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Teufel F, Refsgaard JC, Kasimova MA, Deibler K, Madsen CT, Stahlhut C, Grønborg M, Winther O, Madsen D. Deorphanizing Peptides Using Structure Prediction. J Chem Inf Model 2023; 63:2651-2655. [PMID: 37092865 DOI: 10.1021/acs.jcim.3c00378] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Many endogenous peptides rely on signaling pathways to exert their function, but identifying their cognate receptors remains a challenging problem. We investigate the use of AlphaFold-Multimer complex structure prediction together with transmembrane topology prediction for peptide deorphanization. We find that AlphaFold's confidence metrics have strong performance for prioritizing true peptide-receptor interactions. In a library of 1112 human receptors, the method ranks true receptors in the top percentile on average for 11 benchmark peptide-receptor pairs.
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Affiliation(s)
- Felix Teufel
- Digital Science & Innovation, Novo Nordisk A/S, Måløv 2760, Denmark
- Department of Biology, University of Copenhagen Copenhagen 2200, Denmark
| | - Jan C Refsgaard
- Digital Science & Innovation, Novo Nordisk A/S, Måløv 2760, Denmark
| | | | - Kristine Deibler
- Digital Science & Innovation, Novo Nordisk A/S, Seattle 98109, Washington, United States
| | | | - Carsten Stahlhut
- Digital Science & Innovation, Novo Nordisk A/S, Måløv 2760, Denmark
| | - Mads Grønborg
- Global Translation, Novo Nordisk A/S, Måløv 2760, Denmark
| | - Ole Winther
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Department of Genomic Medicine, Copenhagen University Hospital/Rigshospitalet, Copenhagen 2100, Denmark
| | - Dennis Madsen
- Digital Science & Innovation, Novo Nordisk A/S, Måløv 2760, Denmark
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Li Z, Fu Z, Zhang S, Zhang X, Xue X, Chen Y, Zhang Z, Lai Z, Lin Y. Genome-wide analysis of the GLP gene family and overexpression of GLP1-5-1 to promote lignin accumulation during early somatic embryo development in Dimocarpus longan. BMC Genomics 2023; 24:138. [PMID: 36944911 PMCID: PMC10029309 DOI: 10.1186/s12864-023-09201-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/21/2023] [Indexed: 03/23/2023] Open
Abstract
Longan (Dimocarpus longan Lour.) is an economically important subtropical fruit tree. Its fruit quality and yield are affected by embryo development. As a plant seed germination marker gene, the germin-like protein (GLP) gene plays an important role in embryo development. However, the mechanism underlying the role of the GLP gene in somatic embryos is still unclear. Therefore, we conducted genome-wide identification of the longan GLP (DlGLP) gene and preliminarily verified the function of DlGLP1-5-1. Thirty-five genes were identified as longan GLP genes and divided into 8 subfamilies. Based on transcriptome data and qRT‒PCR results, DlGLP genes exhibited the highest expression levels in the root, and the expression of most DlGLPs was upregulated during the early somatic embryogenesis (SE) in longan and responded to high temperature stress and 2,4-D treatment; eight DlGLP genes were upregulated under MeJA treatment, and four of them were downregulated under ABA treatment. Subcellular localization showed that DlGLP5-8-2 and DlGLP1-5-1 were located in the cytoplasm and extracellular stroma/chloroplast, respectively. Overexpression of DIGLP1-5-1 in the globular embryos (GEs) of longan promoted the accumulation of lignin and decreased the H2O2 content by regulating the activities of ROS-related enzymes. The results provide a reference for the functional analysis of DlGLPs and related research on improving lignin accumulation in the agricultural industry through genetic engineering.
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Affiliation(s)
- Zhuoyun Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhuoran Fu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaodong Xue
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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53
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Tan C, Zhu F, Pan P, Wu A, Li C. Development of multi-epitope vaccines against the monkeypox virus based on envelope proteins using immunoinformatics approaches. Front Immunol 2023; 14:1112816. [PMID: 36993967 PMCID: PMC10040844 DOI: 10.3389/fimmu.2023.1112816] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/21/2023] [Indexed: 03/14/2023] Open
Abstract
BackgroundSince May 2022, cases of monkeypox, a zoonotic disease caused by the monkeypox virus (MPXV), have been increasingly reported worldwide. There are, however, no proven therapies or vaccines available for monkeypox. In this study, several multi-epitope vaccines were designed against the MPXV using immunoinformatics approaches.MethodsThree target proteins, A35R and B6R, enveloped virion (EV) form-derived antigens, and H3L, expressed on the mature virion (MV) form, were selected for epitope identification. The shortlisted epitopes were fused with appropriate adjuvants and linkers to vaccine candidates. The biophysical andbiochemical features of vaccine candidates were evaluated. The Molecular docking and molecular dynamics(MD) simulation were run to understand the binding mode and binding stability between the vaccines and Toll-like receptors (TLRs) and major histocompatibility complexes (MHCs). The immunogenicity of the designed vaccines was evaluated via immune simulation.ResultsFive vaccine constructs (MPXV-1-5) were formed. After the evaluation of various immunological and physicochemical parameters, MPXV-2 and MPXV-5 were selected for further analysis. The results of molecular docking showed that the MPXV-2 and MPXV-5 had a stronger affinity to TLRs (TLR2 and TLR4) and MHC (HLA-A*02:01 and HLA-DRB1*02:01) molecules, and the analyses of molecular dynamics (MD) simulation have further confirmed the strong binding stability of MPXV-2 and MPXV-5 with TLRs and MHC molecules. The results of the immune simulation indicated that both MPXV-2 and MPXV-5 could effectively induce robust protective immune responses in the human body.ConclusionThe MPXV-2 and MPXV-5 have good efficacy against the MPXV in theory, but further studies are required to validate their safety and efficacy.
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Affiliation(s)
- Caixia Tan
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Changsha, Hunan, China
| | - Fei Zhu
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Changsha, Hunan, China
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
| | - Pinhua Pan
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Changsha, Hunan, China
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- *Correspondence: Chunhui Li, ; Anhua Wu, ; Pinhua Pan,
| | - Anhua Wu
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Changsha, Hunan, China
- *Correspondence: Chunhui Li, ; Anhua Wu, ; Pinhua Pan,
| | - Chunhui Li
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Changsha, Hunan, China
- *Correspondence: Chunhui Li, ; Anhua Wu, ; Pinhua Pan,
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Acebal MC, Dalgaard LT, Jørgensen TS, Hansen BW. Embryogenesis of a calanoid copepod analyzed by transcriptomics. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101054. [PMID: 36565589 DOI: 10.1016/j.cbd.2022.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/22/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
The calanoid copepod Acartia tonsa (Dana) has attracted interest because of its use as a copepod model organism as well as its potential economic role as live fish larval feed. While the adult genome and transcriptome of A. tonsa has been investigated, no studies have been performed investigating the genome-wide transcriptional changes during the normal subitaneous embryogenesis. Thus, the aim of the current study was to investigate said transcriptional changes throughout A. tonsa embryonic development. RNA extraction and de novo transcriptome assembly for the subitaneous embryogenesis of the copepod was conducted. The assembly includes for the first-time samples describing quiescent development and overall helps establishing a framework for future studies on the molecular biology of our species of interest. Among the findings reported, sequences annotated to well-known developmental genes, were identified. At the same time are described the molecular changes and gene expression levels throughout the entire 42 h the embryonic development lasts. In conclusion, here we present the most complete genome-wide transcriptional map of early copepod embryonic development to date, enabling further use of A. tonsa as a model organism for crustacean development. Keywords: enrichment of pathways; subitaneous embryogenesis, comparative genomics; transcriptome assembly; invertebrate genomics.
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Affiliation(s)
- Miguel Cifuentes Acebal
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Louise Torp Dalgaard
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Tue Sparholt Jørgensen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark; Department of Environmental Science - Environmental Microbiology and Biotechnology, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark; The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) at the Technical University of Denmark, Building 220, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark(1)
| | - Benni Winding Hansen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark.
