51
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Sahu A, Gaur M, Mahanandia NC, Subudhi E, Swain RP, Subudhi BB. Identification of core therapeutic targets for Monkeypox virus and repurposing potential of drugs against them: An in silico approach. Comput Biol Med 2023; 161:106971. [PMID: 37211001 DOI: 10.1016/j.compbiomed.2023.106971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/23/2023]
Abstract
Monkeypox virus (mpox virus) outbreak has rapidly spread to 82 non-endemic countries. Although it primarily causes skin lesions, secondary complications and high mortality (1-10%) in vulnerable populations have made it an emerging threat. Since there is no specific vaccine/antiviral, it is desirable to repurpose existing drugs against mpox virus. With little knowledge about the lifecycle of mpox virus, identifying potential inhibitors is a challenge. Nevertheless, the available genomes of mpox virus in public databases represent a goldmine of untapped possibilities to identify druggable targets for the structure-based identification of inhibitors. Leveraging this resource, we combined genomics and subtractive proteomics to identify highly druggable core proteins of mpox virus. This was followed by virtual screening to identify inhibitors with affinities for multiple targets. 125 publicly available genomes of mpox virus were mined to identify 69 highly conserved proteins. These proteins were then curated manually. These curated proteins were funnelled through a subtractive proteomics pipeline to identify 4 highly druggable, non-host homologous targets namely; A20R, I7L, Top1B and VETFS. High-throughput virtual screening of 5893 highly curated approved/investigational drugs led to the identification of common as well as unique potential inhibitors with high binding affinities. The common inhibitors, i.e., batefenterol, burixafor and eluxadoline were further validated by molecular dynamics simulation to identify their best potential binding modes. The affinity of these inhibitors suggests their repurposing potential. This work can encourage further experimental validation for possible therapeutic management of mpox.
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Affiliation(s)
- Anshuman Sahu
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751030, India
| | - Mahendra Gaur
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751030, India; Department of Biotechnology, Punjabi University, Patiala, 147002, India
| | - Nimai Charan Mahanandia
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, 110012, India
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751030, India
| | - Ranjit Prasad Swain
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751030, India
| | - Bharat Bhusan Subudhi
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751030, India.
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52
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Rahman A, Sarker MT, Islam MA, Hossain MU, Hasan M, Susmi TF. Targeting Essential Hypothetical Proteins of Pseudomonas aeruginosa PAO1 for Mining of Novel Therapeutics: An In Silico Approach. BIOMED RESEARCH INTERNATIONAL 2023; 2023:1787485. [PMID: 37090194 PMCID: PMC10119676 DOI: 10.1155/2023/1787485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 01/24/2023] [Accepted: 02/06/2023] [Indexed: 04/25/2023]
Abstract
As an omnipresent opportunistic bacterium, Pseudomonas aeruginosa PAO1 is responsible for acute and chronic infection in immunocompromised individuals. Currently, this bacterium is on WHO's red list where new antibiotics are urgently required for the treatment. Finding essential genes and essential hypothetical proteins (EHP) can be crucial in identifying novel druggable targets and therapeutics. This study is aimed at characterizing these EHPs and analyzing subcellular and physiochemical properties, PPI network, nonhomologous analysis against humans, virulence factor and novel drug target prediction, and finally structural analysis of the identified target employing around 42 robust bioinformatics tools/databases, the output of which was evaluated using the ROC analysis. The study discovered 18 EHPs from 336 essential genes, with domain and functional annotation revealing that 50% of these proteins belong to the enzyme category. The majority are cytoplasmic and cytoplasmic membrane proteins, with half being stable proteins subjected to PPIs network analysis. The network contains 261 nodes and 269 edges for 9 proteins of interest, with 11 hubs containing at least three nodes each. Finally, a pipeline builder predicts 7 proteins with novel drug targets, 5 nonhomologous proteins against human proteome, human antitargets, and human gut flora, and 3 virulent proteins. Among these, homology modeling of NP_249450 and NP_251676 was done, and the Ramachandran plot analysis revealed that more than 94% of the residues were in the preferred region. By analyzing functional attributes and virulence characteristics, the findings of this study may facilitate the development of innovative antibacterial drug targets and drugs of Pseudomonas aeruginosa PAO1.
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Affiliation(s)
- Atikur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md. Takim Sarker
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Ashiqul Islam
- Department of Chemistry and Biochemistry, University of Windsor, Canada
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Tasmina Ferdous Susmi
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
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53
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Cromer MK, Majeti KR, Rettig GR, Murugan K, Kurgan GL, Bode NM, Hampton JP, Vakulskas CA, Behlke MA, Porteus MH. Comparative analysis of CRISPR off-target discovery tools following ex vivo editing of CD34 + hematopoietic stem and progenitor cells. Mol Ther 2023; 31:1074-1087. [PMID: 36793210 PMCID: PMC10124080 DOI: 10.1016/j.ymthe.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/11/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
While a number of methods exist to investigate CRISPR off-target (OT) editing, few have been compared head-to-head in primary cells after clinically relevant editing processes. Therefore, we compared in silico tools (COSMID, CCTop, and Cas-OFFinder) and empirical methods (CHANGE-Seq, CIRCLE-Seq, DISCOVER-Seq, GUIDE-Seq, and SITE-Seq) after ex vivo hematopoietic stem and progenitor cell (HSPC) editing. We performed editing using 11 different gRNAs complexed with Cas9 protein (high-fidelity [HiFi] or wild-type versions), then performed targeted next-generation sequencing of nominated OT sites identified by in silico and empirical methods. We identified an average of less than one OT site per guide RNA (gRNA) and all OT sites generated using HiFi Cas9 and a 20-nt gRNA were identified by all OT detection methods with the exception of SITE-seq. This resulted in high sensitivity for the majority of OT nomination tools and COSMID, DISCOVER-Seq, and GUIDE-Seq attained the highest positive predictive value (PPV). We found that empirical methods did not identify OT sites that were not also identified by bioinformatic methods. This study supports that refined bioinformatic algorithms could be developed that maintain both high sensitivity and PPV, thereby enabling more efficient identification of potential OT sites without compromising a thorough examination for any given gRNA.
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Affiliation(s)
- M Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Kiran R Majeti
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Karthik Murugan
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Gavin L Kurgan
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Nicole M Bode
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Jessica P Hampton
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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54
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Gao T, Zhao Y, Zhang L, Wang H. Secondary and Topological Structural Merge Prediction of Alpha-Helical Transmembrane Proteins Using a Hybrid Model Based on Hidden Markov and Long Short-Term Memory Neural Networks. Int J Mol Sci 2023; 24:ijms24065720. [PMID: 36982795 PMCID: PMC10057634 DOI: 10.3390/ijms24065720] [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: 02/07/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Alpha-helical transmembrane proteins (αTMPs) play essential roles in drug targeting and disease treatments. Due to the challenges of using experimental methods to determine their structure, αTMPs have far fewer known structures than soluble proteins. The topology of transmembrane proteins (TMPs) can determine the spatial conformation relative to the membrane, while the secondary structure helps to identify their functional domain. They are highly correlated on αTMPs sequences, and achieving a merge prediction is instructive for further understanding the structure and function of αTMPs. In this study, we implemented a hybrid model combining Deep Learning Neural Networks (DNNs) with a Class Hidden Markov Model (CHMM), namely HDNNtopss. DNNs extract rich contextual features through stacked attention-enhanced Bidirectional Long Short-Term Memory (BiLSTM) networks and Convolutional Neural Networks (CNNs), and CHMM captures state-associative temporal features. The hybrid model not only reasonably considers the probability of the state path but also has a fitting and feature-extraction capability for deep learning, which enables flexible prediction and makes the resulting sequence more biologically meaningful. It outperforms current advanced merge-prediction methods with a Q4 of 0.779 and an MCC of 0.673 on the independent test dataset, which have practical, solid significance. In comparison to advanced prediction methods for topological and secondary structures, it achieves the highest topology prediction with a Q2 of 0.884, which has a strong comprehensive performance. At the same time, we implemented a joint training method, Co-HDNNtopss, and achieved a good performance to provide an important reference for similar hybrid-model training.
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Affiliation(s)
- Ting Gao
- School of Information Science and Technology, Institute of Computational Biology, Northeast Normal University, Changchun 130117, China; (T.G.); (Y.Z.)
| | - Yutong Zhao
- School of Information Science and Technology, Institute of Computational Biology, Northeast Normal University, Changchun 130117, China; (T.G.); (Y.Z.)
| | - Li Zhang
- School of Computer Science and Engineering, Changchun University of Technology, Changchun 130012, China;
| | - Han Wang
- School of Information Science and Technology, Institute of Computational Biology, Northeast Normal University, Changchun 130117, China; (T.G.); (Y.Z.)
- Correspondence:
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55
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Identification and Functional Analysis of Two Mitoferrins, CsMIT1 and CsMIT2, Participating in Iron Homeostasis in Cucumber. Int J Mol Sci 2023; 24:ijms24055050. [PMID: 36902490 PMCID: PMC10003640 DOI: 10.3390/ijms24055050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Mitochondria are one of the major iron sinks in plant cells. Mitochondrial iron accumulation involves the action of ferric reductase oxidases (FRO) and carriers located in the inner mitochondrial membrane. It has been suggested that among these transporters, mitoferrins (mitochondrial iron transporters, MITs) belonging to the mitochondrial carrier family (MCF) function as mitochondrial iron importers. In this study, two cucumber proteins, CsMIT1 and CsMIT2, with high homology to Arabidopsis, rice and yeast MITs were identified and characterized. CsMIT1 and CsMIT2 were expressed in all organs of the two-week-old seedlings. Under Fe-limited conditions as well as Fe excess, the mRNA levels of CsMIT1 and CsMIT2 were altered, suggesting their regulation by iron availability. Analyses using Arabidopsis protoplasts confirmed the mitochondrial localization of cucumber mitoferrins. Expression of CsMIT1 and CsMIT2 restored the growth of the Δmrs3Δmrs4 mutant (defective in mitochondrial Fe transport), but not in mutants sensitive to other heavy metals. Moreover, the altered cytosolic and mitochondrial Fe concentrations, observed in the Δmrs3Δmrs4 strain, were recovered almost to the levels of WT yeast by expressing CsMIT1 or CsMIT2. These results indicate that cucumber proteins are involved in the iron transport from the cytoplasm to the mitochondria.
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56
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Wang YW, McKeon MC, Elmore H, Hess J, Golan J, Gage H, Mao W, Harrow L, Gon ßalves SC, Hull CM, Pringle A. Invasive Californian death caps develop mushrooms unisexually and bisexually. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.525609. [PMID: 36778337 PMCID: PMC9915504 DOI: 10.1101/2023.01.30.525609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Canonical sexual reproduction among basidiomycete fungi involves the fusion of two haploid individuals of different sexes, resulting in a heterokaryotic mycelial body made up of genetically different nuclei 1 . Using population genomics data, we discovered mushrooms of the deadly invasive Amanita phalloides are also homokaryotic, evidence of sexual reproduction by single individuals. In California, genotypes of homokaryotic mushrooms are also found in heterokaryotic mushrooms, implying nuclei of homokaryotic mycelia also promote outcrossing. We discovered death cap mating is controlled by a single mating-type locus ( A. phalloides is bipolar), but the development of homokaryotic mushrooms appears to bypass mating-type gene control. Ultimately, sporulation is enabled by nuclei able to reproduce alone as well as with others, and nuclei competent for both unisexuality and bisexuality have persisted in invaded habitats for at least 17 but potentially as long as 30 years. The diverse reproductive strategies of invasive death caps are likely facilitating its rapid spread, revealing a profound similarity between plant, animal and fungal invasions 2,3 .
