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Prasad R, Kadam A, Padippurackal VV, Pulikuttymadom Balasubramanian A, Kumar Chandrakumaran N, Suresh Rangari K, Dnyaneshwar Khangar P, Ajith H, Natarajan K, Chandramohanadas R, Nelson-Sathi S. Discovery of small molecule entry inhibitors targeting the linoleic acid binding pocket of SARS-CoV-2 spike protein. J Biomol Struct Dyn 2024:1-15. [PMID: 38520147 DOI: 10.1080/07391102.2024.2327537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/02/2024] [Indexed: 03/25/2024]
Abstract
Spike glycoprotein has a significant role in the entry of SARS-CoV-2 to host cells, which makes it a potential drug target. Continued accumulation of non-synonymous mutations in the receptor binding domain of spike protein poses great challenges in identifying antiviral drugs targeting this protein. This study aims to identify potential entry inhibitors of SARS-CoV-2 using virtual screening and molecular dynamics (MD) simulations from three distinct chemical libraries including Pandemic Response Box, Drugbank and DrugCentral, comprising 6971 small molecules. The molecules were screened against a binding pocket identified in the receptor-binding domain (RBD) region of the spike protein which is known as the linoleic acid binding pocket, a highly conserved motif among several SARS-CoV-2 variants. Through virtual screening and binding free energy calculations, we identified four top-scoring compounds, MMV1579787 ([2-Oxo-2-[2-(3-phenoxyphenyl)ethylamino]ethyl]phosphonic acid), Tretinoin, MMV1633963 ((2E,4E)-5-[3-(3,5-dichlorophenoxy)phenyl]penta-2,4-dienoic acid) and Polydatin, which were previously reported to have antibacterial, antifungal or antiviral properties. These molecules showed stable binding on MD simulations over 100 ns and maintained stable interactions with TYR365, PHE338, PHE342, PHE377, TYR369, PHE374 and LEU368 of the spike protein RBD that are found to be conserved among SARS-CoV-2 variants. Our findings were further validated with free energy landscape, principal component analysis and dynamic cross-correlation analysis. Our in silico analysis of binding mode and MD simulation analyses suggest that the identified compounds may impede viral entrance by interacting with the linoleic acid binding site of the spike protein of SARS-CoV-2 regardless of its variants, and they thus demand for further in vitro and in vivo research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Roshny Prasad
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Anil Kadam
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | | | | | - Kartik Suresh Rangari
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | - Harikrishnan Ajith
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Kathiresan Natarajan
- Trans-disciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | - Shijulal Nelson-Sathi
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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Prasad R, Ajith H, Kumar Chandrakumaran N, Dnyaneshwar Khangar P, Mohan A, Nelson-Sathi S. In silico study identifies peptide inhibitors that negate the effect of non-synonymous mutations in major drug targets of SARS-CoV-2 variants. J Biomol Struct Dyn 2023; 41:9551-9561. [PMID: 36377464 DOI: 10.1080/07391102.2022.2143426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/29/2022] [Indexed: 11/16/2022]
Abstract
Since its advent in December 2019, SARS-CoV-2 has diverged into multiple variants with differing levels of virulence owing to the accumulation of mutations in its genome. The structural changes induced by non-synonymous mutations in major drug targets of the virus are known to alter the binding of potential antagonistic inhibitors. Here, we analyzed the effects of non-synonymous mutations in major targets of SARS-CoV-2 in response to potential peptide inhibitors. We screened 12 peptides reported to have anti-viral properties against RBD and 5 peptides against Mpro of SARS-CoV-2 variants using molecular docking and simulation approaches. The mutational landscape of RBD among SARS-CoV-2 variants had 21 non-synonymous mutations across 18 distinct sites. Among these, 14 mutations were present in the RBM region directly interacting with the hACE2 receptor. However, Only 3 non-synonymous mutations were observed in Mpro. We found that LCB1 - a de novo-synthesized peptide has the highest binding affinity to RBD despite non-synonymous mutations in variants and engages key residues of RBD-hACE2 interaction such as K417, E484, N487, and N501. Similarly, an antimicrobial peptide; 2JOS, was identified against Mpro with high binding affinity as it interacts with key residues in dimerization sites such as E166 and F140 crucial for viral replication. MD simulations affirm the stability of RBD-LCB1 and Mpro-2JOS complexes with an average RMSD of 1.902 and 2.476 respectively. We ascertain that LCB1 and 2JOS peptides are promising inhibitors to combat emerging variants of SARS-CoV-2 and thus warrant further investigations using in-vitro and in-vivo analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Roshny Prasad
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Harikrishnan Ajith
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | | | | | - Anand Mohan
