01/26/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023] Open
Abstract
Leafcutter ants farm a fungal cultivar (Leucoagaricus gongylophorus) that converts inedible vegetation into food that sustains colonies with up to millions of workers. Analogous to edible fruits of crops domesticated by humans, L. gongylophorus has evolved specialized nutritional rewards-swollen hyphal cells called gongylidia that package metabolites and are consumed by ant farmers. Yet, little is known about how gongylidia form, and thus how fungal physiology and ant provisioning collectively govern farming performance. We explored the process of gongylidium formation using advanced microscopy to image the cultivar at scales of nanometers, and both in vitro experiments and in silico analyses to examine the mechanisms of gongylidia formation when isolated from ant farmers. We first used transmission electron, fluorescence, and confocal microscopy imaging to see inside hyphal cells. This imaging showed that the cultivar uses a process called autophagy to recycle its own cellular material (e.g. cytosol, mitochondria) and then shuttles the resulting metabolites into a vacuole whose continual expansion displaces other organelles and causes the gongylidium cell's bulging bulb-like appearance. We next used scanning electron microscopy and light microscopy to link this intracellular rearrangement to the external branching patterns of gongylidium cells as they clump together into edible bundles called staphyla. We next confirmed that autophagy plays a critical role in gongylidium formation both: (1) in vitro as gongylidium suppression occurred when isolated fungal cultures were grown on media with autophagy inhibitors, and (2) in silico as differential transcript expression (RNA-seq) analyses showed upregulation of multiple autophagy gene isoforms in gongylidia relative to undifferentiated hyphae. While autophagy is a ubiquitous and often highly derived process across the tree of life, our study reveals a new role for autophagy as a mechanism of functional integration between ant farmers and their fungal crop, and potentially as a signifier of higher-level homeostasis between uniquely life-time committed ectosymbionts.
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Affiliation(s)
- Caio Ambrosio Leal-Dutra
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
| | - Lok Man Yuen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Department of Biology, ETH Zürich, Universitätsstrasse 16, Zürich, 8092, Switzerland
| | - Bruno Augusto Maciel Guedes
- Departamento de Ciências Básicas da Vida, Universidade Federal de Juiz de Fora, Campus Governador Valadares, Governador Valadares, MG, 35020-360, Brazil
| | - Marta Contreras-Serrano
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Pedro Elias Marques
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jonathan Zvi Shik
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
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48
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Craig JM, Kumar S, Hedges SB. The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen. FRONTIERS IN BIOINFORMATICS 2023; 3:1233281. [PMID: 37727796 PMCID: PMC10505794 DOI: 10.3389/fbinf.2023.1233281] [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] [Received: 06/01/2023] [Accepted: 08/07/2023] [Indexed: 09/21/2023] Open
Abstract
The origin of eukaryotes was among the most important events in the history of life, spawning a new evolutionary lineage that led to all complex multicellular organisms. However, the timing of this event, crucial for understanding its environmental context, has been difficult to establish. The fossil and biomarker records are sparse and molecular clocks have thus far not reached a consensus, with dates spanning 2.1-0.91 billion years ago (Ga) for critical nodes. Notably, molecular time estimates for the last common ancestor of eukaryotes are typically hundreds of millions of years younger than the Great Oxidation Event (GOE, 2.43-2.22 Ga), leading researchers to question the presumptive link between eukaryotes and oxygen. We obtained a new time estimate for the origin of eukaryotes using genetic data of both archaeal and bacterial origin, the latter rarely used in past studies. We also avoided potential calibration biases that may have affected earlier studies. We obtained a conservative interval of 2.2-1.5 Ga, with an even narrower core interval of 2.0-1.8 Ga, for the origin of eukaryotes, a period closely aligned with the rise in oxygen. We further reconstructed the history of biological complexity across the tree of life using three universal measures: cell types, genes, and genome size. We found that the rise in complexity was temporally consistent with and followed a pattern similar to the rise in oxygen. This suggests a causal relationship stemming from the increased energy needs of complex life fulfilled by oxygen.
