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Murmu S, Archak S. In-silico study of protein-protein interactions in wheat blast using docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2024; 42:5747-5757. [PMID: 37357445 DOI: 10.1080/07391102.2023.2228907] [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: 02/06/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
Despite advancements in agricultural research and the introduction of modern biotechnological and farming techniques, food security remains a significant issue. Although the efforts of farmers to meet the demands of a growing population, many plant diseases caused by pathogens, through their effects on cell division and tissue growth, lead to the annual loss of countless food crops. The recently emerged wheat blast fungus Magnaporthe oryzae pathotype Triticum (MoT) poses a significant danger to worldwide wheat cultivation. The fungus is a highly varied lineage of the M. oryzae, responsible for causing rice blast disease. In spite of being a significant challenge to successful wheat production in South America since 1985, the underlying biology of the wheat blast pathogen is still not fully understood. The initial outbreak of the wheat blast in South Asia had a severe impact on wheat production, resulting in a complete loss of yield in affected fields. For the purpose of enhancing disease management, it's vital to acquire a comprehensive comprehension of the infection biology of the fungus and its interaction with wheat plants on molecular levels. Host-pathogen protein interactions (HPIs) have the potential to reveal the pathogens' mechanism for overcoming the host organism. The current study delves into the interactions between the host plant wheat and MoT through protein-protein interactions, molecular docking, and 100 ns molecular dynamic simulations. This research uncovers the structural and functional basis of these proteins, leading to improved plant health and production.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sneha Murmu
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunil Archak
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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2
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Deng X, Yao Q, Horvath A, Jiang Z, Zhao J, Fischer T, Sugiyama T. The fission yeast ortholog of Coilin, Mug174, forms Cajal body-like nuclear condensates and is essential for cellular quiescence. Nucleic Acids Res 2024:gkae463. [PMID: 38828770 DOI: 10.1093/nar/gkae463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
The Cajal body, a nuclear condensate, is crucial for ribonucleoprotein assembly, including small nuclear RNPs (snRNPs). While Coilin has been identified as an integral component of Cajal bodies, its exact function remains unclear. Moreover, no Coilin ortholog has been found in unicellular organisms to date. This study unveils Mug174 (Meiosis-upregulated gene 174) as the Coilin ortholog in the fission yeast Schizosaccharomyces pombe. Mug174 forms phase-separated condensates in vitro and is often associated with the nucleolus and the cleavage body in vivo. The generation of Mug174 foci relies on the trimethylguanosine (TMG) synthase Tgs1. Moreover, Mug174 interacts with Tgs1 and U snRNAs. Deletion of the mug174+ gene in S. pombe causes diverse pleiotropic phenotypes, encompassing defects in vegetative growth, meiosis, pre-mRNA splicing, TMG capping of U snRNAs, and chromosome segregation. In addition, we identified weak homology between Mug174 and human Coilin. Notably, human Coilin expressed in fission yeast colocalizes with Mug174. Critically, Mug174 is indispensable for the maintenance of and transition from cellular quiescence. These findings highlight the Coilin ortholog in fission yeast and suggest that the Cajal body is implicated in cellular quiescence, thereby preventing human diseases.