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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Jancy SV, Lupitha SS, Chandrasekharan A, Varadarajan SN, Nelson-Sathi S, Prasad R, Jones S, Easwaran S, Darvin P, Sivasailam A, Santhoshkumar TR. A high-throughput screening system for SARS-CoV-2 entry inhibition, syncytia formation and cell toxicity. Biol Proced Online 2023; 25:22. [PMID: 37495994 PMCID: PMC10373420 DOI: 10.1186/s12575-023-00214-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND The entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into the host cell is mediated through the binding of the SARS-CoV-2 Spike protein via the receptor binding domain (RBD) to human angiotensin-converting enzyme 2 (hACE2). Identifying compounds that inhibit Spike-ACE2 binding would be a promising and safe antiviral approach against COVID-19. METHODS In this study, we used a BSL-2 compatible replication-competent vesicular stomatitis virus (VSV) expressing Spike protein of SARS-CoV-2 with eGFP reporter system (VSV-eGFP-SARS-CoV-2) in a recombinant permissive cell system for high-throughput screening of viral entry blockers. The SARS-CoV-2 permissive reporter system encompasses cells that stably express hACE2-tagged cerulean and H2B tagged with mCherry, as a marker of nuclear condensation, which also enables imaging of fused cells among infected EGFP positive cells and could provide real-time information on syncytia formation. RESULTS A limited high-throughput screening identified six natural products that markedly inhibited VSV-eGFP-SARS-CoV-2 with minimum toxicity. Further studies of Spike-S1 binding using the permissive cells showed Scillaren A and 17-Aminodemethoxygeldanamycin could inhibit S1 binding to ACE2 among the six leads. A real-time imaging revealed delayed inhibition of syncytia by Scillaren A, Proscillaridin, Acetoxycycloheximide and complete inhibition by Didemnin B indicating that the assay is a reliable platform for any image-based drug screening. CONCLUSION A BSL-2 compatible assay system that is equivalent to the infectious SARS-CoV-2 is a promising tool for high-throughput screening of large compound libraries for viral entry inhibitors against SARS-CoV-2 along with toxicity and effects on syncytia. Studies using clinical isolates of SARS-CoV-2 are warranted to confirm the antiviral potency of the leads and the utility of the screening system.
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Affiliation(s)
- Shine Varghese Jancy
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Santhik Subhasingh Lupitha
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Aneesh Chandrasekharan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Shankara Narayanan Varadarajan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Shijulal Nelson-Sathi
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Roshny Prasad
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Sara Jones
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Sreekumar Easwaran
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Pramod Darvin
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Aswathy Sivasailam
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India
| | - Thankayyan Retnabai Santhoshkumar
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thycaud P.O., Thiruvananthapuram, Kerala, 695014, India.
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Reghunandanan K, T P A, Krishnan N, K M D, Prasad R, Nelson-Sathi S, Chandramohanadas R. Search for novel Plasmodium falciparum PfATP4 inhibitors from the MMV Pandemic Response Box through a virtual screening approach. J Biomol Struct Dyn 2023:1-12. [PMID: 37424150 DOI: 10.1080/07391102.2023.2232459] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Owing to its life cycle involving multiple hosts and species-specific biological complexities, a vaccine against Plasmodium, the causative agent of Malaria remains elusive. This makes chemotherapy the only viable means to address the clinical manifestations and spread of this deadly disease. However, rapid surge in antimalarial resistance poses significant challenges to our efforts to eliminate Malaria since the best drug available to-date; Artemisinin and its combinations are also rapidly losing efficacy. Sodium ATPase (PfATP4) of Plasmodium has been recently explored as a suitable target for new antimalarials such as Cipargamin. Prior studies showed that multiple compounds from the Medicines for Malaria Venture (MMV) chemical libraries were efficient PfATP4 inhibitors. In this context, we undertook a structure- based virtual screening approach combined to Molecular Dynamic (MD) simulations to evaluate whether new molecules with binding affinity towards PfATP4 could be identified from the Pandemic Response Box (PRB), a 400-compound library of small molecules launched in 2019 by MMV. Our analysis identified new molecules from the PRB library that showed affinity for distinct binding sites including the previously known G358 site, several of which are clinically used anti-bacterial (MMV1634383, MMV1634402), antiviral (MMV010036, MMV394033) or antifungal (MMV1634494) agents. Therefore, this study highlights the possibility of exploiting PRB molecules against Malaria through abrogation of PfATP4 activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Keerthy Reghunandanan
- DBT-Rajiv Gandhi Centre for Biotechnology, Red Cell Diseases Laboratory, Thiruvananthapuram, India
| | - Akhila T P
- DBT-Rajiv Gandhi Centre for Biotechnology, Red Cell Diseases Laboratory, Thiruvananthapuram, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Nandini Krishnan
- DBT-Rajiv Gandhi Centre for Biotechnology, Red Cell Diseases Laboratory, Thiruvananthapuram, India