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Hernández-Aguirre LE, Peregrino-Uriarte AB, Duarte-Gutiérrez JL, Leyva-Carrillo L, Ezquerra-Brauer JM, Valenzuela-Soto EM, Yepiz-Plascencia G. Shrimp Glucose-6-phosphatase 2 (G6Pase 2): a second isoform of G6Pase in the Pacific white shrimp and regulation of G6Pase 1 and 2 isoforms via HIF-1 during hypoxia and reoxygenation in juveniles. J Bioenerg Biomembr 2023; 55:137-150. [PMID: 36853470 DOI: 10.1007/s10863-023-09960-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
Animals suffer hypoxia when their oxygen consumption is larger than the oxygen available. Hypoxia affects the white shrimp Penaeus (Litopenaeus) vannamei, both in their natural habitat and in cultivation farms. Shrimp regulates some enzymes that participate in energy production pathways as a strategy to survive during hypoxia. Glucose-6-phosphatase (G6Pase) is key to maintain blood glucose homeostasis through gluconeogenesis and glycogenolysis. We previously reported a shrimp G6Pase gene (G6Pase1) and in this work, we report a second isoform that we named G6Pase2. The expression of the two isoforms was evaluated in oxygen limited conditions and during silencing of the transcription factor HIF-1. High G6Pase activity was detected in hepatopancreas followed by muscle and gills under good oxygen and feeding conditions. Gene expression of both isoforms was analyzed in normoxia, hypoxia and reoxygenation in hepatopancreas and gills, and in HIF-1-silenced shrimp. In fed shrimp with normal dissolved oxygen (DO) (5.0 mg L- 1 DO) the expression of G6Pase1 was detected in gills, but not in hepatopancreas or muscle, while G6Pase2 expression was undetectable in all three tissues. In hepatopancreas, G6Pase1 is induced at 3 and 48 h of hypoxia, while G6Pase2 is down-regulated in the same time points but in reoxygenation, both due to the knock-down of HIF-1. In gills, only G6Pase1 was detected, and was induced by the silencing of HIF-1 only after 3 h of reoxygenation. Therefore, the expression of the two isoforms appears to be regulated by HIF-1 at transcriptional level in response to oxygen deprivation and subsequent recovery of oxygen levels.
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Affiliation(s)
- Laura E Hernández-Aguirre
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C, Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col La Victoria, Hermosillo, Sonora, C.P. 83304, México
| | - Alma B Peregrino-Uriarte
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C, Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col La Victoria, Hermosillo, Sonora, C.P. 83304, México
| | - Jorge L Duarte-Gutiérrez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C, Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col La Victoria, Hermosillo, Sonora, C.P. 83304, México
| | - Lilia Leyva-Carrillo
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C, Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col La Victoria, Hermosillo, Sonora, C.P. 83304, México
| | - Josafat M Ezquerra-Brauer
- Departamento de Investigación y Posgrado en Alimentos, Universidad de Sonora, Blvd Luis Encinas y Rosales s/n, Hermosillo, Sonora, CP 83000, México
| | - Elisa M Valenzuela-Soto
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C, Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col La Victoria, Hermosillo, Sonora, C.P. 83304, México
| | - Gloria Yepiz-Plascencia
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C, Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col La Victoria, Hermosillo, Sonora, C.P. 83304, México.
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58
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Exopolysaccharide Biosynthesis in Rhizobium leguminosarum bv. trifolii Requires a Complementary Function of Two Homologous Glycosyltransferases PssG and PssI. Int J Mol Sci 2023; 24:ijms24044248. [PMID: 36835659 PMCID: PMC9961541 DOI: 10.3390/ijms24044248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023] Open
Abstract
The Pss-I region of Rhizobium leguminosarum bv. trifolii TA1 comprises more than 20 genes coding for glycosyltransferases, modifying enzymes, and polymerization/export proteins, altogether determining the biosynthesis of symbiotically relevant exopolysaccharides. In this study, the role of homologous PssG and PssI glycosyltransferases in exopolysaccharide subunit synthesis were analyzed. It was shown that the glycosyltransferase-encoding genes of the Pss-I region were part of a single large transcriptional unit with potential downstream promoters activated in specific conditions. The ΔpssG and ΔpssI mutants produced significantly lower amounts of the exopolysaccharide, while the double deletion mutant ΔpssIΔpssG produced no exopolysaccharide. Complementation of double mutation with individual genes restored exopolysaccharide synthesis, but only to the level similar to that observed for the single ΔpssI or ΔpssG mutants, indicating that PssG and PssI serve complementary functions in the process. PssG and PssI interacted with each other in vivo and in vitro. Moreover, PssI displayed an expanded in vivo interaction network comprising other GTs involved in subunit assembly and polymerization/export proteins. PssG and PssI proteins were shown to interact with the inner membrane through amphipathic helices at their C-termini, and PssG also required other proteins involved in exopolysaccharide synthesis to localize in the membrane protein fraction.
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59
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Native structure of mosquito salivary protein uncovers domains relevant to pathogen transmission. Nat Commun 2023; 14:899. [PMID: 36797290 PMCID: PMC9935623 DOI: 10.1038/s41467-023-36577-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
Female mosquitoes inject saliva into vertebrate hosts during blood feeding. This process transmits mosquito-borne human pathogens that collectively cause ~1,000,000 deaths/year. Among the most abundant and conserved proteins secreted by female salivary glands is a high-molecular weight protein called salivary gland surface protein 1 (SGS1) that facilitates pathogen transmission, but its mechanism remains elusive. Here, we determine the native structure of SGS1 by the cryoID approach, showing that the 3364 amino-acid protein has a Tc toxin-like Rhs/YD shell, four receptor domains, and a set of C-terminal daisy-chained helices. These helices are partially shielded inside the Rhs/YD shell and poised to transform into predicted transmembrane helices. This transformation, and the numerous receptor domains on the surface of SGS1, are likely key in facilitating sporozoite/arbovirus invasion into the salivary glands and manipulating the host's immune response.
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60
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Azizogli AR, Pai V, Coppola F, Jafari R, Dodd-o JB, Harish R, Balasubramanian B, Kashyap J, Acevedo-Jake AM, Král P, Kumar VA. Scalable Inhibitors of the Nsp3-Nsp4 Coupling in SARS-CoV-2. ACS OMEGA 2023; 8:5349-5360. [PMID: 36798146 PMCID: PMC9923439 DOI: 10.1021/acsomega.2c06384] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/29/2022] [Indexed: 06/18/2023]
Abstract
The human Betacoronavirus SARS-CoV-2 is a novel pathogen claiming millions of lives and causing a global pandemic that has disrupted international healthcare systems, economies, and communities. The virus is fast mutating and presenting more infectious but less lethal versions. Currently, some small-molecule therapeutics have received FDA emergency use authorization for the treatment of COVID-19, including Lagevrio (molnupiravir) and Paxlovid (nirmaltrevir/ritonavir), which target the RNA-dependent RNA polymerase and the 3CLpro main protease, respectively. Proteins downstream in the viral replication process, specifically the nonstructural proteins (Nsps1-16), are potential drug targets due to their crucial functions. Of these Nsps, Nsp4 is a particularly promising drug target due to its involvement in the SARS-CoV viral replication and double-membrane vesicle formation (mediated via interaction with Nsp3). Given the degree of sequence conservation of these two Nsps across the Betacoronavirus clade, their protein-protein interactions and functions are likely to be conserved as well in SARS-CoV-2. Through AlphaFold2 and its recent advancements, protein structures were generated of Nsp3 and 4 lumenal loops of interest. Then, using a combination of molecular docking suites and an existing library of lead-like compounds, we virtually screened 7 million ligands to identify five putative ligand inhibitors of Nsp4, which could present an alternative pharmaceutical approach against SARS-CoV-2. These ligands exhibit promising lead-like properties (ideal molecular weight and log P profiles), maintain fixed-Nsp4-ligand complexes in molecular dynamics (MD) simulations, and tightly associate with Nsp4 via hydrophobic interactions. Additionally, alternative peptide inhibitors based on Nsp3 were designed and shown in MD simulations to provide a highly stable binding to the Nsp4 protein. Finally, these therapeutics were attached to dendrimer structures to promote their multivalent binding with Nsp4, especially its large flexible luminal loop (Nsp4LLL). The therapeutics tested in this study represent many different approaches for targeting large flexible protein structures, especially those localized to the ER. This study is the first work targeting the membrane rearrangement system of viruses and will serve as a potential avenue for treating viruses with similar replicative function.
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Affiliation(s)
- Abdul-Rahman Azizogli
- Department
of Biological Sciences, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Varun Pai
- Department
of Biological Sciences, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Francesco Coppola
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
| | - Roya Jafari
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
| | - Joseph B. Dodd-o
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Rohan Harish
- Department
of Electrical and Computer Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Bhavani Balasubramanian
- Department
of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Jatin Kashyap
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Amanda M. Acevedo-Jake
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Petr Král
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
- Departments
of Physics, Pharmaceutical Sciences, and Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Vivek A. Kumar
- Department
of Biological Sciences, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Chemical and Materials Engineering, New
Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department
of Endodontics, Rutgers School of Dental
Medicine, Newark, New Jersey 07103, United States
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61
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Fredericksen M, Fields PD, Du Pasquier L, Ricci V, Ebert D. QTL study reveals candidate genes underlying host resistance in a Red Queen model system. PLoS Genet 2023; 19:e1010570. [PMID: 36730161 PMCID: PMC9894429 DOI: 10.1371/journal.pgen.1010570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/14/2022] [Indexed: 02/03/2023] Open
Abstract
Specific interactions of host and parasite genotypes can lead to balancing selection, maintaining genetic diversity within populations. In order to understand the drivers of such specific coevolution, it is necessary to identify the molecular underpinnings of these genotypic interactions. Here, we investigate the genetic basis of resistance in the crustacean host, Daphnia magna, to attachment and subsequent infection by the bacterial parasite, Pasteuria ramosa. We discover a single locus with Mendelian segregation (3:1 ratio) with resistance being dominant, which we call the F locus. We use QTL analysis and fine mapping to localize the F locus to a 28.8-kb region in the host genome, adjacent to a known resistance supergene. We compare the 28.8-kb region in the two QTL parents to identify differences between host genotypes that are resistant versus susceptible to attachment and infection by the parasite. We identify 13 genes in the region, from which we highlight eight biological candidates for the F locus, based on presence/absence polymorphisms and differential gene expression. The top candidates include a fucosyltransferase gene that is only present in one of the two QTL parents, as well as several Cladoceran-specific genes belonging to a large family that is represented in multiple locations of the host genome. Fucosyltransferases have been linked to resistance in previous studies of Daphnia-Pasteuria and other host-parasite systems, suggesting that P. ramosa spore attachment could be mediated by changes in glycan structures on D. magna cuticle proteins. The Cladoceran-specific candidate genes suggest a resistance strategy that relies on gene duplication. Our results add a new locus to a growing genetic model of resistance in the D. magna-P. ramosa system. The identified candidate genes will be used in future functional genetic studies, with the ultimate aim to test for cycles of allele frequencies in natural populations.