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Affiliation(s)
- Xiaoling Deng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qinglian Yao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Attila Horvath
- The John Curtin School of Medical Research, The Australian National University, Canberra 2601, Australia
| | - Ziling Jiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Junjie Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tamás Fischer
- The John Curtin School of Medical Research, The Australian National University, Canberra 2601, Australia
| | - Tomoyasu Sugiyama
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Moin AT, Rani NA, Patil RB, Robin TB, Ullah MA, Rahim Z, Rahman MF, Zubair T, Hossain M, Mollah AKMM, Absar N, Hossain M, Manchur MA, Islam NN. In-silico formulation of a next-generation polyvalent vaccine against multiple strains of monkeypox virus and other related poxviruses. PLoS One 2024; 19:e0300778. [PMID: 38758816 PMCID: PMC11101047 DOI: 10.1371/journal.pone.0300778] [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: 09/14/2023] [Accepted: 03/05/2024] [Indexed: 05/19/2024] Open
Abstract
Mpox (formerly known as monkeypox) virus and some related poxviruses including smallpox virus pose a significant threat to public health, and effective prevention and treatment strategies are needed. This study utilized a reverse vaccinology approach to retrieve conserved epitopes for monkeypox virus and construct a vaccine that could provide cross-protection against related viruses with similar antigenic properties. The selected virulent proteins of monkeypox virus, MPXVgp165, and Virion core protein P4a, were subjected to epitope mapping for vaccine construction. Two vaccines were constructed using selected T cell epitopes and B cell epitopes with PADRE and human beta-defensins adjuvants conjugated in the vaccine sequence. Both constructs were found to be highly antigenic, non-allergenic, nontoxic, and soluble, suggesting their potential to generate an adequate immune response and be safe for humans. Vaccine construct 1 was selected for molecular dynamic simulation studies. The simulation studies revealed that the TLR8-vaccine complex was more stable than the TLR3-vaccine complex. The lower RMSD and RMSF values of the TLR8 bound vaccine compared to the TLR3 bound vaccine suggested better stability and consistency of hydrogen bonds. The Rg values of the vaccine chain bound to TLR8 indicated overall stability, whereas the vaccine chain bound to TLR3 showed deviations throughout the simulation. These results suggest that the constructed vaccine could be a potential preventive measure against monkeypox and related viruses however, further experimental validation is required to confirm these findings.
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Affiliation(s)
- Abu Tayab Moin
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
| | - Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Maharashtra, India
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md. Asad Ullah
- Faculty of Biological Sciences, Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Zahidur Rahim
- Department of Zoology, Jahangirnagar University, Dhaka, Bangladesh
| | - Md. Foyzur Rahman
- Department of Pharmacy, Dhaka International University, Dhaka, Bangladesh
| | | | - Mohabbat Hossain
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
| | | | - Nurul Absar
- Faculty of Basic Medical and Pharmaceutical Sciences, Department of Biochemistry and Biotechnology, University of Science & Technology Chittagong, Khulshi, Chittagong, Bangladesh
| | - Mahboob Hossain
- Department of Mathematics and Natural Sciences, Microbiology Program, School of Data and Sciences, BRAC University, Dhaka, Bangladesh
| | - Mohammed Abul Manchur
- Faculty of Biological Sciences, Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| | - Nazneen Naher Islam
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
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Rutherford KM, Lera-Ramírez M, Wood V. PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability. Genetics 2024; 227:iyae007. [PMID: 38376816 PMCID: PMC11075564 DOI: 10.1093/genetics/iyae007] [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: 11/28/2023] [Accepted: 01/13/2024] [Indexed: 02/21/2024] Open
Abstract
PomBase (https://www.pombase.org), the model organism database (MOD) for fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition (GBC; https://globalbiodata.org/) after a rigorous selection process. In this MOD review, we present PomBase's continuing growth and improvement over the last 2 years. We describe these improvements in the context of the qualitative GCBR indicators related to scientific quality, comprehensivity, accelerating science, user stories, and collaborations with other biodata resources. This review also showcases the depth of existing connections both within the biocuration ecosystem and between PomBase and its user community.