| | - Darsana K M
- DBT-Rajiv Gandhi Centre for Biotechnology, Red Cell Diseases Laboratory, Thiruvananthapuram, India
| | - Roshny Prasad
- DBT-Rajiv Gandhi Centre for Biotechnology, Bioinformatics Laboratory, Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- DBT-Rajiv Gandhi Centre for Biotechnology, Bioinformatics Laboratory, Thiruvananthapuram, India
| | - Rajesh Chandramohanadas
- DBT-Rajiv Gandhi Centre for Biotechnology, Red Cell Diseases Laboratory, Thiruvananthapuram, India
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Jesmina ARS, Induja DK, Drissya T, Sruthi CR, Raghu KG, Nelson-Sathi S, Kumar BNSAD, Lankalapalli RS. In vitro antibacterial effects of combination of ciprofloxacin with compounds isolated from Streptomyces luteireticuli NIIST-D75. J Antibiot (Tokyo) 2023; 76:198-210. [PMID: 36781977 DOI: 10.1038/s41429-023-00600-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/11/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Three phenazines, 1-methoxyphenazine (1), methyl-6-methoxyphenazine-1-carboxylate (2), 1,6-dimethoxyphenazine (4), and a 2,3-dimethoxy benzamide (3) were isolated from the Streptomyces luteireticuli NIIST-D75, and the antibacterial effects of compounds 1-3, each in combination with ciprofloxacin, were investigated. The in vitro antibacterial activity was assessed by microdilution, checkerboard, and time-kill assay against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Salmonella typhi. According to the checkerboard assay results, each combination of compounds 1, 2 and 3 with ciprofloxacin resulted in a significantly lower minimum inhibitory concentrations (MICs) of 0.02-1.37 µg ml-1, suggesting synergistic combinations by fractional inhibitory concentration index, and displayed bactericidal activity in time-kill kinetics within 48 h. SEM analysis was carried out to determine the changes in morphology in S. aureus and E. coli during treatment with individual combination of ciprofloxacin and compounds (1-3), which revealed drastic changes in the cells such as dent formation, biofilm disruption, cell bursting, and doughnut-like formation, change in surface morphology in S. aureus, and cell elongation, cell burst with ruptured cell, and change in surface morphology in E. coli. Hep G2 cell viability was not affected by the compounds (1-3) that were tested for cytotoxicity up to 250 µM.
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Affiliation(s)
- Abdul Rasheed Safiya Jesmina
- Agro-Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - D K Induja
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, India
| | - Thankappan Drissya
- Agro-Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Chakiniplackal Rajan Sruthi
- Agro-Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kozhiparambil Gopalan Raghu
- Agro-Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shijulal Nelson-Sathi
- Transdisciplinary Biology, Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Bhaskaran Nair Saraswathy Amma Dileep Kumar
- Agro-Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Ravi S Lankalapalli
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, India.
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John J, Narendrakumar L, Thomas S, Nelson-Sathi S. Hybrid genome assembly and annotation of multidrug-resistant Staphylococcus aureus genotype ST672-SCCmec type IVd (2B). J Glob Antimicrob Resist 2023; 32:74-77. [PMID: 36708767 DOI: 10.1016/j.jgar.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/14/2022] [Accepted: 12/26/2022] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVES The emergence of multidrug-resistant Staphylococcus aureus strains is mainly mediated by mobile genetic elements, such as Staphylococcal Cassette Chromosome mec (SCCmec). Currently, SCCmec elements in S. aureus are classified into 15 types, with type IV being the most common in hospital and community-associated methicillin-resistant S. aureus. Among different subtypes of SCCmec type IV strains (IVa-IVn), the complete genome sequence of the SCCmec IVd (2B) subtype is still lacking. Here, we report the complete genome sequence of multidrug-resistant S. aureus SCCmec typeIVd (2B) isolate, S. aureus S145. METHODS Staphylococcus aureus S145 was subjected to phenotypic and genotypic characterization. The whole-genome sequencing of S145 was performed using a hybrid-genome approach. The antibiotic-resistance genes were detected and compared with 112 publicly available S. aureus genomes. RESULTS We obtained a complete genome of S145 with 2.7 Mbp length, Guanine-Cytosine (GC) content of 32.8%, and 2,548 protein-coding regions with 79 virulence factors and 90 antibiotic resistance genes. The S145 has ∼17-kb SCCmec, which encodes genes such as mecA, mecR1, ccrA2B2, and SCCmec IVd (2B) subtype gene CG002. We detected a ∼30-kb multidrug-resistant plasmid with eight antibiotic-resistant genes forming three clusters. Cluster1 encoded for penicillin (blaI-blaZ-blaR1), Cluster2 for aminoglycoside-streptothricin (aph(3')-IIIa-sat4-ΔANT(6)-Ia), and Cluster3 for macrolides (msr(A)-mph(C)) resistance genes. Comparative analysis of Cluster1-Cluster3 revealed that the genetic organization of these clusters resembles resistance genes present in plasmids of USA300 S. aureus SCCmec type IVa strains. CONCLUSION Here, we report the complete genome sequence of S. aureus SCCmec IVd (2B) that can be used as a reference genome for further comparative genomic analysis.