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Affiliation(s)
- Maridel Fredericksen
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
- * E-mail:
| | - Peter D. Fields
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Louis Du Pasquier
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Virginie Ricci
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
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62
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Llanos MA, Alberca LN, Ruiz MD, Sbaraglini ML, Miranda C, Pino-Martinez A, Fraccaroli L, Carrillo C, Alba Soto CD, Gavernet L, Talevi A. A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity. J Comput Aided Mol Des 2023; 37:75-90. [PMID: 36494599 DOI: 10.1007/s10822-022-00491-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Chagas disease, also known as American trypanosomiasis, is a neglected tropical disease caused by the protozoa Trypanosoma cruzi, affecting nearly 7 million people only in the Americas. Polyamines are essential compounds for parasite growth, survival, and differentiation. However, because trypanosomatids are auxotrophic for polyamines, they must be obtained from the host by specific transporters. In this investigation, an ensemble of QSAR classifiers able to identify polyamine analogs with trypanocidal activity was developed. Then, a multi-template homology model of the dimeric polyamine transporter of T. cruzi, TcPAT12, was created with Rosetta, and then refined by enhanced sampling molecular dynamics simulations. Using representative snapshots extracted from the trajectory, a docking model able to discriminate between active and inactive compounds was developed and validated. Both models were applied in a parallel virtual screening campaign to repurpose known drugs as anti-trypanosomal compounds inhibiting polyamine transport in T. cruzi. Montelukast, Quinestrol, Danazol, and Dutasteride were selected for in vitro testing, and all of them inhibited putrescine uptake in biochemical assays, confirming the predictive ability of the computational models. Furthermore, all the confirmed hits proved to inhibit epimastigote proliferation, and Quinestrol and Danazol were able to inhibit, in the low micromolar range, the viability of trypomastigotes and the intracellular growth of amastigotes.
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Affiliation(s)
- Manuel A Llanos
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| | - Lucas N Alberca
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| | - María D Ruiz
- Laboratorio de Biología Molecular y Bioquímica en Trypanosoma cruzi y otros agentes infecciosos, Instituto de Ciencia y Tecnología (ICT) Milstein - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - María L Sbaraglini
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| | - Cristian Miranda
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires., Buenos Aires, Argentina
| | - Agustina Pino-Martinez
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires., Buenos Aires, Argentina
| | - Laura Fraccaroli
- Laboratorio de Biología Molecular y Bioquímica en Trypanosoma cruzi y otros agentes infecciosos, Instituto de Ciencia y Tecnología (ICT) Milstein - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Carolina Carrillo
- Laboratorio de Biología Molecular y Bioquímica en Trypanosoma cruzi y otros agentes infecciosos, Instituto de Ciencia y Tecnología (ICT) Milstein - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Catalina D Alba Soto
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires., Buenos Aires, Argentina
| | - Luciana Gavernet
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina.
| | - Alan Talevi
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
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63
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Sun J, Kulandaisamy A, Liu J, Hu K, Gromiha MM, Zhang Y. Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications. Comput Struct Biotechnol J 2023; 21:1205-1226. [PMID: 36817959 PMCID: PMC9932300 DOI: 10.1016/j.csbj.2023.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
Membrane proteins mediate a wide spectrum of biological processes, such as signal transduction and cell communication. Due to the arduous and costly nature inherent to the experimental process, membrane proteins have long been devoid of well-resolved atomic-level tertiary structures and, consequently, the understanding of their functional roles underlying a multitude of life activities has been hampered. Currently, computational tools dedicated to furthering the structure-function understanding are primarily focused on utilizing intelligent algorithms to address a variety of site-wise prediction problems (e.g., topology and interaction sites), but are scattered across different computing sources. Moreover, the recent advent of deep learning techniques has immensely expedited the development of computational tools for membrane protein-related prediction problems. Given the growing number of applications optimized particularly by manifold deep neural networks, we herein provide a review on the current status of computational strategies mainly in membrane protein type classification, topology identification, interaction site detection, and pathogenic effect prediction. Meanwhile, we provide an overview of how the entire prediction process proceeds, including database collection, data pre-processing, feature extraction, and method selection. This review is expected to be useful for developing more extendable computational tools specific to membrane proteins.
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Affiliation(s)
- Jianfeng Sun
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Headington, Oxford OX3 7LD, UK
| | - Arulsamy Kulandaisamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - Jacklyn Liu
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Kai Hu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India,Corresponding authors.
| | - Yuan Zhang
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China,Corresponding authors.
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Südfeld C, Kiyani A, Wefelmeier K, Wijffels RH, Barbosa MJ, D’Adamo S. Expression of glycerol-3-phosphate acyltransferase increases non-polar lipid accumulation in Nannochloropsis oceanica. Microb Cell Fact 2023; 22:12. [PMID: 36647076 PMCID: PMC9844033 DOI: 10.1186/s12934-022-01987-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023] Open
Abstract
Microalgae are considered a suitable production platform for high-value lipids and oleochemicals. Several species including Nannochloropsis oceanica produce large amounts of essential [Formula: see text]-3 polyunsaturated fatty acids (PUFAs) which are integral components of food and feed and have been associated with health-promoting effects. N. oceanica can further accumulate high contents of non-polar lipids with chemical properties that render them a potential replacement for plant oils such as palm oil. However, biomass and lipid productivities obtained with microalgae need to be improved to reach commercial feasibility. Genetic engineering can improve biomass and lipid productivities, for instance by increasing carbon flux to lipids. Here, we report the overexpression of glycerol-3-phosphate acyltransferase (GPAT) in N. oceanica during favorable growth conditions as a strategy to increase non-polar lipid content. Transformants overproducing either an endogenous (NoGPAT) or a heterologous (Acutodesmus obliquus GPAT) GPAT enzyme targeted to the endoplasmic reticulum had up to 42% and 51% increased non-polar lipid contents, respectively, compared to the wild type. Biomass productivities of transformant strains were not substantially impaired, resulting in lipid productivities that were increased by up to 37% and 42% for NoGPAT and AoGPAT transformants, respectively. When exposed to nutrient stress, transformants and wild type had similar lipid contents, suggesting that GPAT enzyme exerts strong flux control on lipid synthesis in N. oceanica under favorable growth conditions. NoGPAT transformants further accumulated PUFAs in non-polar lipids, reaching a total of 6.8% PUFAs per biomass, an increase of 24% relative to the wild type. Overall, our results indicate that GPAT is an interesting target for engineering of lipid metabolism in microalgae, in order to improve non-polar lipid and PUFAs accumulation in microalgae.
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Affiliation(s)
- Christian Südfeld
- grid.4818.50000 0001 0791 5666Wageningen University, Bioprocess Engineering, PO Box 16, 6700 AA Wageningen, Netherlands
| | - Aamna Kiyani
- grid.4818.50000 0001 0791 5666Wageningen University, Bioprocess Engineering, PO Box 16, 6700 AA Wageningen, Netherlands ,grid.412621.20000 0001 2215 1297Department of Microbiology, Quaid-I-Azam University, Islamabad, 45320 Pakistan
| | - Katrin Wefelmeier
- grid.4818.50000 0001 0791 5666Wageningen University, Bioprocess Engineering, PO Box 16, 6700 AA Wageningen, Netherlands
| | - René H. Wijffels
- grid.4818.50000 0001 0791 5666Wageningen University, Bioprocess Engineering, PO Box 16, 6700 AA Wageningen, Netherlands ,grid.465487.cFaculty of Biosciences and Aquaculture, Nord University, N-8049 Bodø, Norway
| | - Maria J. Barbosa
- grid.4818.50000 0001 0791 5666Wageningen University, Bioprocess Engineering, PO Box 16, 6700 AA Wageningen, Netherlands
| | - Sarah D’Adamo
- grid.4818.50000 0001 0791 5666Wageningen University, Bioprocess Engineering, PO Box 16, 6700 AA Wageningen, Netherlands
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65
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A New Face of the Old Gene: Deletion of the PssA, Encoding Monotopic Inner Membrane Phosphoglycosyl Transferase in Rhizobium leguminosarum, Leads to Diverse Phenotypes That Could Be Attributable to Downstream Effects of the Lack of Exopolysaccharide. Int J Mol Sci 2023; 24:ijms24021035. [PMID: 36674551 PMCID: PMC9860679 DOI: 10.3390/ijms24021035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
The biosynthesis of subunits of rhizobial exopolysaccharides is dependent on glycosyltransferases, which are usually encoded by large gene clusters. PssA is a member of a large family of phosphoglycosyl transferases catalyzing the transfer of a phosphosugar moiety to polyprenol phosphate; thus, it can be considered as priming glycosyltransferase commencing synthesis of the EPS repeating units in Rhizobium leguminosarum. The comprehensive analysis of PssA protein features performed in this work confirmed its specificity for UDP-glucose and provided evidence that PssA is a monotopic inner membrane protein with a reentrant membrane helix rather than a transmembrane segment. The bacterial two-hybrid system screening revealed interactions of PssA with some GTs involved in the EPS octasaccharide synthesis. The distribution of differentially expressed genes in the transcriptome of the ΔpssA mutant into various functional categories indicated complexity of cell response to the deletion, which can mostly be attributed to the lack of exopolysaccharide and downstream effects caused by such deficiency. The block in the EPS biosynthesis at the pssA step, potentially leading to an increased pool of UDP-glucose, is likely to be filtered through to other pathways, and thus the absence of EPS may indirectly affect the expression of proteins involved in these pathways.
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66
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Tiwari V, Sowdhamini R. Structural modelling and dynamics of full-length of TLR10 sheds light on possible modes of dimerization, ligand binding and mechanism of action. Curr Res Struct Biol 2023; 5:100097. [PMID: 36911652 PMCID: PMC9996232 DOI: 10.1016/j.crstbi.2023.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/01/2023] [Accepted: 02/05/2023] [Indexed: 02/22/2023] Open
Abstract
Toll like receptors (TLRs) play a pivotal role in innate and adaptive immunity. There are 10 TLRs in the human genome, of which TLR10 is the least characterized. Genetic polymorphism of TLR10 has been shown to be associated with multiple diseases including tuberculosis and rheumatoid arthritis. TLR10 consists of an extracellular domain (ECD), a single-pass transmembrane (TM) helix and intracellular TIR (Toll/Interleukin-1 receptor) domain. ECD is employed for ligand recognition and the intracellular domain interacts with other TIR domain-containing adapter proteins for signal transduction. Experimental structure of ECD or TM domain is not available for TLR10. In this study, we have modelled multiple forms of TLR10-ECD dimers, such as closed and open forms, starting from available structures of homologues. Subsequently, multiple full-length TLR10 homodimer models were generated by utilizing homology modelling and protein-protein docking. The dynamics of these models in membrane-aqueous environment revealed the global motion of ECD and TIR domain towards membrane bilayer. The TIR domain residues exhibited high root mean square fluctuation compared to ECD. The 'closed form' model was observed to be energetically more favorable than 'open form' model. The evaluation of persistent interchain interactions, along with their conservation score, unveiled critical residues for each model. Further, the binding of dsRNA to TLR10 was modelled by defined and blind docking approaches. Differential binding of dsRNA to the protomers of TLR10 was observed upon simulation that could provide clues on ligand disassociation. Dynamic network analysis revealed that the 'open form' model can be the functional form while 'closed form' model can be the apo form of TLR10.