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Affiliation(s)
- Kim M Rutherford
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Manuel Lera-Ramírez
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Valerie Wood
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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Borujeni PM, Salavati R. Functional domain annotation by structural similarity. NAR Genom Bioinform 2024; 6:lqae005. [PMID: 38298181 PMCID: PMC10830352 DOI: 10.1093/nargab/lqae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/03/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
Traditional automated in silico functional annotation uses tools like Pfam that rely on sequence similarities for domain annotation. However, structural conservation often exceeds sequence conservation, suggesting an untapped potential for improved annotation through structural similarity. This approach was previously overlooked before the AlphaFold2 introduction due to the need for more high-quality protein structures. Leveraging structural information especially holds significant promise to enhance accurate annotation in diverse proteins across phylogenetic distances. In our study, we evaluated the feasibility of annotating Pfam domains based on structural similarity. To this end, we created a database from segmented full-length protein structures at their domain boundaries, representing the structure of Pfam seeds. We used Trypanosoma brucei, a phylogenetically distant protozoan parasite as our model organism. Its structome was aligned with our database using Foldseek, the ultra-fast structural alignment tool, and the top non-overlapping hits were annotated as domains. Our method identified over 400 new domains in the T. brucei proteome, surpassing the benchmark set by sequence-based tools, Pfam and Pfam-N, with some predictions validated manually. We have also addressed limitations and suggested avenues for further enhancing structure-based domain annotation.
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Affiliation(s)
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
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Chen W, Son YE, Cho HJ, Choi D, Park HS, Yu JH. Phylogenomics analysis of velvet regulators in the fungal kingdom. Microbiol Spectr 2024; 12:e0371723. [PMID: 38179919 PMCID: PMC10845976 DOI: 10.1128/spectrum.03717-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/03/2023] [Indexed: 01/06/2024] Open
Abstract
All life forms have evolved to respond appropriately to various environmental and internal cues. In the animal kingdom, the prototypical regulator class of such cellular responses is the Rel homology domain proteins including nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Fungi, the close relatives of animals, have also evolved with their own NF-κB-like regulators called velvet family proteins to govern cellular and chemical development. Here, we conducted a detailed investigation of the taxonomic broad presence of velvet proteins. We observed that velvet proteins are widely distributed in the fungal kingdom. Moreover, we have identified and characterized 21 major velvet clades in fungi. We have further revealed that the highly conserved velvet domain is composed of three distinct motifs and acts as an evolutionarily independent domain, which can be shuffled with various functional domains. Such rearrangements of the velvet domain have resulted in the functional and type diversity of the present velvet regulators. Importantly, our in-deep analyses of the primary and 3D structures of the various velvet domains showed that the fungal velvet domains can be divided into two major clans: the VelB and the VosA clans. The 3D structure comparisons revealed a close similarity of the velvet domain with many other eukaryotic DNA-binding proteins, including those of the Rel, Runt, and signal transducer and activator of transcription families, sharing a common β-sandwich fold. Altogether, this study improves our understanding of velvet regulators in the fungal kingdom.IMPORTANCEFungi are the relatives of animals in Opisthokonta and closely associated with human life by interactive ways such as pathogenicity, food, and secondary metabolites including beneficial ones like penicillin and harmful ones like the carcinogenic aflatoxins. Similar to animals, fungi have also evolved with NF-κB-like velvet family regulators. The velvet proteins constitute a large protein family of fungal transcription factors sharing a common velvet domain and play a key role in coordinating fungal secondary metabolism, developmental and differentiation processes. Our current understanding on velvet regulators is mostly from Ascomycota fungi; however, they remain largely unknown outside Ascomycota. Therefore, this study performed a taxonomic broad investigation of velvet proteins across the fungal kingdom and conducted a detailed analysis on velvet distribution, structure, diversity, and evolution. The results provide a holistic view of velvet regulatory system in the fungal kingdom.