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Affiliation(s)
- Jiffy John
- Bioinformatics Laboratory, Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India; Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Lekshmi Narendrakumar
- Department of Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Sabu Thomas
- Department of Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- Bioinformatics Laboratory, Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India.
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Lupitha SS, Darvin P, Chandrasekharan A, Varadarajan SN, Divakaran SJ, Easwaran S, Nelson-Sathi S, Umasankar PK, Jones S, Joseph I, Pillai MR, Santhoshkumar TR. A rapid bead-based assay for screening of SARS-CoV-2 neutralising antibodies. Antib Ther 2022; 5:100-110. [PMID: 35437514 PMCID: PMC8992333 DOI: 10.1093/abt/tbac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/13/2022] [Accepted: 03/08/2022] [Indexed: 12/01/2022] Open
Abstract
Quantitative determination of neutralizing antibodies against Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) is paramount in immunodiagnostics, vaccine efficacy testing, and immune response profiling among the vaccinated population. Cost-effective, rapid, easy-to-perform assays are essential to support the vaccine development process and immunosurveillance studies. We describe a bead-based screening assay for S1-neutralization using recombinant fluorescent proteins of hACE2 and SARS-CoV2-S1, immobilized on solid beads employing nanobodies/metal-affinity tags. Nanobody-mediated capture of SARS-CoV-2-Spike (S1) on agarose beads served as the trap for soluble recombinant ACE2-GFPSpark, inhibited by neutralizing antibody. The first approach demonstrates single-color fluorescent imaging of ACE2-GFPSpark binding to His-tagged S1-Receptor Binding Domain (RBD-His) immobilized beads. The second approach is dual-color imaging of soluble ACE2-GFPSpark to S1-Orange Fluorescent Protein (S1-OFPSpark) beads. Both methods showed a good correlation with the gold standard pseudovirion assay and can be adapted to any fluorescent platforms for screening.
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Affiliation(s)
- Santhik Subhasingh Lupitha
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Pramod Darvin
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Aneesh Chandrasekharan
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | | | - Soumya Jaya Divakaran
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Sreekumar Easwaran
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Perunthottathu K Umasankar
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Sara Jones
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Iype Joseph
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - M Radhakrishna Pillai
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - T R Santhoshkumar
- Corona Research and Intervention Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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Garg SG, Kapust N, Lin W, Knopp M, Tria FDK, Nelson-Sathi S, Gould SB, Fan L, Zhu R, Zhang C, Martin WF. Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea. Genome Biol Evol 2020; 13:5988511. [PMID: 33462601 DOI: 10.1093/gbe/evaa238] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2020] [Indexed: 01/20/2023] Open
Abstract
Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here, we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.
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Affiliation(s)
- Sriram G Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Nils Kapust
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Weili Lin
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Michael Knopp
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Fernando D K Tria
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Transdisciplinary Biology, Computational Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Lu Fan
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Ruixin Zhu
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
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John J, George S, Nori SRC, Nelson-Sathi S. Phylogenomic Analysis Reveals the Evolutionary Route of Resistant Genes in Staphylococcus aureus. Genome Biol Evol 2020; 11:2917-2926. [PMID: 31589296 PMCID: PMC6808081 DOI: 10.1093/gbe/evz213] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 01/02/2023] Open
Abstract
Multidrug-resistant Staphylococcus aureus is a leading concern worldwide. Coagulase-Negative Staphylococci are claimed to be the reservoir and source of important resistant elements in S. aureus. However, the origin and evolutionary route of resistant genes in S. aureus are still remaining unknown. Here, we performed a detailed phylogenomic analysis of 152 completely sequenced S. aureus strains in comparison with 7,529 non-Staphylococcus aureus reference bacterial genomes. Our results reveal that S. aureus has a large open pan-genome where 97 (55%) of its known resistant-related genes belonging to its accessory genome. Among these genes, 47 (27%) were located within the Staphylococcal Cassette Chromosome mec (SCCmec), a transposable element responsible for resistance against major classes of antibiotics including beta-lactams, macrolides, and aminoglycosides. However, the physically linked mec-box genes (MecA–MecR–MecI) that are responsible for the maintenance of SCCmec elements is not unique to S. aureus, instead it is widely distributed within Staphylococcaceae family. The phyletic patterns of SCCmec-encoded resistant genes in Staphylococcus species are significantly different from that of its core genes indicating frequent exchange of these genes between Staphylococcus species. Our in-depth analysis of SCCmec-resistant gene phylogenies reveals that genes such as blaZ, ble, kmA, and tetK that are responsible for beta-lactam, bleomycin, kanamycin, and tetracycline resistance in S. aureus were laterally transferred from non-Staphylococcus sources. In addition, at least 11 non-SCCmec-encoded resistant genes in S. aureus, were laterally acquired from distantly related species. Our study evidently shows that gene transfers played a crucial role in shaping the evolution of antibiotic resistance in S. aureus.