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Affiliation(s)
- Jack M. Craig
- Center for Biodiversity, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Sudhir Kumar
- Center for Biodiversity, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - S. Blair Hedges
- Center for Biodiversity, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
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49
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Will I, Attardo GM, de Bekker C. Multiomic interpretation of fungus-infected ant metabolomes during manipulated summit disease. Sci Rep 2023; 13:14363. [PMID: 37658067 PMCID: PMC10474057 DOI: 10.1038/s41598-023-40065-0] [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: 05/10/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023] Open
Abstract
Camponotus floridanus ants show altered behaviors followed by a fatal summiting phenotype when infected with manipulating Ophiocordyceps camponoti-floridani fungi. Host summiting as a strategy to increase transmission is also observed with parasite taxa beyond fungi, including aquatic and terrestrial helminths and baculoviruses. The drastic phenotypic changes can sometimes reflect significant molecular changes in gene expression and metabolite concentrations measured in manipulated hosts. Nevertheless, the underlying mechanisms still need to be fully characterized. To investigate the small molecules producing summiting behavior, we infected C. floridanus ants with O. camponoti-floridani and sampled their heads for LC-MS/MS when we observed the characteristic summiting phenotype. We link this metabolomic data with our previous genomic and transcriptomic data to propose mechanisms that underlie manipulated summiting behavior in "zombie ants." This "multiomic" evidence points toward the dysregulation of neurotransmitter levels and neuronal signaling. We propose that these processes are altered during infection and manipulation based on (1) differential expression of neurotransmitter synthesis and receptor genes, (2) altered abundance of metabolites and neurotransmitters (or their precursors) with known behavioral effects in ants and other insects, and (3) possible suppression of a connected immunity pathway. We additionally report signals for metabolic activity during manipulation related to primary metabolism, detoxification, and anti-stress protectants. Taken together, these findings suggest that host manipulation is likely a multi-faceted phenomenon, with key processes changing at multiple levels of molecular organization.
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Affiliation(s)
- I Will
- Biology Department, University of Central Florida, Orlando, USA.
| | - G M Attardo
- Entomology and Nematology Department, University of California-Davis, Davis, USA
| | - C de Bekker
- Biology Department, University of Central Florida, Orlando, USA.
- Biology Department, Utrecht University, Utrecht, The Netherlands.
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50
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Wiberg RAW, Brand JN, Viktorin G, Mitchell JO, Beisel C, Schärer L. Genome assemblies of the simultaneously hermaphroditic flatworms Macrostomum cliftonense and Macrostomum hystrix. G3 (BETHESDA, MD.) 2023; 13:jkad149. [PMID: 37398989 PMCID: PMC10468722 DOI: 10.1093/g3journal/jkad149] [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: 04/28/2023] [Revised: 06/05/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023]
Abstract
The free-living, simultaneously hermaphroditic flatworms of the genus Macrostomum are increasingly used as model systems in various contexts. In particular, Macrostomum lignano, the only species of this group with a published genome assembly, has emerged as a model for the study of regeneration, reproduction, and stem-cell function. However, challenges have emerged due to M. lignano being a hidden polyploid, having recently undergone whole-genome duplication and chromosome fusion events. This complex genome architecture presents a significant roadblock to the application of many modern genetic tools. Hence, additional genomic resources for this genus are needed. Here, we present such resources for Macrostomum cliftonense and Macrostomum hystrix, which represent the contrasting mating behaviors of reciprocal copulation and hypodermic insemination found in the genus. We use a combination of PacBio long-read sequencing and Illumina shot-gun sequencing, along with several RNA-Seq data sets, to assemble and annotate highly contiguous genomes for both species. The assemblies span ∼227 and ∼220 Mb and are represented by 399 and 42 contigs for M. cliftonense and M. hystrix, respectively. Furthermore, high BUSCO completeness (∼84-85%), low BUSCO duplication rates (8.3-6.2%), and low k-mer multiplicity indicate that these assemblies do not suffer from the same assembly ambiguities of the M. lignano genome assembly, which can be attributed to the complex karyology of this species. We also show that these resources, in combination with the prior resources from M. lignano, offer an excellent foundation for comparative genomic research in this group of organisms.
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Affiliation(s)
- R Axel W Wiberg
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Gudrun Viktorin
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Jack O Mitchell
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
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