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Affiliation(s)
- Wanping Chen
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, South Korea
| | - Ye-Eun Son
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, South Korea
| | - He-Jin Cho
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, South Korea
| | - Dasol Choi
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, South Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, South Korea
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
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7
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Vijayakumar S, Swetha RG, Bakthavatchalam YD, Vasudevan K, Abirami Shankar B, Kirubananthan A, Walia K, Ramaiah S, Biswas I, Veeraraghavan B, Anbarasu A. Genomic investigation unveils colistin resistance mechanism in carbapenem-resistant Acinetobacter baumannii clinical isolates. Microbiol Spectr 2024; 12:e0251123. [PMID: 38214512 PMCID: PMC10846133 DOI: 10.1128/spectrum.02511-23] [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: 06/15/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
Colistin resistance in Acinetobacter baumannii is mediated by multiple mechanisms. Recently, mutations within pmrABC two-component system and overexpression of eptA gene due to upstream insertion of ISAba1 have been shown to play a major role. Thus, the aim of our study is to characterize colistin resistance mechanisms among the clinical isolates of A. baumannii in India. A total of 207 clinical isolates of A. baumannii collected from 2016 to 2019 were included in this study. Mutations within lipid A biosynthesis and pmrABC genes were characterized by whole-genome shotgun sequencing. Twenty-eight complete genomes were further characterized by hybrid assembly approach to study insertional inactivation of lpx genes and the association of ISAba1-eptA. Several single point mutations (SNPs), like M12I in pmrA, A138T and A444V in pmrB, and E117K in lpxD, were identified. We are the first to report two novel SNPs (T7I and V383I) in the pmrC gene. Among the five colistin-resistant A. baumannii isolates where complete genome was available, the analysis showed that three of the five isolates had ISAba1 insertion upstream of eptA. No mcr genes were identified among the isolates. We mapped the SNPs on the respective protein structures to understand the effect on the protein activity. We found that majority of the SNPs had little effect on the putative protein function; however, some SNPs might destabilize the local structure. Our study highlights the diversity of colistin resistance mechanisms occurring in A. baumannii, and ISAba1-driven eptA overexpression is responsible for colistin resistance among the Indian isolates.IMPORTANCEAcinetobacter baumannii is a Gram-negative, emerging and opportunistic bacterial pathogen that is often associated with a wide range of nosocomial infections. The treatment of these infections is hindered by increase in the occurrence of A. baumannii strains that are resistant to most of the existing antibiotics. The current drug of choice to treat the infection caused by A. baumannii is colistin, but unfortunately, the bacteria started to show resistance to the last-resort antibiotic. The loss of lipopolysaccharides and mutations in lipid A biosynthesis genes are the main reasons for the colistin resistance. The present study characterized 207 A. baumannii clinical isolates and constructed complete genomes of 28 isolates to recognize the mechanisms of colistin resistance. We showed the mutations in the colistin-resistant variants within genes essential for lipid A biosynthesis and that cause these isolates to lose the ability to produce lipopolysaccharides.
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Affiliation(s)
- Saranya Vijayakumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rayapadi G. Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | | | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
- Department of Biotechnology, School of Applied Sciences, REVA University, Bangalore, India
| | - Baby Abirami Shankar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Kamini Walia
- Division of Epidemiology and Communicable Diseases, Indian Council for Medical Research, New Delhi, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas, USA
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
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Correa Marrero M, Capdevielle S, Huang W, Al-Subhi AM, Busscher M, Busscher-Lange J, van der Wal F, de Ridder D, van Dijk ADJ, Hogenhout SA, Immink RGH. Protein interaction mapping reveals widespread targeting of development-related host transcription factors by phytoplasma effectors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1281-1297. [PMID: 37965720 DOI: 10.1111/tpj.16546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
Phytoplasmas are pathogenic bacteria that reprogram plant host development for their own benefit. Previous studies have characterized a few different phytoplasma effector proteins that destabilize specific plant transcription factors. However, these are only a small fraction of the potential effectors used by phytoplasmas; therefore, the molecular mechanisms through which phytoplasmas modulate their hosts require further investigation. To obtain further insights into the phytoplasma infection mechanisms, we generated a protein-protein interaction network between a broad set of phytoplasma effectors and a large, unbiased collection of Arabidopsis thaliana transcription factors and transcriptional regulators. We found widespread, but specific, interactions between phytoplasma effectors and host transcription factors, especially those related to host developmental processes. In particular, many unrelated effectors target specific sets of TCP transcription factors, which regulate plant development and immunity. Comparison with other host-pathogen protein interaction networks shows that phytoplasma effectors have unusual targets, indicating that phytoplasmas have evolved a unique and unusual infection strategy. This study contributes a rich and solid data source that guides further investigations of the functions of individual effectors, as demonstrated for some herein. Moreover, the dataset provides insights into the underlying molecular mechanisms of phytoplasma infection.