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Affiliation(s)
- Jiffy John
- Computational Biology Laboratory, Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Sinumol George
- Computational Biology Laboratory, Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India
| | - Sai Ravi Chandra Nori
- Computational Biology Laboratory, Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- Computational Biology Laboratory, Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India
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10
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Jaya Divakaran S, Sara Philip J, Chereddy P, Nori SRC, Jaya Ganesh A, John J, Nelson-Sathi S. Insights into the Bacterial Profiles and Resistome Structures Following the Severe 2018 Flood in Kerala, South India. Microorganisms 2019; 7:E474. [PMID: 31635115 PMCID: PMC6843399 DOI: 10.3390/microorganisms7100474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 09/27/2019] [Accepted: 10/08/2019] [Indexed: 12/11/2022] Open
Abstract
Extreme flooding is one of the major risk factors for human health, and it can significantly influence the microbial communities and enhance the mobility of infectious disease agents within the affected areas. The flood crisis in 2018 was one of the severe natural calamities recorded in the southern state of India (Kerala) that significantly affected its economy and ecological habitat. We utilized a combination of shotgun metagenomics and bioinformatics approaches to understand the bacterial profile and the abundance of pathogenic and antibiotic-resistant bacteria in extremely flooded areas of Kuttanad, Kerala (4-10 feet below sea level). Here we report the bacterial profiles of flooded sites that are abundant with virulent and resistant bacteria. The flooded sites were heavily contaminated with faecal contamination indicators such as Escherichia coli and Enterococcus faecalis and multidrug-resistant strains of Pseudomonas aeruginosa, Salmonella typhi/typhimurium, Klebsiella pneumoniae, Vibrio cholerae. The resistome of the flooded sites contains 103 known resistant genes, of which 38% are plasmid-encoded, where most of them are known to be associated with pathogenic bacteria. Our results reveal an overall picture of the bacterial profile and resistome of sites following a devastating flood event, which might increase the levels of pathogens and its associated risks.
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Affiliation(s)
- Soumya Jaya Divakaran
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695 014, Kerala, India.
| | - Jamiema Sara Philip
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695 014, Kerala, India.
| | - Padma Chereddy
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695 014, Kerala, India.
| | - Sai Ravi Chandra Nori
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695 014, Kerala, India.
| | - Akshay Jaya Ganesh
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695 014, Kerala, India.
| | - Jiffy John
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695 014, Kerala, India.
| | - Shijulal Nelson-Sathi
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695 014, Kerala, India.
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11
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Jones S, Nelson-Sathi S, Wang Y, Prasad R, Rayen S, Nandel V, Hu Y, Zhang W, Nair R, Dharmaseelan S, Chirundodh DV, Kumar R, Pillai RM. Evolutionary, genetic, structural characterization and its functional implications for the influenza A (H1N1) infection outbreak in India from 2009 to 2017. Sci Rep 2019; 9:14690. [PMID: 31604969 PMCID: PMC6789102 DOI: 10.1038/s41598-019-51097-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 09/20/2019] [Indexed: 12/27/2022] Open
Abstract
Influenza A (H1N1) continues to be a major public health threat due to possible emergence of a more virulent H1N1 strain resulting from dynamic changes in virus adaptability consequent to functional mutations and antigenic drift in the hemagglutinin (HA) and neuraminidase (NA) surface proteins. In this study, we describe the genetic and evolutionary characteristics of H1N1 strains that circulated in India over a period of nine years from 2009 to 2017 in relation to global strains. The finding is important from a global perspective since previous phylogenetic studies have suggested that the tropics contributed substantially to the global circulation of influenza viruses. Bayesian phylogenic analysis of HA sequences along with global strains indicated that there is a temporal pattern of H1N1 evolution and clustering of Indian isolates with globally circulating strains. Interestingly, we observed four new amino acid substitutions (S179N, I233T, S181T and I312V) in the HA sequence of H1N1 strains isolated during 2017 and two (S181T and I312V) were found to be unique in Indian isolates. Structurally these two unique mutations could lead to altered glycan specificity of the HA gene. Similarly, sequence and structural analysis of NA domain revealed that the presence of K432E mutation in H1N1 strains isolated after 2015 from India and in global strains found to induce a major loop shift in the vicinity of the catalytic site. The findings presented here offer an insight as to how these acquired mutations could be associated to an improved adaptability of the virus for efficient human transmissibility.