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55
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Jabeur R, Guyon V, Toth S, Pereira AE, Huynh MP, Selmani Z, Boland E, Bosio M, Beuf L, Clark P, Vallenet D, Achouak W, Audiffrin C, Torney F, Paul W, Heulin T, Hibbard BE, Toepfer S, Sallaud C. A novel binary pesticidal protein from Chryseobacterium arthrosphaerae controls western corn rootworm by a different mode of action to existing commercial pesticidal proteins. PLoS One 2023; 18:e0267220. [PMID: 36800363 PMCID: PMC9937505 DOI: 10.1371/journal.pone.0267220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/04/2022] [Indexed: 02/18/2023] Open
Abstract
The western corn rootworm (WCR) Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae) remains one of the economically most important pests of maize (Zea mays) due to its adaptive capabilities to pest management options. This includes the ability to develop resistance to some of the commercial pesticidal proteins originating from different strains of Bacillus thuringiensis. Although urgently needed, the discovery of new, environmentally safe agents with new modes of action is a challenge. In this study we report the discovery of a new family of binary pesticidal proteins isolated from several Chryseobacterium species. These novel binary proteins, referred to as GDI0005A and GDI0006A, produced as recombinant proteins, prevent growth and increase mortality of WCR larvae, as does the bacteria. These effects were found both in susceptible and resistant WCR colonies to Cry3Bb1 and Cry34Ab1/Cry35Ab1 (reassigned Gpp34Ab1/Tpp35Ab1). This suggests GDI0005A and GDI0006A may not share the same binding sites as those commercially deployed proteins and thereby possess a new mode of action. This paves the way towards the development of novel biological or biotechnological management solutions urgently needed against rootworms.
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Affiliation(s)
- Rania Jabeur
- Limagrain Europe, Centre de recherche, Chappes, France
| | | | - Szabolcs Toth
- Integrated Pest Management Department, Hungarian University of Agriculture and Life Sciences—MATE, Godollo, Hungary
- CABI Switzerland, c/o Plant Protection and Soil Conservation Directorate, Hodmezovasarhely, Hungary
| | - Adriano E. Pereira
- Division of Plant Science & Technology, University of Missouri, Columbia, MO, United States of America
| | - Man P. Huynh
- Division of Plant Science & Technology, University of Missouri, Columbia, MO, United States of America
| | - Zakia Selmani
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediène, USTHB, Alger, Algérie
| | - Erin Boland
- Genective USA Corp, Champaign, IL, United States of America
| | - Mickael Bosio
- Limagrain Europe, Centre de recherche, Chappes, France
| | - Laurent Beuf
- Limagrain Europe, Centre de recherche, Chappes, France
| | - Pete Clark
- Genective USA Corp, Champaign, IL, United States of America
| | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Evry, Université Paris-Saclay, CNRS, Evry, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Saint Paul-Lez-Durance, France
| | | | | | - Wyatt Paul
- Limagrain Europe, Centre de recherche, Chappes, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Saint Paul-Lez-Durance, France
| | - Bruce E. Hibbard
- USDA-ARS, Plant Genetics Research Unit, Univ. Missouri, Columbia, MO, United States of America
| | - Stefan Toepfer
- CABI Switzerland, c/o Plant Protection and Soil Conservation Directorate, Hodmezovasarhely, Hungary
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Sürmeli Y, Şanlı-Mohamed G. Engineering of xylanases for the development of biotechnologically important characteristics. Biotechnol Bioeng 2023; 120:1171-1188. [PMID: 36715367 DOI: 10.1002/bit.28339] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Xylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.
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Affiliation(s)
- Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
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Grasso S, Dabene V, Hendriks MMW, Zwartjens P, Pellaux R, Held M, Panke S, van Dijl JM, Meyer A, van Rij T. Signal Peptide Efficiency: From High-Throughput Data to Prediction and Explanation. ACS Synth Biol 2023; 12:390-404. [PMID: 36649479 PMCID: PMC9942255 DOI: 10.1021/acssynbio.2c00328] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The passage of proteins across biological membranes via the general secretory (Sec) pathway is a universally conserved process with critical functions in cell physiology and important industrial applications. Proteins are directed into the Sec pathway by a signal peptide at their N-terminus. Estimating the impact of physicochemical signal peptide features on protein secretion levels has not been achieved so far, partially due to the extreme sequence variability of signal peptides. To elucidate relevant features of the signal peptide sequence that influence secretion efficiency, an evaluation of ∼12,000 different designed signal peptides was performed using a novel miniaturized high-throughput assay. The results were used to train a machine learning model, and a post-hoc explanation of the model is provided. By describing each signal peptide with a selection of 156 physicochemical features, it is now possible to both quantify feature importance and predict the protein secretion levels directed by each signal peptide. Our analyses allow the detection and explanation of the relevant signal peptide features influencing the efficiency of protein secretion, generating a versatile tool for the de novo design and in silico evaluation of signal peptides.
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Affiliation(s)
- Stefano Grasso
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, Groningen 9700 RB, The Netherlands,DSM
Biotechnology Center, Alexander Fleminglaan 1, Delft 2613 AX, Netherlands
| | - Valentina Dabene
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, Basel 4058, Switzerland,FGen
AG, Hochbergerstrasse
60C, Basel 4057, Switzerland
| | | | - Priscilla Zwartjens
- DSM
Biotechnology Center, Alexander Fleminglaan 1, Delft 2613 AX, Netherlands
| | - René Pellaux
- FGen
AG, Hochbergerstrasse
60C, Basel 4057, Switzerland
| | - Martin Held
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, Basel 4058, Switzerland
| | - Sven Panke
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, Basel 4058, Switzerland
| | - Jan Maarten van Dijl
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, Groningen 9700 RB, The Netherlands,. Phone: +31503615187
| | - Andreas Meyer
- FGen
AG, Hochbergerstrasse
60C, Basel 4057, Switzerland
| | - Tjeerd van Rij
- DSM
Biotechnology Center, Alexander Fleminglaan 1, Delft 2613 AX, Netherlands,. Phone: +31628441843
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Afshari E, Cohan RA, Sotoodehnejadnematalahi F, Mousavi SF. In-silico design and evaluation of an epitope-based serotype-independent promising vaccine candidate for highly cross-reactive regions of pneumococcal surface protein A. J Transl Med 2023; 21:13. [PMID: 36627666 PMCID: PMC9830136 DOI: 10.1186/s12967-022-03864-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The pathogenicity of pneumococcus with high morbidity, mortality, and multi-drug resistance patterns has been increasing. The limited coverage of the licensed polysaccharide-based vaccines and the replacement of the non-vaccine serotypes are the main reasons for producing a successful serotype-independent vaccine. Pneumococcal surface protein A (PspA) is an extremely important virulence factor and an interesting candidate for conserved protein-based pneumococcal vaccine classified into two prominent families containing five clades. PspA family-elicited immunity is clade-dependent, and the level of the PspA cross-reactivity is restricted to the same family. METHODS To cover and overcome the clade-dependent immunity of the PspAs in this study, we designed and tested a PspA1-5c+p vaccine candidate composed of the highest immunodominant coverage of B- and T-cell epitope truncated domain of each clade focusing on two cross-reactive B and C regions of the PspAs. The antigenicity, toxicity, physicochemical properties, 3D structure prediction, stability and flexibility of the designed protein using molecular dynamic (MD) simulation, molecular docking of the construct withHLADRB1*(01:01) and human lactoferrin N-lop, and immune simulation were assessed using immunoinformatics tools. In the experimental section, after intraperitoneal immunization of the mice with Alum adjuvanted recombinant PspA1-5c+p, we evaluated the immune response, cross-reactivity, and functionality of the Anti-PspA1-5c+p antibody using ELISA, Opsonophagocytic killing activity, and serum bactericidal assay. RESULTS For the first time, this work suggested a novel PspA-based vaccine candidate using immunoinformatics tools. The designed PspA1-5c+p protein is predicted to be highly antigenic, non-toxic, soluble, stable with low flexibility in MD simulation, and able to stimulate both humoral and cellular immune responses. The designed protein also could interact strongly with HLADRB1*(01:01) and human lactoferrin N-lop in the docking study. Our immunoinformatics predictions were validated using experimental data. Results showed that the anti-PspA1-5c+p IgG not only had a high titer with strong and same cross-reactivity coverage against all pneumococcal serotypes used but also had high and effective bioactivity for pneumococcal clearance using complement system and phagocytic cells. CONCLUSION Our findings elucidated the potential application of the PspA1-5c+p vaccine candidate as a serotype-independent pneumococcal vaccine with a strong cross-reactivity feature. Further in-vitro and in-vivo investigations against other PspA clades should be performed to confirm the full protection of the PspA1-5c+p vaccine candidate.