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Affiliation(s)
- Miguel Correa Marrero
- Bioinformatics Group, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Sylvain Capdevielle
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Weijie Huang
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Ali M Al-Subhi
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, 11 Al Khod 123, al-Seeb, Oman
| | - Marco Busscher
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Jacqueline Busscher-Lange
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Froukje van der Wal
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Richard G H Immink
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
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Peng J, Zhao L. The origin and structural evolution of de novo genes in Drosophila. Nat Commun 2024; 15:810. [PMID: 38280868 PMCID: PMC10821953 DOI: 10.1038/s41467-024-45028-1] [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: 02/23/2023] [Accepted: 01/09/2024] [Indexed: 01/29/2024] Open
Abstract
Recent studies reveal that de novo gene origination from previously non-genic sequences is a common mechanism for gene innovation. These young genes provide an opportunity to study the structural and functional origins of proteins. Here, we combine high-quality base-level whole-genome alignments and computational structural modeling to study the origination, evolution, and protein structures of lineage-specific de novo genes. We identify 555 de novo gene candidates in D. melanogaster that originated within the Drosophilinae lineage. Sequence composition, evolutionary rates, and expression patterns indicate possible gradual functional or adaptive shifts with their gene ages. Surprisingly, we find little overall protein structural changes in candidates from the Drosophilinae lineage. We identify several candidates with potentially well-folded protein structures. Ancestral sequence reconstruction analysis reveals that most potentially well-folded candidates are often born well-folded. Single-cell RNA-seq analysis in testis shows that although most de novo gene candidates are enriched in spermatocytes, several young candidates are biased towards the early spermatogenesis stage, indicating potentially important but less emphasized roles of early germline cells in the de novo gene origination in testis. This study provides a systematic overview of the origin, evolution, and protein structural changes of Drosophilinae-specific de novo genes.
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Affiliation(s)
- Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA.
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10
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Rumpf M, Pautz S, Drebes B, Herberg FW, Müller HAJ. Microtubule-Associated Serine/Threonine (MAST) Kinases in Development and Disease. Int J Mol Sci 2023; 24:11913. [PMID: 37569286 PMCID: PMC10419289 DOI: 10.3390/ijms241511913] [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: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Microtubule-Associated Serine/Threonine (MAST) kinases represent an evolutionary conserved branch of the AGC protein kinase superfamily in the kinome. Since the discovery of the founding member, MAST2, in 1993, three additional family members have been identified in mammals and found to be broadly expressed across various tissues, including the brain, heart, lung, liver, intestine and kidney. The study of MAST kinases is highly relevant for unraveling the molecular basis of a wide range of different human diseases, including breast and liver cancer, myeloma, inflammatory bowel disease, cystic fibrosis and various neuronal disorders. Despite several reports on potential substrates and binding partners of MAST kinases, the molecular mechanisms that would explain their involvement in human diseases remain rather obscure. This review will summarize data on the structure, biochemistry and cell and molecular biology of MAST kinases in the context of biomedical research as well as organismal model systems in order to provide a current profile of this field.