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Affiliation(s)
- Vikas Tiwari
- National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore, 560 065, India
| | - R Sowdhamini
- National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore, 560 065, India
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67
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Langó T, Kuffa K, Tóth G, Turiák L, Drahos L, Tusnády GE. Comprehensive Discovery of the Accessible Primary Amino Group-Containing Segments from Cell Surface Proteins by Fine-Tuning a High-Throughput Biotinylation Method. Int J Mol Sci 2022; 24:ijms24010273. [PMID: 36613715 PMCID: PMC9820203 DOI: 10.3390/ijms24010273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Cell surface proteins, including transmembrane and other surface-anchored proteins, play a key role in several critical cellular processes and have a strong diagnostic value. The development of quick and robust experimental methods remains vital for the accurate and comprehensive characterization of the cell surface subproteome of individual cells. Here we present a high-throughput technique which relies on the biotinylation of the accessible primary amino groups in the extracellular segments of the proteins, using HL60 as a model cell line. Several steps of the method have been thoroughly optimized to capture labeled surface proteins selectively and in larger quantities. These include the following: improving the efficiency of the cell surface biotinylation; reducing the endogen protease activity; applying an optimal amount of affinity column and elution steps for labeled peptide enrichment; and examining the effect of various solid-phase extraction methods, different HPLC gradients, and various tandem mass spectrometry settings. Using the optimized workflow, we identified at least 1700 surface-associated individual labeled peptides (~6000-7000 redundant peptides) from the model cell surface in a single nanoHPLC-MS/MS run. The presented method can provide a comprehensive and specific list of the cell surface available protein segments that could be potential targets in various bioinformatics and molecular biology research.
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Affiliation(s)
- Tamás Langó
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
- Correspondence:
| | - Katalin Kuffa
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány P. stny. 1/C, H-1117 Budapest, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
| | - Gábor E. Tusnády
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
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68
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Huang TC, Fischer WB. Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach. Biomolecules 2022; 12:biom12121844. [PMID: 36551274 PMCID: PMC9775931 DOI: 10.3390/biom12121844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
A de novo assembly algorithm is provided to propose the assembly of bitopic transmembrane domains (TMDs) of membrane proteins. The algorithm is probed using, in particular, viral channel forming proteins (VCPs) such as M2 of influenza A virus, E protein of severe acute respiratory syndrome corona virus (SARS-CoV), 6K of Chikungunya virus (CHIKV), SH of human respiratory syncytial virus (hRSV), and Vpu of human immunodeficiency virus type 2 (HIV-2). The generation of the structures is based on screening a 7-dimensional space. Assembly of the TMDs can be achieved either by simultaneously docking the individual TMDs or via a sequential docking. Scoring based on estimated binding energies (EBEs) of the oligomeric structures is obtained by the tilt to decipher the handedness of the bundles. The bundles match especially well for all-atom models of M2 referring to an experimentally reported tetrameric bundle. Docking of helical poly-peptides to experimental structures of M2 and E protein identifies improving EBEs for positively charged (K,R,H) and aromatic amino acids (F,Y,W). Data are improved when using polypeptides for which the coordinates of the amino acids are adapted to the Cα coordinates of the respective experimentally derived structures of the TMDs of the target proteins.
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69
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Dobson L, Szekeres LI, Gerdán C, Langó T, Zeke A, Tusnády GE. TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures. Nucleic Acids Res 2022; 51:D517-D522. [PMID: 36318239 PMCID: PMC9825488 DOI: 10.1093/nar/gkac928] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/20/2022] [Accepted: 10/07/2022] [Indexed: 12/12/2022] Open
Abstract
AI-driven protein structure prediction, most notably AlphaFold2 (AF2) opens new frontiers for almost all fields of structural biology. As traditional structure prediction methods for transmembrane proteins were both complicated and error prone, AF2 is a great help to the community. Complementing the relatively meager number of experimental structures, AF2 provides 3D predictions for thousands of new alpha-helical membrane proteins. However, the lack of reliable structural templates and the fact that AF2 was not trained to handle phase boundaries also necessitates a delicate assessment of structural correctness. In our new database, Transmembrane AlphaFold database (TmAlphaFold database), we apply TMDET, a simple geometry-based method to visualize the likeliest position of the membrane plane. In addition, we calculate several parameters to evaluate the location of the protein into the membrane. This also allows TmAlphaFold database to show whether the predicted 3D structure is realistic or not. The TmAlphaFold database is available at https://tmalphafold.ttk.hu/.
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Affiliation(s)
- Laszlo Dobson
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Levente I Szekeres
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - Csongor Gerdán
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - Tamás Langó
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - András Zeke
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - Gábor E Tusnády
- To whom correspondence should be addressed. Tel: +36 1 382 6709;
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The extracellular domain of site-2-metalloprotease RseP is important for sensitivity to bacteriocin EntK1. J Biol Chem 2022; 298:102593. [PMID: 36244452 PMCID: PMC9672952 DOI: 10.1016/j.jbc.2022.102593] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
Enterocin K1 (EntK1), a bacteriocin that is highly potent against vancomycin-resistant enterococci, depends on binding to an intramembrane protease of the site-2 protease family, RseP, for its antimicrobial activity. RseP is highly conserved in both EntK1-sensitive and EntK1-insensitive bacteria, and the molecular mechanisms underlying the interaction between RseP and EntK1 and bacteriocin sensitivity are unknown. Here, we describe a mutational study of RseP from EntK1-sensitive Enterococcus faecium to identify regions of RseP involved in bacteriocin binding and activity. Mutational effects were assessed by studying EntK1 sensitivity and binding with strains of naturally EntK1-insensitive Lactiplantibacillus plantarum–expressing various RseP variants. We determined that site-directed mutations in conserved sequence motifs related to catalysis and substrate binding, and even deletion of two such motifs known to be involved in substrate binding, did not abolish bacteriocin sensitivity, with one exception. A mutation of a highly conserved asparagine, Asn359, in the extended so-called LDG motif abolished both binding of and killing by EntK1. By constructing various hybrids of the RseP proteins from sensitive E. faecium and insensitive L. plantarum, we showed that the extracellular PDZ domain is the key determinant of EntK1 sensitivity. Taken together, these data may provide valuable insight for guided construction of novel bacteriocins and may contribute to establishing RseP as an antibacterial target.
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71
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Heterologously secreted MbxA from Moraxella bovis induces a membrane blebbing response of the human host cell. Sci Rep 2022; 12:17825. [PMID: 36280777 PMCID: PMC9592583 DOI: 10.1038/s41598-022-22480-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/14/2022] [Indexed: 01/20/2023] Open
Abstract
Many proteins of the Repeats in Toxins (RTX) protein family are toxins of Gram-negative pathogens including hemolysin A (HlyA) of uropathogenic E. coli. RTX proteins are secreted via Type I secretion systems (T1SS) and adopt their native conformation in the Ca2+-rich extracellular environment. Here we employed the E. coli HlyA T1SS as a heterologous surrogate system for the RTX toxin MbxA from the bovine pathogen Moraxella bovis. In E. coli the HlyA system successfully activates the heterologous MbxA substrate by acylation and secretes the precursor proMbxA and active MbxA allowing purification of both species in quantities sufficient for a variety of investigations. The activating E. coli acyltransferase HlyC recognizes the acylation sites in MbxA, but unexpectedly in a different acylation pattern as for its endogenous substrate HlyA. HlyC-activated MbxA shows host species-independent activity including a so-far unknown toxicity against human lymphocytes and epithelial cells. Using live-cell imaging, we show an immediate MbxA-mediated permeabilization and a rapidly developing blebbing of the plasma membrane in epithelial cells, which is associated with immediate cell death.
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72
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A structure and evolutionary-based classification of solute carriers. iScience 2022; 25:105096. [PMID: 36164651 PMCID: PMC9508557 DOI: 10.1016/j.isci.2022.105096] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/22/2022] [Accepted: 09/04/2022] [Indexed: 11/22/2022] Open
Abstract
Solute carriers are an operationally defined diverse family of membrane proteins involved in the transport of nutrients, metabolites, xenobiotics, and drugs. Here, we provide an integrative classification of solute carriers by combining evolutionary information with proteome-wide structure models recently made available through the AlphaFold resource. Analyses of orthologous relations among 455 protein-coding genes currently classified as human solute carriers, over the fully sequenced genomes of 2,100 species, suggest no more than approximately 180 independent evolutionary origins. Structural comparative analyses provided further insight revealing a total of 24 structurally distinct transmembrane folds, increasing by approximately 40% the number of previously described SLC structural folds. In addition, a structural comparative analysis identified a new human solute carrier member and revealed details of noncanonical ones. Our analyses uncover new ancestral relations between solute carrier genes, provide insights into the evolution of remote homologs and a platform to test hypotheses of functional deorphanization.
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73
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Knoot CJ, Wantuch PL, Robinson LS, Rosen DA, Scott NE, Harding CM. Discovery and characterization of a new class of O-linking oligosaccharyltransferases from the Moraxellaceae family. Glycobiology 2022; 33:57-74. [PMID: 36239418 PMCID: PMC9829042 DOI: 10.1093/glycob/cwac070] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 01/12/2023] Open
Abstract
Bacterial protein glycosylation is commonly mediated by oligosaccharyltransferases (OTases) that transfer oligosaccharides en bloc from preassembled lipid-linked precursors to acceptor proteins. Natively, O-linking OTases usually transfer a single repeat unit of the O-antigen or capsular polysaccharide to the side chains of serine or threonine on acceptor proteins. Three major families of bacterial O-linking OTases have been described: PglL, PglS, and TfpO. TfpO is limited to transferring short oligosaccharides both in its native context and when heterologously expressed in glycoengineered Escherichia coli. On the other hand, PglL and PglS can transfer long-chain polysaccharides when expressed in glycoengineered E. coli. Herein, we describe the discovery and functional characterization of a novel family of bacterial O-linking OTases termed TfpM from Moraxellaceae bacteria. TfpM proteins are similar in size and sequence to TfpO enzymes but can transfer long-chain polysaccharides to acceptor proteins. Phylogenetic analyses demonstrate that TfpM proteins cluster in distinct clades from known bacterial OTases. Using a representative TfpM enzyme from Moraxella osloensis, we determined that TfpM glycosylates a C-terminal threonine of its cognate pilin-like protein and identified the minimal sequon required for glycosylation. We further demonstrated that TfpM has broad substrate tolerance and can transfer diverse glycans including those with glucose, galactose, or 2-N-acetyl sugars at the reducing end. Last, we find that a TfpM-derived bioconjugate is immunogenic and elicits serotype-specific polysaccharide IgG responses in mice. The glycan substrate promiscuity of TfpM and identification of the minimal TfpM sequon renders this enzyme a valuable additional tool for expanding the glycoengineering toolbox.
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Affiliation(s)
- Cory J Knoot
- Omniose, 4340 Duncan Ave, Suite 202, St. Louis, MO 63110, USA
| | - Paeton L Wantuch
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, 4990 Children’s Place, St. Louis, MO 63110, USA
| | | | - David A Rosen
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, 4990 Children’s Place, St. Louis, MO 63110, USA,Department of Molecular Microbiology, Washington University School of Medicine, 660 Euclid Ave, St. Louis, MO 63110, USA
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
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74
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MPAD: A Database for Binding Affinity of Membrane Protein–protein Complexes and their Mutants. J Mol Biol 2022:167870. [DOI: 10.1016/j.jmb.2022.167870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
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75
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Jain P, Iyer S, Straka J, Surrey LF, Pogoriler J, Han H, Smith T, Busch C, Fox E, Li M, Waanders AJ, Resnick A, Davare MA. Discovery and functional characterization of the oncogenicity and targetability of a novel NOTCH1-ROS1 gene fusion in pediatric angiosarcoma. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006222. [PMID: 36307212 PMCID: PMC9632357 DOI: 10.1101/mcs.a006222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023] Open
Abstract
Angiosarcomas are rare, malignant soft tissue tumors in children that arise in a wide range of anatomical locations and have limited targeted therapies available. Here, we report a rare case of a pediatric angiosarcoma (pAS) with Li-Fraumeni syndrome (LFS) expressing a novel NOTCH1-ROS1 gene fusion. Although both NOTCH1 and ROS1 are established proto-oncogenes, our study is the first to describe the mechanistic role of NOTCH1-ROS1 fusion arising via intrachromosomal rearrangement. NOTCH1-ROS1 displayed potent neoplastic transformation propensity in vitro, and harbors tumorigenic potential in vivo, where it induced oncogenic activation of the MAPK, PI3K/mTOR, and JAK-STAT signaling pathways in a murine allograft model. We found an unexpected contribution of the NOTCH1 extracellular region in mediating NOTCH1-ROS1 activation and oncogenic function, highlighting the contribution of both NOTCH1 and ROS1 fusion partners in driving tumorigenicity. Interestingly, neither membrane localization nor fusion protein dimerization were found to be essential for NOTCH1-ROS1 fusion oncogenicity. To target NOTCH1-ROS1-driven tumors, we tested both NOTCH1-directed inhibitors and ROS1-targeted tyrosine kinase inhibitors (TKI) in heterologous models (NIH3T3, Ba/F3). Although NOTCH1 inhibitors did not suppress NOTCH1-ROS1-driven oncogenic growth, we found that oral entrectinib treatment effectively suppressed the growth of NOTCH-ROS1-driven tumors. Taken together, we report the first known pAS case with a novel NOTCH1-ROS1 alteration along with a detailed report on the function and therapeutic targeting of NOTCH1-ROS1. Our study highlights the importance of genomic profiling of rare cancers such as pAS to reveal actionable drivers and improve patient outcomes.