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Affiliation(s)
- Elnaz Afshari
- grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Reza Ahangari Cohan
- grid.420169.80000 0000 9562 2611Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Fattah Sotoodehnejadnematalahi
- grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Seyed Fazlollah Mousavi
- grid.420169.80000 0000 9562 2611Department of Microbiology, Pasteur Institute of Iran, 69 Pasteur Ave., Tehran, 13164 Iran
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Kunze M. Computational Evaluation of Peroxisomal Targeting Signals in Metazoa. Methods Mol Biol 2023; 2643:391-404. [PMID: 36952201 DOI: 10.1007/978-1-0716-3048-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Most soluble proteins enclosed in peroxisomes encode either type-1 or type-2 peroxisomal targeting signals (PTS1 or PTS2), which act as postal codes and define the proteins' intracellular destination. Thus, various computational programs have been developed to evaluate the probability of specific peptide sequences for being a functional PTS or to scan the primary sequence of proteins for such signals. Among these prediction algorithms the PTS1-predictor ( https://mendel.imp.ac.at/pts1/ ) has been amply used, but the research logic of this and other PTS1 prediction tools is occasionally misjudged giving rise to characteristic pitfalls. Here, a proper utilization of the PTS1-predictor is introduced together with a framework of additional tests to increase the validity of the interpretation of results. Moreover, a list of possible causes for a mismatch between results of such predictions and experimental outcomes is provided. However, the foundational arguments apply to other prediction tools for PTS1 motifs as well.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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Cui Z, Wu W, Fan F, Wang F, Liu D, Di D, Wang H. Transcriptome analysis of Lr19-virulent mutants provides clues for the AvrLr19 of Puccinia triticina. Front Microbiol 2023; 14:1062548. [PMID: 37032911 PMCID: PMC10073493 DOI: 10.3389/fmicb.2023.1062548] [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: 10/06/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Wheat leaf rust caused by Puccinia triticina (Pt) remains one of the most destructive diseases of common wheat worldwide. Understanding the pathogenicity mechanisms of Pt is important to control wheat leaf rust. Methods The urediniospores of Pt race PHNT (wheat leaf rust resistance gene Lr19-avirulent isolate) were mutagenized with ethyl methanesulfonate (EMS), and two Lr19-virulent mutants named M1 and M2 were isolated. RNA sequencing was performed on samples collected from wheat cultivars Chinese Spring and TcLr19 infected with wild-type (WT) PHNT, M1, and M2 isolates at 14 days post-inoculation (dpi), respectively. Screening AvrLr19 candidates by quantitative reverse transcription PCR (qPCR) and Agrobacterium-mediated transient assays in Nicotiana benthamiana. Results 560 genes with single nucleotide polymorphisms (SNPs) and insertions or deletions (Indels) from non-differentially expressed genes were identified. Among them, 10 secreted proteins were screened based on their fragments per kilobase of exon model per million mapped reads (FPKM) values in the database. qPCR results showed that the expression profiles of 7 secreted proteins including PTTG_27471, PTTG_12441, PTTG_28324, PTTG_26499, PTTG_06910, PTTG_26516, and PTTG_03570 among 10 secreted proteins in mutants were significantly different with that in wild-type isolate after infection wheat TcLr19 and might be related to the recognition between Lr19 and AvrLr19. In addition, a total of 216 differentially expressed genes (DEGs) were obtained from three different sample comparisons including M1-vs-WT, M2-vs-WT, and M1-vs-M2. Among 216 DEGs, 15 were predicted to be secreted proteins. One secreted protein named PTTG_04779 could inhibit programmed progress of cell death (PCD) induced by apoptosis-controlling genes B-cell lymphoma-2 associated X protein (BAX) on Nicotiana benthamiana, indicating that it might play a virulence function in plant. Taken together, total 8 secreted proteins, PTTG_04779, PTTG_27471, PTTG_12441, PTTG_28324, PTTG_26499, PTTG_06910, PTTG_26516, PTTG_03570 are identified as AvrLr19 candidates. Discussion Our results showed that a large number of genes participate in the interaction between Pt and TcLr19, which will provide valuable resources for the identification of AvrLr19 candidates and pathogenesis-related genes.
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Affiliation(s)
- Zhongchi Cui
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Wenyue Wu
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Fan Fan
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Fei Wang
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Daqun Liu
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Dianping Di
- Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding, Hebei, China
- *Correspondence: Dianping Di,
| | - Haiyan Wang
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
- Haiyan Wang,
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Khurshid B, Jackson DJ, Engilberge S, Motreuil S, Broussard C, Thomas J, Immel F, Harrington MJ, Crowley PB, Vielzeuf D, Perrin J, Marin F. Molecular characterization of accripin11, a soluble shell protein with an acidic C-terminus, identified in the prismatic layer of the Mediterranean fan mussel Pinna nobilis (Bivalvia, Pteriomorphia). FEBS Open Bio 2022; 13:10-25. [PMID: 36219517 PMCID: PMC9808598 DOI: 10.1002/2211-5463.13497] [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: 06/13/2022] [Revised: 08/23/2022] [Accepted: 10/10/2022] [Indexed: 01/07/2023] Open
Abstract
We have identified a novel shell protein, accripin11, as a major soluble component of the calcitic prisms of the fan mussel Pinna nobilis. Initially retrieved from a cDNA library, its full sequence is confirmed here by transcriptomic and proteomic approaches. The sequence of the mature protein is 103 residues with a theoretical molecular weight of 11 kDa and is moderately acidic (pI 6.74) except for its C-terminus which is highly enriched in aspartic acid. The protein exhibits a peculiar cysteine pattern in its central domain. The full sequence shares similarity with six other uncharacterized molluscan shell proteins from the orders Ostreida, Pteriida and Mytilida, all of which are pteriomorphids and produce a phylogenetically restricted pattern of nacro-prismatic shell microstructures. This suggests that accripin11 is a member of a family of clade-specific shell proteins. A 3D model of accripin11 was predicted with AlphaFold2, indicating that it possesses three short alpha helices and a disordered C-terminus. Recombinant accripin11 was tested in vitro for its ability to influence the crystallization of CaCO3 , while a polyclonal antibody was able to locate accripin11 to prismatic extracts, particularly in the acetic acid-soluble matrix. The putative functions of accripin11 are further discussed in relation to shell biomineralization.
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Affiliation(s)
- Benazir Khurshid
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance,Synchrotron SOLEILBeamline ANATOMIXGif‐sur‐YvetteFrance
| | | | - Sylvain Engilberge
- Structural Biology GroupEuropean Synchrotron Radiation FacilityGrenobleFrance
| | - Sébastien Motreuil
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
| | | | - Jérôme Thomas
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
| | - Françoise Immel
- Chrono‐Environnement, UMR 6249 CNRSUniversité de Bourgogne Franche‐ComtéBesançonFrance
| | | | - Peter B. Crowley
- School of Biological and Chemical SciencesNational University of IrelandGalwayIreland
| | | | | | - Frédéric Marin
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
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Heterologous Expression of Extracellular Proteinase pAsPs of Aspergillus pseudotamarii in Komagataella phaffii. Int J Mol Sci 2022; 23:ijms232315035. [PMID: 36499360 PMCID: PMC9739362 DOI: 10.3390/ijms232315035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
Neutral protease pAsPs gene was obtained by sequence optimization of NpI protease from Aspergillus pseudotamarii. pAsPs was for the first time integrated in the genome of yeast strain Komagataella phaffii T07, and then produced in a 5 L bioreactor with an enzyme yield of 150,800 U/mL of culture liquid towards casein. The specific activity of the pAsPs was 7,657,000 U/mg toward casein, 2320 U/mg toward hemoglobin, and 25,344 U/mg toward azocasein per 1 mg of the protein. The enzyme was found to be inhibited by Cu2+. Optimal activity pH was shown in the range of pH 6.5-8.0, and optimal temperature-50-60 °C. The molecular mass of the recombinant protease pAsPs was shown to be 67.5 kDa. Mass-spectrometric analysis confirmed the identity of the amino acid sequence of the obtained pAsPs preparation with the predicted sequence, with 17% coverage and protein score 288. Thus, the novel neutral protease pAsPs is a promising candidate for large-scale use in manufacturing, including the food industry.