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Affiliation(s)
- Sara Jones
- Pathogen Biology Program, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Shijulal Nelson-Sathi
- Interdiciplinary Biology Program, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Raji Prasad
- Pathogen Biology Program, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Sabrina Rayen
- Interdiciplinary Biology Program, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Vibhuti Nandel
- Interdiciplinary Biology Program, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Yueming Hu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Wei Zhang
- Shenzhen Gen Read Technology, Shenzhen, 518000, China
| | - Radhakrishnan Nair
- Laboratory Medicine and Molecular Diagnostics Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Sanjai Dharmaseelan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | | | - Rakesh Kumar
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India.
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12
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Sharma C, Nelson-Sathi S, Singh A, Radhakrishna Pillai M, Chowdhary A. Genomic perspective of triazole resistance in clinical and environmental Aspergillus fumigatus isolates without cyp51A mutations. Fungal Genet Biol 2019; 132:103265. [PMID: 31465846 DOI: 10.1016/j.fgb.2019.103265] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 11/24/2022]
Abstract
Aspergillus fumigatus is the most common etiologic agent of primarily all clinical manifestations of aspergillosis. A steady increase in the number of azole resistant A. fumigatus (ARAF) isolates from environment and clinical samples leading to therapeutic failures in clinical settings have alarmed the mycologists and clinicians worldwide. Although mutations in azole target cyp51A gene have been implicated in conferring azole resistance in A. fumigatus, recent studies have demonstrated occurrence of azole resistant strains without cyp51A mutations. In this study, next generation sequencing techniques and the expression profiling of transporter genes with single nucleotide polymorphisms (SNPs) in clinical and environmental ARAF isolates with (G54E) and without known cyp51A mutations was undertaken to understand the genetic background and role of transporters in azole resistance. The raw reads of four ARAF strains when mapped to Af293 reference genome (>100X depth) covered at least 93.1% of the reference genome. Among all four strains, a total of 212,711 SNPs was identified with 37,829 were common in at least two isolates. The expression analysis suggested the overexpression of MFS transporter, namely, mfsC in all ARAF isolates. None of the resistant strain showed significant upregulation of cyp51A and cyp51B gene. On the other hand, abcD was upregulated (5-fold) in the isolates with cyp 51A mutation (G54E). The whole genome sequence analysis showed the presence of two previously described amino acid substitutions S269F and F390Y in HMG1 gene in a clinical panazole resistant strain without cyp51A mutations. These mutations have been previously associated with azole resistance in A. fumigatus strains without cyp51A mutations. Further, several punctual mutations and a large-segment deletion among different strains were observed suggesting the involvement of resistance mechanisms other than cyp51A.
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Affiliation(s)
- Cheshta Sharma
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Shijulal Nelson-Sathi
- Interdiciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Ashutosh Singh
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | | | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India.
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13
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Gould SB, Garg SG, Handrich M, Nelson-Sathi S, Gruenheit N, Tielens AGM, Martin WF. Adaptation to life on land at high O 2 via transition from ferredoxin-to NADH-dependent redox balance. Proc Biol Sci 2019; 286:20191491. [PMID: 31431166 PMCID: PMC6732389 DOI: 10.1098/rspb.2019.1491] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pyruvate : ferredoxin oxidoreductase (PFO) and iron only hydrogenase ([Fe]-HYD) are common enzymes among eukaryotic microbes that inhabit anaerobic niches. Their function is to maintain redox balance by donating electrons from food oxidation via ferredoxin (Fd) to protons, generating H2 as a waste product. Operating in series, they constitute a soluble electron transport chain of one-electron transfers between FeS clusters. They fulfil the same function—redox balance—served by two electron-transfers in the NADH- and O2-dependent respiratory chains of mitochondria. Although they possess O2-sensitive FeS clusters, PFO, Fd and [Fe]-HYD are also present among numerous algae that produce O2. The evolutionary persistence of these enzymes among eukaryotic aerobes is traditionally explained as adaptation to facultative anaerobic growth. Here, we show that algae express enzymes of anaerobic energy metabolism at ambient O2 levels (21% v/v), Chlamydomonas reinhardtii expresses them with diurnal regulation. High O2 environments arose on Earth only approximately 450 million years ago. Gene presence/absence and gene expression data indicate that during the transition to high O2 environments and terrestrialization, diverse algal lineages retained enzymes of Fd-dependent one-electron-based redox balance, while the land plant and land animal lineages underwent irreversible specialization to redox balance involving the O2-insensitive two-electron carrier NADH.