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Affiliation(s)
- Payal Jain
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Sudarshan Iyer
- Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon 97239, USA
| | - Joshua Straka
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lea F. Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jennifer Pogoriler
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Harry Han
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Tiffany Smith
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Christine Busch
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Elizabeth Fox
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Marilyn Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Angela J. Waanders
- Department of Pediatrics, Feinberg School of Medicine Northwestern University, Chicago, Illinois 60611, USA;,Division of Hematology, Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Adam Resnick
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Monika A. Davare
- Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon 97239, USA
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76
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Bernhofer M, Rost B. TMbed: transmembrane proteins predicted through language model embeddings. BMC Bioinformatics 2022; 23:326. [PMID: 35941534 PMCID: PMC9358067 DOI: 10.1186/s12859-022-04873-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/03/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Despite the immense importance of transmembrane proteins (TMP) for molecular biology and medicine, experimental 3D structures for TMPs remain about 4-5 times underrepresented compared to non-TMPs. Today's top methods such as AlphaFold2 accurately predict 3D structures for many TMPs, but annotating transmembrane regions remains a limiting step for proteome-wide predictions. RESULTS Here, we present TMbed, a novel method inputting embeddings from protein Language Models (pLMs, here ProtT5), to predict for each residue one of four classes: transmembrane helix (TMH), transmembrane strand (TMB), signal peptide, or other. TMbed completes predictions for entire proteomes within hours on a single consumer-grade desktop machine at performance levels similar or better than methods, which are using evolutionary information from multiple sequence alignments (MSAs) of protein families. On the per-protein level, TMbed correctly identified 94 ± 8% of the beta barrel TMPs (53 of 57) and 98 ± 1% of the alpha helical TMPs (557 of 571) in a non-redundant data set, at false positive rates well below 1% (erred on 30 of 5654 non-membrane proteins). On the per-segment level, TMbed correctly placed, on average, 9 of 10 transmembrane segments within five residues of the experimental observation. Our method can handle sequences of up to 4200 residues on standard graphics cards used in desktop PCs (e.g., NVIDIA GeForce RTX 3060). CONCLUSIONS Based on embeddings from pLMs and two novel filters (Gaussian and Viterbi), TMbed predicts alpha helical and beta barrel TMPs at least as accurately as any other method but at lower false positive rates. Given the few false positives and its outstanding speed, TMbed might be ideal to sieve through millions of 3D structures soon to be predicted, e.g., by AlphaFold2.
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Affiliation(s)
- Michael Bernhofer
- Department of Informatics, Bioinformatics and Computational Biology ‑ i12, Technical University of Munich (TUM), Boltzmannstr. 3, 85748, Garching, Germany. .,TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany.
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology ‑ i12, Technical University of Munich (TUM), Boltzmannstr. 3, 85748, Garching, Germany.,Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748, Garching, Germany.,TUM School of Life Sciences Weihenstephan (TUM-WZW), Alte Akademie 8, Freising, Germany
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77
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Barylko B, Hedde PN, Taylor CA, Binns DD, Huang YK, Molinaro G, Huber KM, Jameson DM, Albanesi JP. Palmitoylation-regulated interactions of the pseudokinase calmodulin kinase-like vesicle-associated with membranes and Arc/Arg3.1. Front Synaptic Neurosci 2022; 14:926570. [PMID: 35965782 PMCID: PMC9371321 DOI: 10.3389/fnsyn.2022.926570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Calmodulin kinase-like vesicle-associated (CaMKv), a pseudokinase belonging to the Ca2+/calmodulin-dependent kinase family, is expressed predominantly in brain and neural tissue. It may function in synaptic strengthening during spatial learning by promoting the stabilization and enrichment of dendritic spines. At present, almost nothing is known regarding CaMKv structure and regulation. In this study we confirm prior proteomic analyses demonstrating that CaMKv is palmitoylated on Cys5. Wild-type CaMKv is enriched on the plasma membrane, but this enrichment is lost upon mutation of Cys5 to Ser. We further show that CaMKv interacts with another regulator of synaptic plasticity, Arc/Arg3.1, and that the interaction between these two proteins is weakened by mutation of the palmitoylated cysteine in CamKv.
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Affiliation(s)
- Barbara Barylko
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Per Niklas Hedde
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, United States
| | - Clinton A. Taylor
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Derk D. Binns
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yu-Kai Huang
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, United States
| | - Gemma Molinaro
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Kimberly M. Huber
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - David M. Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Joseph P. Albanesi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
- *Correspondence: Joseph P. Albanesi,
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78
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Evolution of the Membrane Transport Protein Domain. Int J Mol Sci 2022; 23:ijms23158094. [PMID: 35897663 PMCID: PMC9330825 DOI: 10.3390/ijms23158094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 01/27/2023] Open
Abstract
Membrane transport proteins are widely present in all living organisms, however, their function, transported substrate, and mechanism of action are unknown. Here we use diverse bioinformatics tools to investigate the evolution of MTPs, analyse domain organisation and loop topology, and study the comparative alignment of modelled 3D structures. Our results suggest a high level of conservancy between MTPs from different taxa on both amino acids and structural levels, which imply some degree of functional similarities. The presence of loop/s of different lengths in various positions suggests tax-on-specific adaptation to transported substrates, intracellular localisation, accessibility for post-translation modifications, and interaction with other proteins. The comparison of modelled structures proposes close relations and a common origin for MTP and Na/H exchanger. Further, a high level of amino acid similarity and identity between archaeal and bacterial MTPs and Na/H exchangers imply conservancy of ion transporting function at least for archaeal and bacterial MTPs.
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79
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Delmas P, Parpaite T, Coste B. PIEZO channels and newcomers in the mammalian mechanosensitive ion channel family. Neuron 2022; 110:2713-2727. [PMID: 35907398 DOI: 10.1016/j.neuron.2022.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/25/2022] [Accepted: 07/01/2022] [Indexed: 10/16/2022]
Abstract
Many ion channels have been described as mechanosensitive according to various criteria. Most broadly defined, an ion channel is called mechanosensitive if its activity is controlled by application of a physical force. The last decade has witnessed a revolution in mechanosensory physiology at the molecular, cellular, and system levels, both in health and in diseases. Since the discovery of the PIEZO proteins as prototypical mechanosensitive channel, many proteins have been proposed to transduce mechanosensory information in mammals. However, few of these newly identified candidates have all the attributes of bona fide, pore-forming mechanosensitive ion channels. In this perspective, we will cover and discuss new data that have advanced our understanding of mechanosensation at the molecular level.
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Affiliation(s)
- Patrick Delmas
- SomatoSens, Laboratory for Cognitive Neuroscience, Aix-Marseille University, CNRS UMR 7291, Marseilles, France.
| | - Thibaud Parpaite
- SomatoSens, Laboratory for Cognitive Neuroscience, Aix-Marseille University, CNRS UMR 7291, Marseilles, France
| | - Bertrand Coste
- SomatoSens, Laboratory for Cognitive Neuroscience, Aix-Marseille University, CNRS UMR 7291, Marseilles, France
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80
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Bulatova L, Savenkova D, Nurgalieva A, Reshetnikova D, Timonina A, Skripova V, Bogdanov M, Kiyamova R. Toward a Topology-Based Therapeutic Design of Membrane Proteins: Validation of NaPi2b Topology in Live Ovarian Cancer Cells. Front Mol Biosci 2022; 9:895911. [PMID: 35911971 PMCID: PMC9335355 DOI: 10.3389/fmolb.2022.895911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
NaPi2b is a sodium-dependent phosphate transporter that belongs to the SLC34 family of transporters which is mainly responsible for phosphate homeostasis in humans. Although NaPi2b is widely expressed in normal tissues, its overexpression has been demonstrated in ovarian, lung, and other cancers. A valuable set of antibodies, including L2 (20/3) and MX35, and its humanized versions react strongly with an antigen on the surface of ovarian and other carcinoma cells. Although the topology of NaPi2b was predicted in silico, no direct experimental data are available for the orientation of NaPi2b extracellular domains in cancer cells. The presented results of antibody mapping of untagged NaPi2b in live ovarian carcinoma cells OVCAR-4 provide a platform for current and future epitope-based cancer therapies and serological diagnostics.
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Affiliation(s)
- Leisan Bulatova
- Research Laboratory “Biomarker”, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Daria Savenkova
- Research Laboratory “Biomarker”, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Alsina Nurgalieva
- Research Laboratory “Biomarker”, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Daria Reshetnikova
- Research Laboratory “Biomarker”, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Arina Timonina
- Research Laboratory “Biomarker”, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Vera Skripova
- Research Laboratory “Biomarker”, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Mikhail Bogdanov
- Research Laboratory “Biomarker”, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
- Department of Biochemistry and Molecular Biology, McGovern Medical School, the University of Texas Health Science Center, Houston, TX, United States
- *Correspondence: Ramziya Kiyamova, ; Mikhail Bogdanov,
| | - Ramziya Kiyamova
- Research Laboratory “Biomarker”, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
- *Correspondence: Ramziya Kiyamova, ; Mikhail Bogdanov,
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81
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Seniya SP, Jain V. Decoding phage resistance by mpr and its role in survivability of Mycobacterium smegmatis. Nucleic Acids Res 2022; 50:6938-6952. [PMID: 35713559 PMCID: PMC9262609 DOI: 10.1093/nar/gkac505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/09/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
Bacteria and bacteriophages co-evolve in a constant arms race, wherein one tries and finds newer ways to overcome the other. Phage resistance poses a great threat to the development of phage therapy. Hence, it is both essential and important to understand the mechanism of phage resistance in bacteria. First identified in Mycobacterium smegmatis, the gene mpr, upon overexpression, confers resistance against D29 mycobacteriophage. Presently, the mechanism behind phage resistance by mpr is poorly understood. Here we show that Mpr is a membrane-bound DNA exonuclease, which digests DNA in a non-specific manner independent of the sequence, and shares no sequence or structural similarity with any known nuclease. Exonuclease activity of mpr provides resistance against phage infection, but the role of mpr may very well go beyond just phage resistance. Our experiments show that mpr plays a crucial role in the appearance of mutant colonies (phage resistant strains). However, the molecular mechanism behind the emergence of these mutant/resistant colonies is yet to be understood. Nevertheless, it appears that mpr is involved in the survival and evolution of M. smegmatis against phage. A similar mechanism may be present in other organisms, which requires further exploration.