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Cheng BX, Shao GY, Li Y, Tian QQ, Wang SY, Liu F. Molecular cloning and characterisation of the PmEglin cDNA in the leech Hirudinaria sp. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01277-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Peritrophin-like Genes Are Associated with Delousing Drug Response and Sensitivity in the Sea Louse Caligus rogercresseyi. Int J Mol Sci 2022; 23:ijms232113341. [DOI: 10.3390/ijms232113341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Caligus rogercresseyi is the main ectoparasite that affects the salmon industry in Chile. The mechanisms used by the parasite to support its life strategy are of great interest for developing control strategies. Due to the critical role of insect peritrophins in host–parasite interactions and response to pest control drugs, this study aimed to identify and characterize the peritrophin-like genes present in C. rogercresseyi. Moreover, the expression of peritrophin-like genes was evaluated on parasites exposed to delousing drugs such as pyrethroids and azamethiphos. Peritrophin genes were identified by homology analysis among the sea louse transcriptome database and arthropods peritrophin-protein database obtained from GenBank and UniProt. Moreover, the gene loci in the parasite genome were located. Furthermore, peritrophin gene expression levels were evaluated by RNA-Seq analysis in sea louse developmental stages and sea lice exposed to delousing drugs deltamethrin, cypermethrin, and azamethiphos. Seven putative peritrophin-like genes were identified in C. rogercresseyi with high homology with other crustacean peritrophins. Differences in the presence of signal peptides, the number of chitin-binding domains, and the position of conserved cysteines were found. In addition, seven peritrophin-like gene sequences were identified in the C. rogercresseyi genome. Gene expression analysis revealed a stage-dependent expression profile. Notably, differential regulation of peritrophin genes in resistant and susceptible populations to delousing drugs was found. These data are the first report and characterization of peritrophin genes in the sea louse C. rogercresseyi, representing valuable knowledge to understand sea louse biology. Moreover, this study provides evidence for a deeper understanding of the molecular basis of C. rogercresseyi response to delousing drugs.
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Bindics J, Khan M, Uhse S, Kogelmann B, Baggely L, Reumann D, Ingole KD, Stirnberg A, Rybecky A, Darino M, Navarrete F, Doehlemann G, Djamei A. Many ways to TOPLESS - manipulation of plant auxin signalling by a cluster of fungal effectors. THE NEW PHYTOLOGIST 2022; 236:1455-1470. [PMID: 35944559 DOI: 10.1111/nph.18315] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Plant biotrophic pathogens employ secreted molecules, called effectors, to suppress the host immune system and redirect the host's metabolism and development in their favour. Putative effectors of the gall-inducing maize pathogenic fungus Ustilago maydis were analysed for their ability to induce auxin signalling in plants. Using genetic, biochemical, cell-biological, and bioinformatic approaches we functionally elucidate a set of five, genetically linked effectors, called Topless (TPL) interacting protein (Tips) effectors that induce auxin signalling. We show that Tips induce auxin signalling by interfering with central corepressors of the TPL family. CRISPR-Cas9 mutants and deletion strain analysis indicate that the auxin signalling inducing subcluster effectors plays a redundant role in virulence. Although none of the Tips seem to have a conserved interaction motif, four of them bind solely to the N-terminal TPL domain and, for Tip1 and Tip4, we demonstrate direct competition with auxin/indole-3-acetic acid transcriptional repressors for their binding to TPL class of corepressors. Our findings reveal that TPL proteins, key regulators of growth-defence antagonism, are a major target of the U. maydis effectome.
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Affiliation(s)
- Janos Bindics
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna Bio Center (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Mamoona Khan
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Nussallee 9, 53115, Bonn, Germany
| | - Simon Uhse
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna Bio Center (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Benjamin Kogelmann
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna Bio Center (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Laura Baggely
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna Bio Center (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Daniel Reumann
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna Bio Center (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Kishor D Ingole
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Nussallee 9, 53115, Bonn, Germany
| | - Alexandra Stirnberg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna Bio Center (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Anna Rybecky
- CEPLAS, Institute for Plant Sciences, University of Cologne, 50674, Cologne, Germany
| | - Martin Darino
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna Bio Center (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Fernando Navarrete
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna Bio Center (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Gunther Doehlemann
- CEPLAS, Institute for Plant Sciences, University of Cologne, 50674, Cologne, Germany
| | - Armin Djamei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna Bio Center (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Nussallee 9, 53115, Bonn, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany
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Abstract
Artificial intelligence (AI) methods have been and are now being increasingly integrated in prediction software implemented in bioinformatics and its glycoscience branch known as glycoinformatics. AI techniques have evolved in the past decades, and their applications in glycoscience are not yet widespread. This limited use is partly explained by the peculiarities of glyco-data that are notoriously hard to produce and analyze. Nonetheless, as time goes, the accumulation of glycomics, glycoproteomics, and glycan-binding data has reached a point where even the most recent deep learning methods can provide predictors with good performance. We discuss the historical development of the application of various AI methods in the broader field of glycoinformatics. A particular focus is placed on shining a light on challenges in glyco-data handling, contextualized by lessons learnt from related disciplines. Ending on the discussion of state-of-the-art deep learning approaches in glycoinformatics, we also envision the future of glycoinformatics, including development that need to occur in order to truly unleash the capabilities of glycoscience in the systems biology era.
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Affiliation(s)
- Daniel Bojar
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 41390, Sweden
- Wallenberg
Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg 41390, Sweden
| | - Frederique Lisacek
- Proteome
Informatics Group, Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
- Computer
Science Department & Section of Biology, University of Geneva, route de Drize 7, CH-1227, Geneva, Switzerland
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67
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Rahman MA, Heme UH, Parvez MAK. In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and adaptational functions to extreme environments. PLoS One 2022; 17:e0276085. [PMID: 36228026 PMCID: PMC9560612 DOI: 10.1371/journal.pone.0276085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2022] Open
Abstract
Members of the Bacillus genus are industrial cell factories due to their capacity to secrete significant quantities of biomolecules with industrial applications. The Bacillus paralicheniformis strain Bac84 was isolated from the Red Sea and it shares a close evolutionary relationship with Bacillus licheniformis. However, a significant number of proteins in its genome are annotated as functionally uncharacterized hypothetical proteins. Investigating these proteins' functions may help us better understand how bacteria survive extreme environmental conditions and to find novel targets for biotechnological applications. Therefore, the purpose of our research was to functionally annotate the hypothetical proteins from the genome of B. paralicheniformis strain Bac84. We employed a structured in-silico approach incorporating numerous bioinformatics tools and databases for functional annotation, physicochemical characterization, subcellular localization, protein-protein interactions, and three-dimensional structure determination. Sequences of 414 hypothetical proteins were evaluated and we were able to successfully attribute a function to 37 hypothetical proteins. Moreover, we performed receiver operating characteristic analysis to assess the performance of various tools used in this present study. We identified 12 proteins having significant adaptational roles to unfavorable environments such as sporulation, formation of biofilm, motility, regulation of transcription, etc. Additionally, 8 proteins were predicted with biotechnological potentials such as coenzyme A biosynthesis, phenylalanine biosynthesis, rare-sugars biosynthesis, antibiotic biosynthesis, bioremediation, and others. Evaluation of the performance of the tools showed an accuracy of 98% which represented the rationality of the tools used. This work shows that this annotation strategy will make the functional characterization of unknown proteins easier and can find the target for further investigation. The knowledge of these hypothetical proteins' potential functions aids B. paralicheniformis strain Bac84 in effectively creating a new biotechnological target. In addition, the results may also facilitate a better understanding of the survival mechanisms in harsh environmental conditions.
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Affiliation(s)
- Md. Atikur Rahman
- Institute of Microbiology, Friedrich Schiller University Jena, Thuringia, Germany
| | - Uzma Habiba Heme
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Thuringia, Germany
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Brunello L, Ménard C, Rousset M, Vignes M, Charnet P, Cens T. Different efficiency of auxiliary/chaperone proteins to promote the functional reconstitution of honeybee glutamate and acetylcholine receptors in Xenopus laevis oocytes. INSECT MOLECULAR BIOLOGY 2022; 31:620-633. [PMID: 35587772 PMCID: PMC9546428 DOI: 10.1111/imb.12791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Heterologous expression systems (e.g., Xenopus laevis oocytes) are useful to study the biophysical properties and pharmacology of ionotropic receptors such as ionotropic glutamate (iGLuRs) and nicotinic acetylcholine (nAChRs) receptors. However, insect receptors often require the co-expression of chaperone proteins to be functional. Only few iGluRs and nAChRs have been successfully expressed in such systems. Here, we compared the efficiency of chaperone proteins to promote the functional expression of one Apis mellifera iGluR and several nAChR subunit combinations (α1α8β1, α7, α2α8β1 and α2α7α8β1) in Xenopus oocytes. To this end, we cloned a new iGluR (GluR-1) and potential chaperone proteins (e.g., SOL-1, Neto, NACHO) and tested more than 40 combinations of human, nematode and honeybee proteins. We obtained robust expression of GluR-1 and α1α8β1 when co-expressed with honeybee chaperone proteins and found that nAChR expression critically depended on the α1 subunit N-terminal sequence. We recorded small ACh-gated currents in few oocytes when the α7 subunit was co-expressed with Caenorhabditis elegans RIC-3, but none of the chaperone proteins allowed efficient expression of α2α8β1 or α2α7α8β1. Our results show that only some protein combinations can reconstitute functional receptors in Xenopus oocytes and that protein combination efficient in one species is not always efficient in another species.