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Affiliation(s)
- S B Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - S G Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - M Handrich
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - S Nelson-Sathi
- Interdisciplinary Biology, Computational Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - N Gruenheit
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - A G M Tielens
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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14
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Abstract
The origin of mitochondria was a crucial event in eukaryote evolution. A recent report claimed to provide evidence, based on branch length variation in phylogenetic trees, that the mitochondrion came late in eukaryotic evolution. Here, we reinvestigate their claim with a reanalysis of the published data. We show that the analyses underpinning a late mitochondrial origin suffer from multiple fatal flaws founded in inappropriate statistical methods and analyses, in addition to erroneous interpretations.
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Affiliation(s)
- William F. Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
- Corresponding author: E-mail:
| | - Mayo Roettger
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Chuan Ku
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Sriram G. Garg
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Computational Biology & Bioinformatics Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | - Giddy Landan
- Institute of Microbiology, Christian-Albrechts-University of Kiel, Germany
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15
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Kapust N, Nelson-Sathi S, Schönfeld B, Hazkani-Covo E, Bryant D, Lockhart PJ, Röttger M, Xavier JC, Martin WF. Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication. Genome Biol Evol 2018; 10:1198-1209. [PMID: 29718211 PMCID: PMC5928405 DOI: 10.1093/gbe/evy080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2018] [Indexed: 12/13/2022] Open
Abstract
In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible.
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Affiliation(s)
- Nils Kapust
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Computational Biology & Bioinformatics Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | | | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
| | - David Bryant
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Peter J Lockhart
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Mayo Röttger
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Joana C Xavier
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
- Corresponding author: E-mail:
| | - William F Martin
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
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16
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Abstract
Genomes record their own history. But if we want to look all the way back to life's beginnings some 4 billion years ago, the record of microbial evolution that is preserved in prokaryotic genomes is not easy to read. Microbiology has a lot in common with geology in that regard. Geologists know that plate tectonics and erosion have erased much of the geological record, with ancient rocks being truly rare. The same is true of microbes. Lateral gene transfer (LGT) and sequence divergence have erased much of the evolutionary record that was once written in genomes, and it is not obvious which genes among sequenced genomes are genuinely ancient. Which genes trace to the last universal ancestor, LUCA? The classical approach has been to look for genes that are universally distributed. Another approach is to make all trees for all genes, and sift out the trees where signals have been overwritten by LGT. What is left ought to be ancient. If we do that, what do we find?
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Affiliation(s)
- William F Martin
- Institute for Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany. ; Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Madeline C Weiss
- Institute for Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany
| | - Sinje Neukirchen
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Shijulal Nelson-Sathi
- Computational Biology & Bioinformatics Group, Rajiv Gandhi Centre for Biotechnology (RGCB), Trivandrum, Kerala 695014, India
| | - Filipa L Sousa
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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17
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Abstract
Bubonic plaque is caused by Yersinia pestis, a deadly pathogen that left deep scars in human history. Rasmussen et al. (2015) have now retrieved Y. pestis genomes from 2,800- to 5,000-year-old human teeth, shedding new light on origins of the strain that brought Black Death to Europe 670 years ago.
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Affiliation(s)
- Shijulal Nelson-Sathi
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.