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Affiliation(s)
- Surya Pratap Seniya
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, India
| | - Vikas Jain
- To whom correspondence should be addressed. Tel: +91 755 2691425; Fax: +91 755 2692392;
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82
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Ricciardi S, Guarino AM, Giaquinto L, Polishchuk EV, Santoro M, Di Tullio G, Wilson C, Panariello F, Soares VC, Dias SSG, Santos JC, Souza TML, Fusco G, Viscardi M, Brandi S, Bozza PT, Polishchuk RS, Venditti R, De Matteis MA. The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle. Nature 2022; 606:761-768. [PMID: 35551511 DOI: 10.1038/s41586-022-04835-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022]
Abstract
SARS-CoV-2, like other coronaviruses, builds a membrane-bound replication organelle (RO) to enable RNA replication1. The SARS-CoV-2 RO is composed of double membrane vesicles (DMVs) tethered to the endoplasmic reticulum (ER) by thin membrane connectors2, but the viral proteins and the host factors involved are currently unknown. Here we identify the viral non-structural proteins (NSPs) that generate the SARS-CoV-2 RO. NSP3 and NSP4 generate the DMVs while NSP6, through oligomerization and an amphipathic helix, zippers ER membranes and establishes the connectors. The NSP6ΔSGF mutant, which arose independently in the α, β, γ, η, ι, and λ variants of SARS-CoV-2, behaves as a gain-of-function mutant with a higher ER-zippering activity. We identified three main roles for NSP6: to act as a filter in RO-ER communication allowing lipid flow but restricting access of ER luminal proteins to the DMVs, to position and organize DMV clusters, and to mediate contact with lipid droplets (LDs) via the LD-tethering complex DFCP1-Rab18. NSP6 thus acts as an organizer of DMV clusters and can provide a selective track to refurbish them with LD-derived lipids. Importantly, both properly formed NSP6 connectors and LDs are required for SARS-CoV-2 replication. Our findings, uncovering the biological activity of NSP6 of SARS-CoV-2 and of other coronaviruses, have the potential to fuel the search for broad antiviral agents.
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Affiliation(s)
- Simona Ricciardi
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy.,Dept. Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Laura Giaquinto
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Elena V Polishchuk
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Michele Santoro
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Giuseppe Di Tullio
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Cathal Wilson
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | | | - Vinicius C Soares
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Programa de Imunologia e Inflamação, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Suelen S G Dias
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Julia C Santos
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Thiago M L Souza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde (CDTS) and National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), FIOCRUZ, Rio de Janeiro, Brazil
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, (Naples), Italy
| | - Maurizio Viscardi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, (Naples), Italy
| | - Sergio Brandi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, (Naples), Italy
| | - Patrícia T Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Roman S Polishchuk
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy.
| | - Rossella Venditti
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy. .,Dept. Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy. .,Dept. Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.
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83
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Cui J, Chen H, Tang X, Zhang H, Chen YQ, Chen W. Characterization and Molecular Mechanism of a Novel Cytochrome b5 Reductase with NAD(P)H Specificity from Mortierella alpina. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5186-5196. [PMID: 35416034 DOI: 10.1021/acs.jafc.1c08108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The electron-transfer capabilities of cytochrome b5 reductase (Cyt b5R) and NADPH supply have been shown to be critical factors in microbial fatty acid synthesis. Unfortunately, Cyt b5R substrate specificity is limited to the coenzyme NADH. In this study, we discovered that a novel Cyt b5R from Mortierella alpina (MaCytb5RII) displays affinity for NADPH and NADH. The enzymatic characteristics of high-purity MaCytb5RII were determined with the Km,NADPH and Km,NADH being 0.42 and 0.07 mM, respectively. MaCytb5RII shows high specific activity at 4 °C and pH 9.0. We anchored the residues that interacted with the coenzymes using the homology models of MaCytb5Rs docking NAD(P)H and FAD. The enzyme activity analysis of the purified mutants MaCytb5RII[S230N], MaCytb5RII[Y242F], and MaCytb5RII[S272A] revealed that Ser230 is essential for MaCytb5RII to have dual NAD(P)H dependence, whereas Tyr242 influences MaCytb5RII's NADPH affinity and Ala272 greatly decreases MaCytb5RII's NADH affinity.
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Affiliation(s)
- Jie Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, P. R. China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, P. R. China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, P. R. China
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27127, United States
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, P. R. China
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84
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Yang C, Cheng J, Lin J, Zheng Y, Yu X, Sun J. Corrigendum: Sex Pheromone Receptors of Lepidopteran Insects. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.900818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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85
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Bartenschlager F, Klymiuk N, Weise C, Kuropka B, Gruber AD, Mundhenk L. Evolutionarily conserved properties of CLCA proteins 1, 3 and 4, as revealed by phylogenetic and biochemical studies in avian homologues. PLoS One 2022; 17:e0266937. [PMID: 35417490 PMCID: PMC9007345 DOI: 10.1371/journal.pone.0266937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 03/30/2022] [Indexed: 12/21/2022] Open
Abstract
Species-specific diversities are particular features of mammalian chloride channel regulator, calcium activated (CLCA) genes. In contrast to four complex gene clusters in mammals, only two CLCA genes appear to exist in chickens. CLCA2 is conserved in both, while only the galline CLCA1 (gCLCA1) displays close genetic distance to mammalian clusters 1, 3 and 4. In this study, sequence analyses and biochemical characterizations revealed that gCLCA1 as a putative avian prototype shares common protein domains and processing features with all mammalian CLCA homologues. It has a transmembrane (TM) domain in the carboxy terminal region and its mRNA and protein were detected in the alimentary canal, where the protein was localized in the apical membrane of enterocytes, similar to CLCA4. Both mammals and birds seem to have at least one TM domain containing CLCA protein with complex glycosylation in the apical membrane of enterocytes. However, some characteristic features of mammalian CLCA1 and 3 including entire protein secretion and expression in cell types other than enterocytes seem to be dispensable for chicken. Phylogenetic analyses including twelve bird species revealed that avian CLCA1 and mammalian CLCA3 form clades separate from a major branch containing mammalian CLCA1 and 4. Overall, our data suggest that gCLCA1 and mammalian CLCA clusters 1, 3 and 4 stem from a common ancestor which underwent complex gene diversification in mammals but not in birds.
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Affiliation(s)
- Florian Bartenschlager
- Faculty of Veterinary Medicine, Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Nikolai Klymiuk
- Large Animal Models in Cardiovascular Research, Internal Medical Department I, Technical University of Munich, Munich, Germany
- Center for Innovative Medical Models, Ludwig-Maximilians University Munich, Munich, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, Freie Universität Berlin, Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, Freie Universität Berlin, Berlin, Germany
| | - Achim D. Gruber
- Faculty of Veterinary Medicine, Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Lars Mundhenk
- Faculty of Veterinary Medicine, Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
- * E-mail:
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86
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Molza AE, Westermaier Y, Moutte M, Ducrot P, Danilowicz C, Godoy-Carter V, Prentiss M, Robert CH, Baaden M, Prévost C. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Front Mol Biosci 2022; 9:826136. [PMID: 35480882 PMCID: PMC9035671 DOI: 10.3389/fmolb.2022.826136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/21/2022] [Indexed: 01/25/2023] Open
Abstract
Recent advances in structural biophysics and integrative modelling methods now allow us to decipher the structures of large macromolecular assemblies. Understanding the dynamics and mechanisms involved in their biological function requires rigorous integration of all available data. We have developed a complete modelling pipeline that includes analyses to extract biologically significant information by consistently combining automated and interactive human-guided steps. We illustrate this idea with two examples. First, we describe the ryanodine receptor, an ion channel that controls ion flux across the cell membrane through transitions between open and closed states. The conformational changes associated with the transitions are small compared to the considerable system size of the receptor; it is challenging to consistently track these states with the available cryo-EM structures. The second example involves homologous recombination, in which long filaments of a recombinase protein and DNA catalyse the exchange of homologous DNA strands to reliably repair DNA double-strand breaks. The nucleoprotein filament reaction intermediates in this process are short-lived and heterogeneous, making their structures particularly elusive. The pipeline we describe, which incorporates experimental and theoretical knowledge combined with state-of-the-art interactive and immersive modelling tools, can help overcome these challenges. In both examples, we point to new insights into biological processes that arise from such interdisciplinary approaches.
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Affiliation(s)
- Anne-Elisabeth Molza
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Yvonne Westermaier
- Biophysics and Modelling Department/In Vitro Pharmacology Unit–IDRS (Servier Research Institute), Croissy-sur-Seine, France
| | | | - Pierre Ducrot
- Biophysics and Modelling Department/In Vitro Pharmacology Unit–IDRS (Servier Research Institute), Croissy-sur-Seine, France
| | | | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA, United States
| | - Charles H. Robert
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Marc Baaden
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Chantal Prévost
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
- *Correspondence: Chantal Prévost ,
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87
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Wang L, Zhong H, Xue Z, Wang Y. Improving the topology prediction of α-helical transmembrane proteins with deep transfer learning. Comput Struct Biotechnol J 2022; 20:1993-2000. [PMID: 35521551 PMCID: PMC9062415 DOI: 10.1016/j.csbj.2022.04.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/09/2022] [Accepted: 04/17/2022] [Indexed: 11/11/2022] Open
Abstract
Transmembrane proteins (TMPs) are essential for cell recognition and communication, and they serve as important drug targets in humans. Transmembrane proteins' 3D structures are critical for determining their functions and drug design but are hard to determine even by experimental methods. Although some computational methods have been developed to predict transmembrane helices (TMHs) and orientation, there is still room for improvement. Considering that the pre-trained language model can make full use of massive unlabeled protein sequences to obtain latent feature representation for TMPs and reduce the dependence on evolutionary information, we proposed DeepTMpred, which used pre-trained self-supervised language models called ESM, convolutional neural networks, attentive neural network and conditional random fields for alpha-TMP topology prediction. Compared with the current state-of-the-art tools on a non-redundant dataset of TMPs, DeepTMpred demonstrated superior predictive performance in most evaluation metrics, especially at the TMH level. Furthermore, DeepTMpred could also obtain reliable prediction results for TMPs without much evolutionary feature in a few seconds. A tutorial on how to use DeepTMpred can be found in the colab notebook (https://colab.research.google.com/github/ISYSLAB-HUST/DeepTMpred/blob/master/notebook/test.ipynb).
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88
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Marques-Pereira C, Pires MN, Gouveia RP, Pereira NN, Caniceiro AB, Rosário-Ferreira N, Moreira IS. SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights. Int J Mol Sci 2022; 23:2986. [PMID: 35328409 PMCID: PMC8948900 DOI: 10.3390/ijms23062986] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 01/27/2023] Open
Abstract
Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) is composed of four structural proteins and several accessory non-structural proteins. SARS-CoV-2's most abundant structural protein, Membrane (M) protein, has a pivotal role both during viral infection cycle and host interferon antagonism. This is a highly conserved viral protein, thus an interesting and suitable target for drug discovery. In this paper, we explain the structural nature of M protein homodimer. To do so, we developed and applied a detailed and robust in silico workflow to predict M protein dimeric structure, membrane orientation, and interface characterization. Single Nucleotide Polymorphisms (SNPs) in M protein were retrieved from over 1.2 M SARS-CoV-2 genomes and proteins from the Global Initiative on Sharing All Influenza Data (GISAID) database, 91 of which were located at the predicted dimer interface. Among those, we identified SNPs in Variants of Concern (VOC) and Variants of Interest (VOI). Binding free energy differences were evaluated for dimer interfacial SNPs to infer mutant protein stabilities. A few high-prevalent mutated residues were found to be especially relevant in VOC and VOI. This realization may be a game-changer to structure-driven formulation of new therapeutics for SARS-CoV-2.