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Affiliation(s)
- Lorène Brunello
- Intitut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCMMontpellierFrance
| | - Claudine Ménard
- Intitut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCMMontpellierFrance
| | - Matthieu Rousset
- Intitut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCMMontpellierFrance
| | - Michel Vignes
- Intitut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCMMontpellierFrance
| | - Pierre Charnet
- Intitut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCMMontpellierFrance
| | - Thierry Cens
- Intitut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCMMontpellierFrance
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Shuai B, Deng T, Xie L, Zhang R. A novel matrix protein PNU5 facilitates the transformation from amorphous calcium carbonate to calcite and aragonite. Int J Biol Macromol 2022; 224:754-765. [DOI: 10.1016/j.ijbiomac.2022.10.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022]
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Rozov SM, Deineko EV. Increasing the Efficiency of the Accumulation of Recombinant Proteins in Plant Cells: The Role of Transport Signal Peptides. PLANTS (BASEL, SWITZERLAND) 2022; 11:2561. [PMID: 36235427 PMCID: PMC9572730 DOI: 10.3390/plants11192561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The problem with increasing the yield of recombinant proteins is resolvable using different approaches, including the transport of a target protein to cell compartments with a low protease activity. In the cell, protein targeting involves short-signal peptide sequences recognized by intracellular protein transport systems. The main systems of the protein transport across membranes of the endoplasmic reticulum and endosymbiotic organelles are reviewed here, as are the major types and structure of the signal sequences targeting proteins to the endoplasmic reticulum and its derivatives, to plastids, and to mitochondria. The role of protein targeting to certain cell organelles depending on specific features of recombinant proteins and the effect of this targeting on the protein yield are discussed, in addition to the main directions of the search for signal sequences based on their primary structure. This knowledge makes it possible not only to predict a protein localization in the cell but also to reveal the most efficient sequences with potential biotechnological utility.
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71
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Sneha, Pandey JP, Pandey DM. Evaluating the role of trypsin in silk degumming: An in silico approach. J Biotechnol 2022; 359:35-47. [PMID: 36126805 DOI: 10.1016/j.jbiotec.2022.09.007] [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: 12/24/2021] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022]
Abstract
The trypsin being universal enzyme forming family of proteases catalyzes the hydrolysis of proteins into amino acids and regenerates the serine hydroxyl an active site. The trypsin enzyme from D. saccharalis, uses sericin as its preferred substrate. Presence of catalytic triad (serine, aspartic acid and histidine) at the substrate binding site of this enzyme is very important for the catalytic activity. In the current study, the interacting mechanism between the substrate sericin protein and enzyme trypsin protein were explored by integrating various computational approaches including physico-chemical properties, biophysical properties, dynamics, gene ontology, molecular docking, protein - protein interactions, binding free energy calculation and structural motifs were studied. The evolutionary study performed by MEGA X showed that trypsin protein sequence (ALE15212.1) is closely related to cocoonase protein sequence (ADG26770.1) from Antheraea pernyi. 3-D models of trypsin and sericin proteins were predicted using I-TASSER and further validated by PROCHECK, and ProSAweb softwares. The predicted trypsin structure model was assigned E.C. no. 3.4.21.4 which refers hydrolytic mechanism. Gene Ontology predicted by QuickGO showed that trypsin has serine hydrolase activity (GO: 00017171), and part of proteolysis (GO: 0006508) as well as protein metabolic process (GO:0019538) actvity. Molecular docking studies between trypsin and sericin proteins were conducted by the HADDOCK 2.4 having best docked protein complex with Z-score - 1.9. 2D and 3D protein-protein interaction was performed with LIGPLOT+ and HAWKDOCK, PDBsum, respectively. The amino acid residues interacting across proteins interface are sericin_chain A representing "Ser133, Tyr214, Thr188, Thr243, Ser225, Ser151, Ser156, His294, Arg293, Gly296″ and trypsin_chain B "Lys120, Tyr246, Asn119, Glu239, Ser62, Tyr194, Ile197, Ser171, Tyr169, Gly170″. Based on our results trypsin shows similarity with cocoonase and presumably trypsin can be used as an alternative source in cocoon degumming.
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Affiliation(s)
- Sneha
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India.
| | - Jay Prakash Pandey
- Central Tasar Research and Training Institute, Piska-Nagri, Ranchi, Jharkhand 835303, India.
| | - Dev Mani Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India.
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Unveiling the Secretome of the Fungal Plant Pathogen Neofusicoccum parvum Induced by In Vitro Host Mimicry. J Fungi (Basel) 2022; 8:jof8090971. [PMID: 36135697 PMCID: PMC9505667 DOI: 10.3390/jof8090971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Neofusicoccum parvum is a fungal plant pathogen of a wide range of hosts but knowledge about the virulence factors of N. parvum and host-pathogen interactions is rather limited. The molecules involved in the interaction between N. parvum and Eucalyptus are mostly unknown, so we used a multi-omics approach to understand pathogen-host interactions. We present the first comprehensive characterization of the in vitro secretome of N. parvum and a prediction of protein-protein interactions using a dry-lab non-targeted interactomics strategy. We used LC-MS to identify N. parvum protein profiles, resulting in the identification of over 400 proteins, from which 117 had a different abundance in the presence of the Eucalyptus stem. Most of the more abundant proteins under host mimicry are involved in plant cell wall degradation (targeting pectin and hemicellulose) consistent with pathogen growth on a plant host. Other proteins identified are involved in adhesion to host tissues, penetration, pathogenesis, or reactive oxygen species generation, involving ribonuclease/ribotoxin domains, putative ricin B lectins, and necrosis elicitors. The overexpression of chitosan synthesis proteins during interaction with the Eucalyptus stem reinforces the hypothesis of an infection strategy involving pathogen masking to avoid host defenses. Neofusicoccum parvum has the molecular apparatus to colonize the host but also actively feed on its living cells and induce necrosis suggesting that this species has a hemibiotrophic lifestyle.
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73
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Yang J, Ge L, Song B, Ma Z, Yang X, Wang B, Dai Y, Xu H, Qiao M. A novel hydrophobin encoded by hgfII from Grifola frondosa exhibiting excellent self-assembly ability. Front Microbiol 2022; 13:990231. [PMID: 36160239 PMCID: PMC9504065 DOI: 10.3389/fmicb.2022.990231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Hydrophobins are small proteins from filamentous fungi, which have remarkable self-assembly properties of great potential, e.g., as drug carriers and as anti-bacterial agents, but different hydrophobins, with improved properties, are needed. HGFI (a hydrophobin from Grifola frondosa) is a class I hydrophobin, which can self-assemble into rodlet structures with a length range 100–150 nm. In this study, we identified a new hydrophobin gene (hgfII) from the mycelium of G. frondosa with a much higher transcriptional level than hgfI. Heterologous expression of hgfII was accomplished in the Pichia pastoris. X-ray photoelectron spectroscopy and water contact angle assay measurements revealed that HGFII can self-assemble into a protein film at the air–solid interface, with circular dichroism and thioflavin T fluorescence studies showing that this effect was accompanied by a decrease in α-helix content and an increase in β-sheet content. Using atomic force microscopy, it was shown that HGFII self-assembled into rodlet-like structures with a diameter of 15–30 nm, showing that it was a class I hydrophobin, with self-assembly behavior different from HGFI. The surface hydrophobicity of HGFII was stronger than that of HGFI, meanwhile, in emulsification trials, HGFII displayed better dispersive capacity to the soybean oil than HGFI, producing a more stable and durable emulsion.