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Affiliation(s)
- Marie Rumpf
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Sabine Pautz
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Benedikt Drebes
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Friedrich W. Herberg
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Hans-Arno J. Müller
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
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11
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Ruperti F, Papadopoulos N, Musser JM, Mirdita M, Steinegger M, Arendt D. Cross-phyla protein annotation by structural prediction and alignment. Genome Biol 2023; 24:113. [PMID: 37173746 PMCID: PMC10176882 DOI: 10.1186/s13059-023-02942-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Protein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a few model organisms. In non-model species, the sequence-based prediction of gene orthology can be used to infer protein identity; however, this approach loses predictive power at longer evolutionary distances. Here we propose a workflow for protein annotation using structural similarity, exploiting the fact that similar protein structures often reflect homology and are more conserved than protein sequences. RESULTS We propose a workflow of openly available tools for the functional annotation of proteins via structural similarity (MorF: MorphologFinder) and use it to annotate the complete proteome of a sponge. Sponges are highly relevant for inferring the early history of animals, yet their proteomes remain sparsely annotated. MorF accurately predicts the functions of proteins with known homology in [Formula: see text] cases and annotates an additional [Formula: see text] of the proteome beyond standard sequence-based methods. We uncover new functions for sponge cell types, including extensive FGF, TGF, and Ephrin signaling in sponge epithelia, and redox metabolism and control in myopeptidocytes. Notably, we also annotate genes specific to the enigmatic sponge mesocytes, proposing they function to digest cell walls. CONCLUSIONS Our work demonstrates that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify homologous proteins over long evolutionary distances. We anticipate this will be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms.
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Affiliation(s)
- Fabian Ruperti
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Collaboration for joint Ph.D. degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Nikolaos Papadopoulos
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department for Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Jacob M Musser
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Milot Mirdita
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany.
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12
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Barrera-Redondo J, Lotharukpong JS, Drost HG, Coelho SM. Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biol 2023; 24:54. [PMID: 36964572 PMCID: PMC10037820 DOI: 10.1186/s13059-023-02895-z] [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: 08/26/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
We present GenEra ( https://github.com/josuebarrera/GenEra ), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.
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Affiliation(s)
- Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - Jaruwatana Sodai Lotharukpong
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Hajk-Georg Drost
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
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13
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Vosseberg J, Stolker D, von der Dunk SHA, Snel B. Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome. Mol Biol Evol 2023; 40:6985000. [PMID: 36631250 PMCID: PMC9887622 DOI: 10.1093/molbev/msad011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/09/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Eukaryotic genes are characterized by the presence of introns that are removed from pre-mRNA by a spliceosome. This ribonucleoprotein complex is comprised of multiple RNA molecules and over a hundred proteins, which makes it one of the most complex molecular machines that originated during the prokaryote-to-eukaryote transition. Previous works have established that these introns and the spliceosomal core originated from self-splicing introns in prokaryotes. Yet, how the spliceosomal core expanded by recruiting many additional proteins remains largely elusive. In this study, we use phylogenetic analyses to infer the evolutionary history of 145 proteins that we could trace back to the spliceosome in the last eukaryotic common ancestor. We found that an overabundance of proteins derived from ribosome-related processes was added to the prokaryote-derived core. Extensive duplications of these proteins substantially increased the complexity of the emerging spliceosome. By comparing the intron positions between spliceosomal paralogs, we infer that most spliceosomal complexity postdates the spread of introns through the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insight into the driving forces behind the emergence of complexes with many proteins during eukaryogenesis.
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Affiliation(s)
- Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands,Laboratory of Microbiology, Wageningen University & Research, 6700 EH Wageningen, the Netherlands
| | - Daan Stolker
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Samuel H A von der Dunk
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
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14
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Sanchez-Pulido L, Ponting CP. OAF: a new member of the BRICHOS family. BIOINFORMATICS ADVANCES 2022; 2:vbac087. [PMID: 36699367 PMCID: PMC9714404 DOI: 10.1093/bioadv/vbac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/03/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
Summary The 10 known BRICHOS domain-containing proteins in humans have been linked to an unusually long list of pathologies, including cancer, obesity and two amyloid-like diseases. BRICHOS domains themselves have been described as intramolecular chaperones that act to prevent amyloid-like aggregation of their proteins' mature polypeptides. Using structural comparison of coevolution-based AlphaFold models and sequence conservation, we identified the Out at First (OAF) protein as a new member of the BRICHOS family in humans. OAF is an experimentally uncharacterized protein that has been proposed as a candidate biomarker for clinical management of coronavirus disease 2019 infections. Our analysis revealed how structural comparison of AlphaFold models can discover remote homology relationships and lead to a better understanding of BRICHOS domain molecular mechanism. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Luis Sanchez-Pulido
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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