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18
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Sousa FL, Nelson-Sathi S, Martin WF. One step beyond a ribosome: The ancient anaerobic core. Biochim Biophys Acta 2016; 1857:1027-1038. [PMID: 27150504 PMCID: PMC4906156 DOI: 10.1016/j.bbabio.2016.04.284] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/03/2016] [Accepted: 04/05/2016] [Indexed: 11/23/2022]
Abstract
Life arose in a world without oxygen and the first organisms were anaerobes. Here we investigate the gene repertoire of the prokaryote common ancestor, estimating which genes it contained and to which lineages of modern prokaryotes it was most similar in terms of gene content. Using a phylogenetic approach we found that among trees for all 8779 protein families shared between 134 archaea and 1847 bacterial genomes, only 1045 have sequences from at least two bacterial and two archaeal groups and retain the ancestral archaeal–bacterial split. Among those, the genes shared by anaerobes were identified as candidate genes for the prokaryote common ancestor, which lived in anaerobic environments. We find that these anaerobic prokaryote common ancestor genes are today most frequently distributed among methanogens and clostridia, strict anaerobes that live from low free energy changes near the thermodynamic limit of life. The anaerobic families encompass genes for bifunctional acetyl-CoA-synthase/CO-dehydrogenase, heterodisulfide reductase subunits C and A, ferredoxins, and several subunits of the Mrp-antiporter/hydrogenase family, in addition to numerous S-adenosyl methionine (SAM) dependent methyltransferases. The data indicate a major role for methyl groups in the metabolism of the prokaryote common ancestor. The data furthermore indicate that the prokaryote ancestor possessed a rotor stator ATP synthase, but lacked cytochromes and quinones as well as identifiable redox-dependent ion pumping complexes. The prokaryote ancestor did possess, however, an Mrp-type H+/Na+ antiporter complex, capable of transducing geochemical pH gradients into biologically more stable Na+-gradients. The findings implicate a hydrothermal, autotrophic, and methyl-dependent origin of life. This article is part of a Special Issue entitled ‘EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2–6, 2016’, edited by Prof. Paolo Bernardi. Life arose without oxygen, the universal ancestor (Luca) was an anaerobe. We used phylogenetic and physiological criteria to identify genes present in Luca. An ancient core of 65 metabolic genes shed light on Luca's anaerobic lifestyle. Ancient core genes are most widespread among modern methanogens and clostridia. The data implicate a major role for methyl groups in Luca's anaerobic metabolism.
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Affiliation(s)
- Filipa L Sousa
- Institute for Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany.
| | - Shijulal Nelson-Sathi
- Institute for Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany
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19
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Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF. Endosymbiotic origin and differential loss of eukaryotic genes. Nature 2015; 524:427-32. [PMID: 26287458 DOI: 10.1038/nature14963] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/20/2015] [Indexed: 01/11/2023]
Abstract
Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.
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Affiliation(s)
- Chuan Ku
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Mayo Roettger
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Filipa L Sousa
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Peter J Lockhart
- Institute of Fundamental Sciences, Massey University, Palmerston North 4474, New Zealand
| | - David Bryant
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
| | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana 43107, Israel
| | - James O McInerney
- Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland.,Michael Smith Building, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Giddy Landan
- Genomic Microbiology Group, Institute of Microbiology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
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20
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Abstract
Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution.
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Affiliation(s)
- Johann-Mattis List
- Research Center Deutscher Sprachatlas, Philipps-University MarburgMarburg, Germany
| | - Shijulal Nelson-Sathi
- Institute of Molecular Evolution, Heinrich-Heine University DüsseldorfDüsseldorf, Germany
| | - Hans Geisler
- Institute of Romance Languages and Literature, Heinrich-Heine University DüsseldorfDüsseldorf, Germany
| | - William Martin
- Institute of Molecular Evolution, Heinrich-Heine University DüsseldorfDüsseldorf, Germany
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21
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Abstract
Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood-Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent-ocean interface via the ATP synthase, (iii) harnessing of Na(+) gradients generated by H(+)/Na(+) antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO2 reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type 'reduced iron → reduced carbon' at the beginning of bioenergetic evolution.
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Affiliation(s)
- Filipa L. Sousa
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Thorsten Thiergart
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Giddy Landan
- Institute of Genomic Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - John F. Allen
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, UK
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK
| | - Nick Lane
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK
| | - William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
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Nelson-Sathi S, List JM, Geisler H, Fangerau H, Gray RD, Martin W, Dagan T. Networks uncover hidden lexical borrowing in Indo-European language evolution. Proc Biol Sci 2010; 278:1794-803. [PMID: 21106583 PMCID: PMC3097823 DOI: 10.1098/rspb.2010.1917] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Language evolution is traditionally described in terms of family trees with ancestral languages splitting into descendent languages. However, it has long been recognized that language evolution also entails horizontal components, most commonly through lexical borrowing. For example, the English language was heavily influenced by Old Norse and Old French; eight per cent of its basic vocabulary is borrowed. Borrowing is a distinctly non-tree-like process--akin to horizontal gene transfer in genome evolution--that cannot be recovered by phylogenetic trees. Here, we infer the frequency of hidden borrowing among 2346 cognates (etymologically related words) of basic vocabulary distributed across 84 Indo-European languages. The dataset includes 124 (5%) known borrowings. Applying the uniformitarian principle to inventory dynamics in past and present basic vocabularies, we find that 1373 (61%) of the cognates have been affected by borrowing during their history. Our approach correctly identified 117 (94%) known borrowings. Reconstructed phylogenetic networks that capture both vertical and horizontal components of evolutionary history reveal that, on average, eight per cent of the words of basic vocabulary in each Indo-European language were involved in borrowing during evolution. Basic vocabulary is often assumed to be relatively resistant to borrowing. Our results indicate that the impact of borrowing is far more widespread than previously thought.
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