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Affiliation(s)
- Jiuxia Yang
- NHC Key Laboratory of Critical Care Medicine, Tianjin First Central Hospital, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Lu Ge
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Bo Song
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhongqiang Ma
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaotian Yang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Bo Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yixin Dai
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Haijin Xu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- *Correspondence: Haijin Xu,
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- The Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- Mingqiang Qiao,
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Ye B, Song Q, Li H, Shen J, Wu C, Shu J, Zhang Y. Cloning and Functional Characterization of a Novel β-GRP Gene From Melanotus cribricollis. JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:4. [PMID: 36082677 PMCID: PMC9459437 DOI: 10.1093/jisesa/ieac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Indexed: 06/15/2023]
Abstract
In this study, a novel β-1,3-glucan recognition protein gene (β-GRP) was identified from Melanotus cribricollis, and its potential role in the immune response was investigated. The full length of β-GRP cDNA (Accession Number: MT941530) was 1644 bp, encoding a protein composed of 428 amino acids. The theoretical molecular weight and the isoelectric point were 51.53 kDa and 6.17, respectively. The amino acid sequence of β-GRP from M. cribricollis was closely related to that of. β-GRP-like from Photinus pyralis, and was predicted to contain conserved GH16 domain without glucanase active site. The results of real-time quantitative PCR showed that fungal infection of Metarhizium pingshaense may significantly upregulated the expression level of β-GRP gene. The RNAi suppression of β-GRP gene expression significantly increased the corrected cumulative mortality. Meanwhile, antimicrobial peptide genes defensin and lysozyme were significantly downregulated after interference of β-GRP. Taken together, these results suggest that β-GRP of M. cribricollis probably participates in the host immune system by mediating the expression of antimicrobial peptides. This study provides comprehensive insights into the innate immune system of insect larvae.
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Affiliation(s)
- Bihuan Ye
- Zhejiang Academy of Forestry, Hangzhou 310023, China
| | - Qiyan Song
- Zhejiang Academy of Forestry, Hangzhou 310023, China
| | - Haibo Li
- Zhejiang Academy of Forestry, Hangzhou 310023, China
| | - Jianjun Shen
- Zhejiang Academy of Forestry, Hangzhou 310023, China
| | | | - Jinping Shu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yabo Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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75
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Giacomucci S, Mathieu-Denoncourt A, Vincent AT, Jannadi H, Duperthuy M. Experimental evolution of Vibrio cholerae identifies hypervesiculation as a way to increase motility in the presence of polymyxin B. Front Microbiol 2022; 13:932165. [PMID: 36090081 PMCID: PMC9454949 DOI: 10.3389/fmicb.2022.932165] [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: 04/29/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022] Open
Abstract
Vibrio cholerae includes strains responsible for the cholera disease and is a natural inhabitant of aquatic environments. V. cholerae possesses a unique polar flagellum essential for motility, adhesion, and biofilm formation. In a previous study, we showed that motility and biofilm formation are altered in the presence of subinhibitory concentrations of polymyxin B in V. cholerae O1 and O139. In this study, we performed an experimental evolution to identify the genes restoring the motility in the presence of a subinhibitory concentration of polymyxin B. Mutations in five genes have been identified in three variants derived from two different parental strains A1552 and MO10: ihfA that encodes a subunit of the integration host factor (IHF), vacJ (mlaA) and mlaF, two genes belonging to the maintenance of the lipid asymmetry (Mla) pathway, dacB that encodes a penicillin-binding protein (PBP4) and involved in cell wall synthesis, and ccmH that encodes a c-type cytochrome maturation protein. We further demonstrated that the variants derived from MO10 containing mutations in vacJ, mlaF, and dacB secrete more and larger membrane vesicles that titer the polymyxin B, which increases the bacterial survival and is expected to limit its impact on the bacterial envelope and participate in the flagellum’s retention and motility.
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Affiliation(s)
- Sean Giacomucci
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | | | - Antony T. Vincent
- Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Hanen Jannadi
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Marylise Duperthuy
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- *Correspondence: Marylise Duperthuy,
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76
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Paliwal D, Thom M, Hussein A, Ravishankar D, Wilkes A, Charleston B, Jones IM. Towards Reverse Vaccinology for Bovine TB: High Throughput Expression of Full Length Recombinant Mycobacterium bovis Proteins. Front Mol Biosci 2022; 9:889667. [PMID: 36032666 PMCID: PMC9402895 DOI: 10.3389/fmolb.2022.889667] [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: 03/04/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Bovine tuberculosis caused by Mycobacterium bovis, is a significant global pathogen causing economic loss in livestock and zoonotic TB in man. Several vaccine approaches are in development including reverse vaccinology which uses an unbiased approach to select open reading frames (ORF) of potential vaccine candidates, produce them as recombinant proteins and assesses their immunogenicity by direct immunization. To provide feasibility data for this approach we have cloned and expressed 123 ORFs from the M. bovis genome, using a mixture of E. coli and insect cell expression. We used a concatenated open reading frames design to reduce the number of clones required and single chain fusion proteins for protein pairs known to interact, such as the members of the PPE-PE family. Over 60% of clones showed soluble expression in one or the other host and most allowed rapid purification of the tagged bTB protein from the host cell background. The catalogue of recombinant proteins represents a resource that may be suitable for test immunisations in the development of an effective bTB vaccine.
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Affiliation(s)
- Deepa Paliwal
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | | | - Areej Hussein
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | | | - Alex Wilkes
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | | | - Ian M. Jones
- School of Biological Sciences, University of Reading, Reading, United Kingdom
- *Correspondence: Ian M. Jones,
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Zadorozhny AV, Ushakov VS, Rozanov AS, Bogacheva NV, Shlyakhtun VN, Voskoboev ME, Korzhuk AV, Romancev VA, Bannikova SV, Mescheryakova IA, Antonov EV, Vasilieva AR, Pavlova EI, Chesnokov DO, Shedko ED, Bryanskaya AV, Bochkov DV, Goryachkovskaya TN, Peltek SE. Heterologous Expression of Xylanase xAor from Aspergillus oryzae in Komagataella phaffii T07. Int J Mol Sci 2022; 23:ijms23158741. [PMID: 35955874 PMCID: PMC9369408 DOI: 10.3390/ijms23158741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/27/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022] Open
Abstract
Xylanases (EC 3.2.1.8) hydrolyze the hemicellulose of plant cell walls. Xylanases are used in the food and paper industries and for bioconversion of lignocellulose to biofuel. In this work, the producer-strain with four copies of the xAor xylanase gene was organized in two tandem copies for optimal expression in Komagataella phaffii T07 yeast. The secreted 35 kDa xylanase was purified from culture medium by gel filtration on Sephadex G-25 and anion exchange chromatography on DEAE-Sepharose 6HF. Tryptic peptides of the recombinant enzyme were analyzed by liquid chromatography-tandem mass spectrometry where the amino acid sequence corresponded to Protein Accession # O94163 for Endo-1,4-beta-xylanase from Aspergillus oryzae RIB40. The recombinant xylanase was produced in a bioreactor where the secreted enzyme hydrolyzed oat xylane with an activity of 258240 IU/mL. High activity in the culture medium suggested xylanase could be used for industrial applications without being purified or concentrated. The pH optimum for xylanase xAor was 7.5, though the enzyme was active from pH 2.5 to pH 10. Xylanase was active at temperatures from 35 °C to 85 °C with a maximum at 60 °C. In conclusion, this protocol yields soluble, secreted xylanase suitable for industrial scale production.
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Affiliation(s)
- Andrey Valentinovich Zadorozhny
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Viktor Sergeevich Ushakov
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Alexei Sergeevich Rozanov
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Natalia Vladimirovna Bogacheva
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | | | | | - Anton Vladimirovich Korzhuk
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | | | | | - Irina Anatolyevna Mescheryakova
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Egor Vladimirovich Antonov
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Asya Rifhatovna Vasilieva
- Kurchatov Genomic Center of the Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Elena Iurevna Pavlova
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Danil Olegovich Chesnokov
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Elizaveta Dmitrievna Shedko
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Correspondence:
| | - Alla Viktorovna Bryanskaya
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | | | - Tatiana Nikolayevna Goryachkovskaya
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Sergey Evgenyevich Peltek
- Laboratory of Molecular Biotechnology, The Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
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78
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Tiedemann K, Tsao S, Komarova SV. Platelets and osteoblasts: secretome connections. Am J Physiol Cell Physiol 2022; 323:C347-C353. [PMID: 35675640 DOI: 10.1152/ajpcell.00187.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Megakaryocyte hyperplasia associated with myeloproliferative neoplasms commonly leads to abnormal bone tissue deposition in the bone marrow, known as osteosclerosis. In this study, we aimed to synthesize the known proteomics literature describing factors released by megakaryocytes and platelets and to examine if any of the secreted factors have a known ability to stimulate the bone-forming cells, osteoblasts. Using a systematic search of Medline, we identified 77 articles reporting on factors secreted by platelets and megakaryocytes. After a full-text screening and analysis of the studies, we selected seven papers that reported proteomics data for factors secreted by platelets from healthy individuals. From 60 proteins reported in at least two studies, we focused on 23 that contained a putative signal peptide, which we searched for a potential osteoblast-stimulatory function. From nine proteins with a positive effect on osteoblast formation and function, two extracellular matrix (ECM) proteins, secreted protein acidic and rich in cysteine (SPARC) and tissue inhibitor of metalloproteinase-1 (TIMP1), and three cellular proteins with known extracellular function, the 70-kDa heat shock protein (HSP70), thymosin-β4 (TB4), and super dismutase (SOD), were identified as hypothetical candidate molecules to be examined as potential mediators in mouse models of osteomyelofibrosis. Thus, careful analysis of prior literature can be beneficial in assisting the planning of future experimental studies.