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Affiliation(s)
- Catarina Marques-Pereira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- IIIs—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Manuel N. Pires
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- Department of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Raquel P. Gouveia
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Nádia N. Pereira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Ana B. Caniceiro
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Nícia Rosário-Ferreira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- CQC—Coimbra Chemistry Center, Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Irina S. Moreira
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-535 Coimbra, Portugal
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89
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Gallois N, Alpha-Bazin B, Bremond N, Ortet P, Barakat M, Piette L, Mohamad Ali A, Lemaire D, Legrand P, Theodorakopoulos N, Floriani M, Février L, Den Auwer C, Arnoux P, Berthomieu C, Armengaud J, Chapon V. Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria. THE ISME JOURNAL 2022; 16:705-716. [PMID: 34556817 PMCID: PMC8857325 DOI: 10.1038/s41396-021-01113-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO22+ and Fe3+. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.
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Affiliation(s)
- Nicolas Gallois
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Béatrice Alpha-Bazin
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Nicolas Bremond
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Philippe Ortet
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Laurie Piette
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Abbas Mohamad Ali
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - David Lemaire
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Pierre Legrand
- grid.426328.9Synchrotron SOLEIL. L’Orme des Merisiers Saint-Aubin. BP 48, 91192 Gif-sur-Yvette, France
| | - Nicolas Theodorakopoulos
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France ,grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Magali Floriani
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Laureline Février
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Christophe Den Auwer
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, CNRS, ICN, 06108 Nice, France
| | - Pascal Arnoux
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Catherine Berthomieu
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Jean Armengaud
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Virginie Chapon
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France.
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90
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Yang C, Cheng J, Lin J, Zheng Y, Yu X, Sun J. Sex Pheromone Receptors of Lepidopteran Insects. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.797287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The sex pheromone receptors (SPRs) of Lepidopteran insects play important roles in chemical communication. In the sex pheromone detection processes, sex pheromone molecule (SPM), SPR, co-receptor (Orco), pheromone binding protein (PBP), sensory neuron membrane protein (SNMP), and pheromone degradation enzyme (PDE) play individual and cooperative roles. Commonly known as butterfly and moth, the Lepidopteran insects are widely distributed throughout the world, most of which are pests. Comprehensive knowledge of the SPRs of Lepidopteran insects would help the development of sex lure technology and the sex communication pathway research. In this review, we summarized SPR/Orco information from 10 families of Lepidopteran insects from corresponding studies. According to the research progress in the literature, we speculated the evolution of SPRs/Orcos and phylogenetically analyzed the Lepidopteran SPRs and Orcos with the neighbor-joining tree and further concluded the relationship between the cluster of SPRs and their ligands; we analyzed the predicted structural features of SPRs and gave our prediction results of SPRs and Orcos with Consensus Constrained TOPology Prediction (CCTOP) and SwissModel; we summarized the functional characterization of Lepidopteran SPRs and SPR-ligand interaction and then described the progress in the sex pheromone signaling pathways and metabotropic ion channel. Further studies are needed to work out the cryo-electron microscopy (EM) structure of SPR and the SPR-ligand docking pattern in a biophysical perspective, which will directly facilitate the understanding of sex pheromone signal transduction pathways and provide guidance in the sex lure technology in field pest control.
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91
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Bernat-Silvestre C, Ma Y, Johnson K, Ferrando A, Aniento F, Marcote MJ. Characterization of Arabidopsis Post-Glycosylphosphatidylinositol Attachment to Proteins Phospholipase 3 Like Genes. FRONTIERS IN PLANT SCIENCE 2022; 13:817915. [PMID: 35222477 PMCID: PMC8874281 DOI: 10.3389/fpls.2022.817915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Lipid remodeling of Glycosylphosphatidylinositol (GPI) anchors is required for their maturation and may influence the localization and function of GPI-anchored proteins (GPI-APs). Maturation of GPI-anchors is well characterized in animals and fungi but very little is known about this process in plants. In yeast, the GPI-lipid remodeling occurs entirely at the ER and is initiated by the remodeling enzyme Bst1p (Post-Glycosylphosphatidylinositol Attachment to Proteins inositol deacylase 1 -PGAP1- in mammals and Arabidopsis). Next, the remodeling enzyme Per1p (Post-Glycosylphosphatidylinositol Attachment to Proteins phospholipase 3 -PGAP3- in mammals) removes a short, unsaturated fatty acid of phosphatidylinositol (PI) that is replaced with a very long-chain saturated fatty acid or ceramide to complete lipid remodeling. In mammals, lipid remodeling starts at the ER and is completed at the Golgi apparatus. Studies of the Arabidopsis PGAP1 gene showed that the lipid remodeling of the GPI anchor is critical for the final localization of GPI-APs. Here we characterized loss-of-function mutants of Arabidopsis Per1/PGAP3 like genes (AtPGAP3A and AtPGAP3B). Our results suggest that PGAP3A function is required for the efficient transport of GPI-anchored proteins from the ER to the plasma membrane/cell wall. In addition, loss of function of PGAP3A increases susceptibility to salt and osmotic stresses that may be due to the altered localization of GPI-APs in this mutant. Furthermore, PGAP3B complements a yeast strain lacking PER1 gene suggesting that PGAP3B and Per1p are functional orthologs. Finally, subcellular localization studies suggest that PGAP3A and PGAP3B cycle between the ER and the Golgi apparatus.
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Affiliation(s)
- Cesar Bernat-Silvestre
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Valencia, Spain
| | - Yingxuan Ma
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture and Food, La Trobe University, Bundoora, VIC, Australia
| | - Kim Johnson
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture and Food, La Trobe University, Bundoora, VIC, Australia
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Fernando Aniento
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Valencia, Spain
| | - María Jesús Marcote
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Valencia, Spain
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92
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Tsunoda T, Riku M, Yamada N, Tsuchiya H, Tomita T, Suzuki M, Kizuki M, Inoko A, Ito H, Murotani K, Murakami H, Saeki Y, Kasai K. ENTREP/FAM189A2 encodes a new ITCH ubiquitin ligase activator that is downregulated in breast cancer. EMBO Rep 2022; 23:e51182. [PMID: 34927784 PMCID: PMC8811627 DOI: 10.15252/embr.202051182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/13/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022] Open
Abstract
The HECT-type ubiquitin E3 ligases including ITCH regulate many aspects of cellular function through ubiquitinating various substrates. These ligases are known to be allosterically autoinhibited and to require an activator protein to fully achieve the ubiquitination of their substrates. Here we demonstrate that FAM189A2, a downregulated gene in breast cancer, encodes a new type of ITCH activator. FAM189A2 is a transmembrane protein harboring PPxY motifs, and the motifs mediate its association with and ubiquitination by ITCH. FAM189A2 also associates with Epsin and accumulates in early and late endosomes along with ITCH. Intriguingly, FAM189A2 facilitates the association of a chemokine receptor CXCR4 with ITCH and enhances ITCH-mediated ubiquitination of CXCR4. FAM189A2-knockout prohibits CXCL12-induced endocytosis of CXCR4, thereby enhancing the effects of CXCL12 on the chemotaxis and mammosphere formation of breast cancer cells. In comparison to other activators or adaptors known in the previous studies, FAM189A2 is a unique activator for ITCH to desensitize CXCR4 activity, and we here propose that FAM189A2 be renamed as ENdosomal TRansmembrane binding with EPsin (ENTREP).
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Affiliation(s)
- Takumi Tsunoda
- Department of PathologyAichi Medical University School of MedicineNagakuteJapan
| | - Miho Riku
- Department of PathologyAichi Medical University School of MedicineNagakuteJapan
| | - Norika Yamada
- Department of PathologyAichi Medical University School of MedicineNagakuteJapan
| | - Hikaru Tsuchiya
- Protein Metabolism ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Takuya Tomita
- Protein Metabolism ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Minako Suzuki
- Department of PathologyAichi Medical University School of MedicineNagakuteJapan
| | - Mari Kizuki
- Department of PathologyAichi Medical University School of MedicineNagakuteJapan
| | - Akihito Inoko
- Department of PathologyAichi Medical University School of MedicineNagakuteJapan
- Division of Cancer Epidemiology and PreventionAichi Cancer Center Research InstituteNagoyaJapan
| | - Hideaki Ito
- Department of PathologyAichi Medical University School of MedicineNagakuteJapan
| | | | - Hideki Murakami
- Department of PathologyAichi Medical University School of MedicineNagakuteJapan
| | - Yasushi Saeki
- Protein Metabolism ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Kenji Kasai
- Department of PathologyAichi Medical University School of MedicineNagakuteJapan
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93
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Duan Y, Zhu W, Zhao X, Merzendorfer H, Chen J, Zou X, Yang Q. Choline transporter-like protein 2 interacts with chitin synthase 1 and is involved in insect cuticle development. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 141:103718. [PMID: 34982980 DOI: 10.1016/j.ibmb.2021.103718] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Chitin is an aminopolysaccharide present in insects as a major structural component of the cuticle. However, current knowledge on the chitin biosynthetic machinery, especially its constituents and mechanism, is limited. Using three independent binding assays, including co-immunoprecipitation, split-ubiquitin membrane yeast two-hybrid assay, and pull-down assay, we demonstrate that choline transporter-like protein 2 (Ctl2) interacts with krotzkopf verkehrt (kkv) in Drosophila melanogaster. The global knockdown of Ctl2 by RNA interference (RNAi) induced lethality at the larval stage. Tissue-specific RNAi to silence Ctl2 in the tracheal system and in the epidermis of the flies resulted in lethality at the first larval instar. The knockdown of Ctl2 in wings led to shrunken wings containing accumulated fluid. Calcofluor White staining demonstrated reduced chitin content in the first longitudinal vein of Ctl2 knockdown wings. The pro-cuticle, which was thinner compared to wildtype, exhibited a reduced number of chitin laminar layers. Phylogenetic analyses revealed orthologues of Ctl2 in different insect orders with highly conserved domains. Our findings provide new insights into cuticle formation, wherein Ctl2 plays an important role as a chitin-synthase interacting protein.
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Affiliation(s)
- Yanwei Duan
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian, 116024, China
| | - Weixing Zhu
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian, 116024, China
| | - Xiaoming Zhao
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Hans Merzendorfer
- Institute of Biology, University of Siegen, Adolf-Reichwein-Strasse 2, Siegen, 57068, Germany
| | - Jiqiang Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing, 100193, China
| | - Xu Zou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing, 100193, China
| | - Qing Yang
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian, 116024, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing, 100193, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No 7 Pengfei Road, Shenzhen, 518120, China.
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94
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Hegedűs T, Geisler M, Lukács GL, Farkas B. Ins and outs of AlphaFold2 transmembrane protein structure predictions. Cell Mol Life Sci 2022; 79:73. [PMID: 35034173 PMCID: PMC8761152 DOI: 10.1007/s00018-021-04112-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/25/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022]
Abstract
Transmembrane (TM) proteins are major drug targets, but their structure determination, a prerequisite for rational drug design, remains challenging. Recently, the DeepMind's AlphaFold2 machine learning method greatly expanded the structural coverage of sequences with high accuracy. Since the employed algorithm did not take specific properties of TM proteins into account, the reliability of the generated TM structures should be assessed. Therefore, we quantitatively investigated the quality of structures at genome scales, at the level of ABC protein superfamily folds and for specific membrane proteins (e.g. dimer modeling and stability in molecular dynamics simulations). We tested template-free structure prediction with a challenging TM CASP14 target and several TM protein structures published after AlphaFold2 training. Our results suggest that AlphaFold2 performs well in the case of TM proteins and its neural network is not overfitted. We conclude that cautious applications of AlphaFold2 structural models will advance TM protein-associated studies at an unexpected level.