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Affiliation(s)
- Kerstin Tiedemann
- Faculty of Dental Medicine and Oral Health Sciences, Shriners Hospital for Children-Canada, Montreal, Quebec, Canada
| | - Serena Tsao
- Faculty of Dental Medicine and Oral Health Sciences, Shriners Hospital for Children-Canada, Montreal, Quebec, Canada
| | - Svetlana V Komarova
- Faculty of Dental Medicine and Oral Health Sciences, Shriners Hospital for Children-Canada, Montreal, Quebec, Canada
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79
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Botkin J, Chanda AK, Martin FN, Hirsch CD. A Reference Genome Sequence Resource for the Sugar Beet Root Rot Pathogen Aphanomyces cochlioides. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:706-710. [PMID: 35834412 DOI: 10.1094/mpmi-11-21-0277-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Jacob Botkin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Ashok K Chanda
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
- University of Minnesota, Northwest Research and Outreach Center, Crookston, MN 56716, U.S.A
| | - Frank N Martin
- USDA, Agricultural Research Service, Salinas, CA 93905, U.S.A
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
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80
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Nagaki K, Kataoka N, Theeragool G, Matsutani M, Ano Y, Matsushita K, Yakushi T. Periplasmic dehydroshikimate dehydratase combined with quinate oxidation in Gluconobacter oxydans for protocatechuate production. Biosci Biotechnol Biochem 2022; 86:1151-1159. [PMID: 35675214 DOI: 10.1093/bbb/zbac090] [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: 04/15/2022] [Accepted: 05/29/2022] [Indexed: 11/14/2022]
Abstract
Protocatechuate (3,4-dihydroxybenzoate) has antioxidant properties and is a raw material for the production of muconic acid, which is a key compound in the synthesis of polymers such as nylon and polyethylene terephthalate. Gluconobacter oxydans strain NBRC3244 has a periplasmic system for oxidation of quinate to produce 3-dehydroquinate. Previously, a periplasmic 3-dehydroshikimate production system was constructed by heterologously expressing Gluconacetobacter diazotrophicus dehydroquinate dehydratase in the periplasm of G. oxydans strain NBRC3244. 3-Dehydroshikimate is converted to protocatechuate by dehydration. In this study, we constructed a G. oxydans strain that expresses the Acinetobacter baylyi quiC gene, which encodes a dehydroshikimate dehydratase of which the subcellular localization is likely the periplasm. We attempted to produce protocatechuate by co-cultivation of two recombinant G. oxydans strains-one expressing the periplasmically targeted dehydroquinate dehydratase and the other expressing A. baylyi dehydroshikimate dehydratase. The co-cultivation system produced protocatechuate from quinate in a nearly quantitative manner.
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Affiliation(s)
- Kakeru Nagaki
- Joint Degree Program of Kasetsart University and Yamaguchi University, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Naoya Kataoka
- Division of Agricultural Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan.,Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
| | - Gunjana Theeragool
- Joint Degree Program of Kasetsart University and Yamaguchi University, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan.,Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | - Yoshitaka Ano
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Japan
| | - Kazunobu Matsushita
- Division of Agricultural Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan.,Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
| | - Toshiharu Yakushi
- Joint Degree Program of Kasetsart University and Yamaguchi University, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan.,Division of Agricultural Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan.,Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
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81
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Chevignon G, Dotto-Maurel A, Serpin D, Chollet B, Arzul I. De Novo Transcriptome Assembly and Analysis of the Flat Oyster Pathogenic Protozoa Bonamia Ostreae. Front Cell Infect Microbiol 2022; 12:921136. [PMID: 35909967 PMCID: PMC9329632 DOI: 10.3389/fcimb.2022.921136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/22/2022] [Indexed: 12/05/2022] Open
Abstract
The flat oyster Ostrea edulis is an oyster species native to Europe. It has declined to functional extinction in many areas of the NE Atlantic for several decades. Factors explaining this decline include over-exploitation of natural populations and diseases like bonamiosis, regulated across both the EU and the wider world and caused by the intracellular protozoan parasite Bonamia ostreae. To date, very limited sequence data are available for this Haplosporidian species. We present here the first transcriptome of B. ostreae. As this protozoan is not yet culturable, it remains extremely challenging to obtain high-quality -omic data. Thanks to a specific parasite isolation protocol and a dedicated bioinformatic pipeline, we were able to obtain a high-quality transcriptome for an intracellular marine micro-eukaryote, which will be very helpful to better understand its biology and to consider the development of new relevant diagnostic tools.
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82
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He Y, Wang C, Jiao R, Ni Q, Wang Y, Gao Q, Zhang Y, Xu G. Biochemical characterization of a novel glucose-tolerant GH3 β-glucosidase (Bgl1973) from Leifsonia sp. ZF2019. Appl Microbiol Biotechnol 2022; 106:5063-5079. [PMID: 35833950 DOI: 10.1007/s00253-022-12064-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/27/2022] [Accepted: 07/02/2022] [Indexed: 11/25/2022]
Abstract
Beta-glucosidase (Bgl) is an enzyme with considerable food, beverage, and biofuel processing potential. However, as many Bgls are inhibited by their reaction end product glucose, their industrial applications are greatly limited. In this study, a novel Bgl gene (Bgl1973) was cloned from Leifsonia sp. ZF2019 and heterologously expressed in E. coli. Sequence analysis and structure modeling revealed that Bgl1973 was 748 aa, giving it a molecular weight of 78 kDa, and it showed high similarity with the glycoside hydrolase 3 (GH3) family Bgls with which its active site residues were conserved. By using pNPGlc (p-nitrophenyl-β-D-glucopyranoside) as substrate, the optimum temperature and pH of Bgl1973 were shown to be 50 °C and 7.0, respectively. Bgl1973 was insensitive to most metal ions (12.5 mM), 1% urea, and even 0.1% Tween-80. This enzyme maintained 60% of its original activity in the presence of 20% NaCl, demonstrating its excellent salt tolerance. Furthermore, it still had 83% residual activity in 1 M of glucose, displaying its outstanding glucose tolerance. The Km, Vmax, and kcat of Bgl1973 were 0.22 mM, 44.44 μmol/min mg, and 57.78 s-1, respectively. Bgl1973 had a high specific activity for pNPGlc (19.10 ± 0.59 U/mg) and salicin (20.43 ± 0.92 U/mg). Furthermore, molecular docking indicated that the glucose binding location and the narrow and deep active channel geometry might contribute to the glucose tolerance of Bgl1973. Our results lay a foundation for the studying of this glucose-tolerant β-glucosidase and its applications in many industrial settings. KEY POINTS: • A novel β-glucosidase from GH3 was obtained from Leifsonia sp. ZF2019. • Bgl1973 demonstrated excellent glucose tolerance. • The glucose tolerance of Bgl1973 was explained using molecular docking analysis.
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Affiliation(s)
- Yi He
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Chenxi Wang
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Ronghu Jiao
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Qinxue Ni
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yan Wang
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Qianxin Gao
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Youzuo Zhang
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Guangzhi Xu
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China.