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Affiliation(s)
- Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
- TKI, Eötvös Loránd Research Network, Budapest, Hungary.
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Bianka Farkas
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
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95
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Llebrés MT, Castro-Rodríguez V, Pascual MB, Avila C, Cánovas FM. The amino acid permease PpAAP1 mediates arginine transport in maritime pine. TREE PHYSIOLOGY 2022; 42:175-188. [PMID: 34296278 DOI: 10.1093/treephys/tpab089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/07/2021] [Indexed: 05/16/2023]
Abstract
Forest trees have access to diverse nitrogenous compounds in the soil such as ammonium, nitrate and amino acids. Recent progress has been made in the identification and characterization of ammonium and nitrate transporters. However, much more limited is our current knowledge of amino acid transport systems despite their relevance to fully understanding nitrogen nutrition in trees. In the present study, we have identified 10 genes encoding putative amino acid permeases of the AAP family in maritime pine (Pinus pinaster Ait.). Four members of this family, PpAAP1, PpAAP2, PpAAP3 and PpAAP4 were phylogenetically related to AtAAP5, involved in arginine transport in Arabidopsis thaliana. One of these genes, PpAAP1, exhibited enhanced expression levels in maritime pine roots when arginine was externally supplied. PpAAP1 was functionally characterized by complementation of a yeast mutant strain defective in the transport of arginine, allowing yeast to take up [14C]-arginine with high affinity. Furthermore, PpAAP1 was able to restore the severely affected root uptake of arginine displayed by AtAAP5 T-DNA mutants. Uptake rates of 15N-labelled arginine were significantly higher in PpAAP1-overexpressing plants when compared to wild-type and AtAAP5 mutant plants. Taken together, our results indicate that PpAAP1 is a high-affinity arginine transporter in maritime pine.
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Affiliation(s)
- María Teresa Llebrés
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Vanessa Castro-Rodríguez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - María Belén Pascual
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Concepción Avila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
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96
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Shahrear S, Afroj Zinnia M, Sany MRU, Islam ABMMK. Functional Analysis of Hypothetical Proteins of Vibrio parahaemolyticus Reveals the Presence of Virulence Factors and Growth-Related Enzymes With Therapeutic Potential. Bioinform Biol Insights 2022; 16:11779322221136002. [PMID: 36386863 PMCID: PMC9661560 DOI: 10.1177/11779322221136002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022] Open
Abstract
Vibrio parahaemolyticus, an aquatic pathogen, is a major concern in the shrimp aquaculture industry. Several strains of this pathogen are responsible for causing acute hepatopancreatic necrosis disease as well as other serious illness, both of which result in severe economic losses. The genome sequence of two pathogenic strains of V. parahaemolyticus, MSR16 and MSR17, isolated from Bangladesh, have been reported to gain a better understanding of their diversity and virulence. However, the prevalence of hypothetical proteins (HPs) makes it challenging to obtain a comprehensive understanding of the pathogenesis of V. parahaemolyticus. The aim of the present study is to provide a functional annotation of the HPs to elucidate their role in pathogenesis employing several in silico tools. The exploration of protein domains and families, similarity searches against proteins with known function, gene ontology enrichment, along with protein-protein interaction analysis of the HPs led to the functional assignment with a high level of confidence for 656 proteins out of a pool of 2631 proteins. The in silico approach used in this study was important for accurately assigning function to HPs and inferring interactions with proteins with previously described functions. The HPs with function predicted were categorized into various groups such as enzymes involved in small-compound biosynthesis pathway, iron binding proteins, antibiotics resistance proteins, and other proteins. Several proteins with potential druggability were identified among them. In addition, the HPs were investigated in search of virulent factors, which led to the identification of proteins that have the potential to be exploited as vaccine candidate. The findings of the study will be effective in gaining a better understanding of the molecular mechanisms of bacterial pathogenesis. They may also provide an insight into the process of evaluating promising targets for the development of drugs and vaccines against V. parahaemolyticus.
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Affiliation(s)
- Sazzad Shahrear
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | | - Md. Rabi Us Sany
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
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97
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Kumar P, Bhardwaj T, Garg N, Giri R. Microsecond simulations and CD spectroscopy reveals the intrinsically disordered nature of SARS-CoV-2 spike-C-terminal cytoplasmic tail (residues 1242-1273) in isolation. Virology 2022; 566:42-55. [PMID: 34864296 PMCID: PMC8626822 DOI: 10.1016/j.virol.2021.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/01/2021] [Accepted: 11/17/2021] [Indexed: 01/04/2023]
Abstract
All available SARS-CoV-2 spike protein crystal and cryo-EM structures have shown missing electron densities for cytosolic C-terminal regions (CTR). Generally, the missing electron densities point towards the intrinsically disordered nature of the protein region (IDPR). This curiosity has led us to investigate the cytosolic CTR of the spike glycoprotein of SARS-CoV-2 in isolation. The spike CTR is supposed to be from 1235 to 1273 residues or 1242-1273 residues based on our used prediction. Therefore, we have demonstrated the structural conformation of cytosolic region and its dynamics through computer simulations up to microsecond timescale using OPLS and CHARMM forcefields. The simulations have revealed the unstructured conformation of cytosolic region. Further, we have validated our computational observations with circular dichroism (CD) spectroscopy-based experiments and found its signature spectra at 198 nm. We believe that our findings will surely help in understanding the structure-function relationship of the spike protein's cytosolic region.
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Affiliation(s)
- Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Taniya Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Neha Garg
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India,Corresponding author
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98
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Cui J, Chen H, Tang X, Zhang H, Chen YQ, Chen W. Consensus mutagenesis and computational simulation provide insight into the desaturation catalytic mechanism for delta 6 fatty acid desaturase. Biochem Biophys Res Commun 2022; 586:74-80. [PMID: 34837835 DOI: 10.1016/j.bbrc.2021.11.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/14/2021] [Indexed: 12/29/2022]
Abstract
Fatty acid desaturase (FADS) generates double bond at a certain position of the corresponding polyunsaturated fatty acids (PUFAs) with high selectivity, the enzyme activity and PUFAs products of which are essential to biological systems and are associated with a variety of physiological diseases. Little is known about the structure of FADSs and their amino acid residues related to catalytic activities. Identifying key residues of Micromonas pusilla delta 6 desaturase (MpFADS6) provides a point of departure for a better understanding of desaturation. In this study, conserved amino acids were anchored through gene consensus analysis, thereby generating corresponding variants by site-directed mutagenesis. To achieve stable and high-efficiency expression of MpFADS6 and its variants in Saccharomyces cerevisiae, the key points of induced expression were optimized. The contribution of conserved residues to the function of enzyme was determined by analyzing enzyme activity of the variants. Molecular modeling indicated that these residues are essential to catalytic activities, or substrate binding. Mutants MpFADS6[Q409R] and MpFADS6[M242P] abolished desaturation, while MpFADS6[F419V] and MpFADS6[A374Q] significantly reduced catalytic activities. Given that certain residues have been identified to have a significant impact on MpFADS6 activities, it is put forward that histidine-conserved region III of FADS6 is related to electronic transfer during desaturation, while histidine-conserved regions I and II are related to desaturation. These findings provide new insights and methods to determine the structure, mechanism and directed transformation of membrane-bound desaturases.
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Affiliation(s)
- Jie Cui
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China.
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China.
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China.
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, PR China; Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, 214122, PR China.
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 5, 27127, USA.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, PR China.
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99
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Ting SY, LaCourse KD, Ledvina HE, Zhang R, Radey MC, Kulasekara HD, Somavanshi R, Bertolli SK, Gallagher LA, Kim J, Penewit KM, Salipante SJ, Xu L, Peterson SB, Mougous JD. Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism. eLife 2022; 11:74658. [PMID: 35175195 PMCID: PMC8926400 DOI: 10.7554/elife.74658] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial survival is fraught with antagonism, including that deriving from viruses and competing bacterial cells. It is now appreciated that bacteria mount complex antiviral responses; however, whether a coordinated defense against bacterial threats is undertaken is not well understood. Previously, we showed that Pseudomonas aeruginosa possess a danger-sensing pathway that is a critical fitness determinant during competition against other bacteria. Here, we conducted genome-wide screens in P. aeruginosa that reveal three conserved and widespread interbacterial antagonism resistance clusters (arc1-3). We find that although arc1-3 are coordinately activated by the Gac/Rsm danger-sensing system, they function independently and provide idiosyncratic defense capabilities, distinguishing them from general stress response pathways. Our findings demonstrate that Arc3 family proteins provide specific protection against phospholipase toxins by preventing the accumulation of lysophospholipids in a manner distinct from previously characterized membrane repair systems. These findings liken the response of P. aeruginosa to bacterial threats to that of eukaryotic innate immunity, wherein threat detection leads to the activation of specialized defense systems.
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Affiliation(s)
- See-Yeun Ting
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Kaitlyn D LaCourse
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Hannah E Ledvina
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Rutan Zhang
- Department of Medicinal Chemistry, University of Washington School of PharmacySeattleUnited States
| | - Matthew C Radey
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Hemantha D Kulasekara
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Rahul Somavanshi
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Savannah K Bertolli
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Larry A Gallagher
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Jennifer Kim
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Kelsi M Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of MedicineSeattleUnited States
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of MedicineSeattleUnited States
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington School of PharmacySeattleUnited States
| | - S Brook Peterson
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Joseph D Mougous
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States,Department of Biochemistry, University of Washington School of MedicineSeattleUnited States,Howard Hughes Medical Institute, University of WashingtonSeattleUnited States
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100
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Caldeira JB, Chung AP, Piedade AP, Morais PV, Branco R. A DedA Family Membrane Protein in Indium Extrusion in Rhodanobacter sp. B2A1Ga4. Front Microbiol 2021; 12:772127. [PMID: 34925279 PMCID: PMC8679861 DOI: 10.3389/fmicb.2021.772127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/20/2021] [Indexed: 01/27/2023] Open
Abstract
Indium (In) is a critical metal widely used in electronic equipment, and the supply of this precious metal is a major challenge for sustainable development. The use of microorganisms for the recovery of this critical high-tech element has been considered an excellent eco-friendly strategy. The Rhodanobacter sp. B2A1Ga4 strain, highly resistant to In, was studied in order to disclose the bacterial mechanisms closely linked to the ability to cope with this metal. The mutation of the gene encoding for a DedA protein homolog, YqaA, affected drastically the In resistance and the cellular metabolic activity of strain Rhodanobacter sp. B2A1Ga4 in presence of this metal. This indicates that this protein plays an important role in its In resistance phenotype. The negative impact of In might be related to the high accumulation of the metal into the mutant cells showing In concentration up to approximately 4-fold higher than the native strain. In addition, the expression of the yqaA gene in this mutant reverted the bacterial phenotype with a significant decrease of In accumulation levels into the cells and an increase of In resistance. Membrane potential measurements showed similar values for native and mutant cells, suggesting that there was no loss of proton-motive force in the mutant cells. The results from this study suggest a potential role of this DedA family protein as a membrane transporter involved in the In efflux process. The mutant strain also has the potential to be used as a biotool in bioaccumulation strategies, for the recovery of In in biomining activities.
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Affiliation(s)
- Joana B Caldeira
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, Coimbra, Portugal
| | - Ana Paula Chung
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, Coimbra, Portugal
| | - Ana Paula Piedade
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Mechanical Engineering, Coimbra, Portugal
| | - Paula V Morais
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, Coimbra, Portugal
| | - Rita Branco
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, Coimbra, Portugal
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