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83
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Otazo-Pérez A, Asensio-Calavia P, González-Acosta S, Baca-González V, López MR, Morales-delaNuez A, Pérez de la Lastra JM. Antimicrobial Activity of Cathelicidin-Derived Peptide from the Iberian Mole Talpa occidentalis. Vaccines (Basel) 2022; 10:vaccines10071105. [PMID: 35891269 PMCID: PMC9323388 DOI: 10.3390/vaccines10071105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023] Open
Abstract
The immune systems of all vertebrates contain cathelicidins, a family of antimicrobial peptides. Cathelicidins are a type of innate immune effector that have a number of biological functions, including a well-known direct antibacterial action and immunomodulatory function. In search of new templates for antimicrobial peptide discovery, we have identified and characterized the cathelicidin of the small mammal Talpa occidentalis. We describe the heterogeneity of cathelicidin in the order Eulipotyphla in relation to the Iberian mole and predict its antibacterial activity using bioinformatics tools. In an effort to correlate these findings, we derived the putative active peptide and performed in vitro hemolysis and antimicrobial activity assays, confirming that Iberian mole cathelicidins are antimicrobial. Our results showed that the Iberian mole putative peptide, named To-KL37 (KLFGKVGNLLQKGWQKIKNIGRRIKDFFRNIRPMQEA) has antibacterial and antifungal activity. Understanding the antimicrobial defense of insectivores may help scientists prevent the spread of pathogens to humans. We hope that this study can also provide new, effective antibacterial peptides for future drug development.
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Affiliation(s)
- Andrea Otazo-Pérez
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de la Laguna, Spain; (A.O.-P.); (P.A.-C.); (S.G.-A.); (V.B.-G.); (M.R.L.); (A.M.-d.)
- Escuela de Doctorado y Estudios de Posgrado, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, SN. Edificio Calabaza-Apdo. 456, 38200 San Cristóbal de La Laguna, Spain
| | - Patricia Asensio-Calavia
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de la Laguna, Spain; (A.O.-P.); (P.A.-C.); (S.G.-A.); (V.B.-G.); (M.R.L.); (A.M.-d.)
- Escuela de Doctorado y Estudios de Posgrado, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, SN. Edificio Calabaza-Apdo. 456, 38200 San Cristóbal de La Laguna, Spain
| | - Sergio González-Acosta
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de la Laguna, Spain; (A.O.-P.); (P.A.-C.); (S.G.-A.); (V.B.-G.); (M.R.L.); (A.M.-d.)
- Escuela de Doctorado y Estudios de Posgrado, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, SN. Edificio Calabaza-Apdo. 456, 38200 San Cristóbal de La Laguna, Spain
| | - Victoria Baca-González
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de la Laguna, Spain; (A.O.-P.); (P.A.-C.); (S.G.-A.); (V.B.-G.); (M.R.L.); (A.M.-d.)
| | - Manuel R. López
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de la Laguna, Spain; (A.O.-P.); (P.A.-C.); (S.G.-A.); (V.B.-G.); (M.R.L.); (A.M.-d.)
| | - Antonio Morales-delaNuez
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de la Laguna, Spain; (A.O.-P.); (P.A.-C.); (S.G.-A.); (V.B.-G.); (M.R.L.); (A.M.-d.)
| | - José Manuel Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de la Laguna, Spain; (A.O.-P.); (P.A.-C.); (S.G.-A.); (V.B.-G.); (M.R.L.); (A.M.-d.)
- Correspondence: ; Tel.: +34-922260112
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Thumuluri V, Almagro Armenteros JJ, Johansen A, Nielsen H, Winther O. DeepLoc 2.0: multi-label subcellular localization prediction using protein language models. Nucleic Acids Res 2022; 50:W228-W234. [PMID: 35489069 PMCID: PMC9252801 DOI: 10.1093/nar/gkac278] [Citation(s) in RCA: 167] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/07/2022] [Accepted: 04/19/2022] [Indexed: 12/19/2022] Open
Abstract
The prediction of protein subcellular localization is of great relevance for proteomics research. Here, we propose an update to the popular tool DeepLoc with multi-localization prediction and improvements in both performance and interpretability. For training and validation, we curate eukaryotic and human multi-location protein datasets with stringent homology partitioning and enriched with sorting signal information compiled from the literature. We achieve state-of-the-art performance in DeepLoc 2.0 by using a pre-trained protein language model. It has the further advantage that it uses sequence input rather than relying on slower protein profiles. We provide two means of better interpretability: an attention output along the sequence and highly accurate prediction of nine different types of protein sorting signals. We find that the attention output correlates well with the position of sorting signals. The webserver is available at services.healthtech.dtu.dk/service.php?DeepLoc-2.0.
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Affiliation(s)
| | - José Juan Almagro Armenteros
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford 94305, CA, USA
| | - Alexander Rosenberg Johansen
- Department of Computer Science, Stanford University, Stanford 94305, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford 94305, CA, USA
| | - Henrik Nielsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Ole Winther
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
- Department of Biology, Bioinformatics Centre, University of Copenhagen, Copenhagen 2200, Denmark
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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85
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Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI, Tsirigos KD, Winther O, Brunak S, von Heijne G, Nielsen H. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat Biotechnol 2022. [PMID: 34980915 DOI: 10.1038/s41587-41021-01156-41583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects all five SP types and is applicable to metagenomic data.
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Affiliation(s)
- Felix Teufel
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - José Juan Almagro Armenteros
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Magnús Halldór Gíslason
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen, Denmark
| | - Silas Irby Pihl
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Ole Winther
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen, Denmark.,Department of Biology, Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.,Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Henrik Nielsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
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86
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SpySwitch enables pH- or heat-responsive capture and release for plug-and-display nanoassembly. Nat Commun 2022; 13:3714. [PMID: 35764623 PMCID: PMC9240080 DOI: 10.1038/s41467-022-31193-8] [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: 01/06/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
Proteins can be empowered via SpyTag for anchoring and nanoassembly, through covalent bonding to SpyCatcher partners. Here we generate a switchable version of SpyCatcher, allowing gentle purification of SpyTagged proteins. We introduce numerous histidines adjacent to SpyTag’s binding site, giving moderate pH-dependent release. After phage-based selection, our final SpySwitch allows purification of SpyTag- and SpyTag003-fusions from bacterial or mammalian culture by capture at neutral pH and release at pH 5, with purity far beyond His-tag methods. SpySwitch is also thermosensitive, capturing at 4 °C and releasing at 37 °C. With flexible choice of eluent, SpySwitch-purified proteins can directly assemble onto multimeric scaffolds. 60-mer multimerization enhances immunogenicity and we use SpySwitch to purify receptor-binding domains from SARS-CoV-2 and 11 other sarbecoviruses. For these receptor-binding domains we determine thermal resilience (for mosaic vaccine development) and cross-recognition by antibodies. Antibody EY6A reacts across all tested sarbecoviruses, towards potential application against new coronavirus pandemic threats. The SpyCatcher-SpyTag system allows protein anchoring and nanoassembly. Here, the authors engineer SpySwitch, a dually switchable Catcher which allows gentle purification of SpyTagged proteins prior to downstream applications such as the assembly of virus-like particles.
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87
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de Jong RM, Singh SK, Teelen K, van de Vegte-Bolmer M, van Gemert GJ, Stone WJR, Locke E, Plieskatt J, Theisen M, Bousema T, Jore MM. Heterologous Expression and Evaluation of Novel Plasmodium falciparum Transmission Blocking Vaccine Candidates. Front Immunol 2022; 13:909060. [PMID: 35812379 PMCID: PMC9259988 DOI: 10.3389/fimmu.2022.909060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 11/27/2022] Open
Abstract
Malaria transmission blocking vaccines (TBV) aim to induce antibodies that can interrupt Plasmodium falciparum development in the mosquito midgut and thereby prevent onward malaria transmission. A limited number of TBV candidates have been identified and only three (Pfs25, Pfs230 and Pfs48/45) have entered clinical testing. While one of these candidates may emerge as a highly potent TBV candidate, it is premature to determine if they will generate sufficiently potent and sustained responses. It is therefore important to explore novel candidate antigens. We recently analyzed sera from naturally exposed individuals and found that the presence and/or intensity of antibodies against 12 novel putative surface expressed gametocyte antigens was associated with transmission reducing activity. In this study, protein fragments of these novel TBV candidates were designed and heterologously expressed in Drosophila melanogaster S2 cells and Lactococcus lactis. Eleven protein fragments, covering seven TBV candidates, were successfully produced. All tested antigens were recognized by antibodies from individuals living in malaria-endemic areas, indicating that native epitopes are present. All antigens induced antigen-specific antibody responses in mice. Two antigens induced antibodies that recognized a native protein in gametocyte extract, and antibodies elicited by four antigens recognized whole gametocytes. In particular, we found that antigen Pf3D7_0305300, a putative transporter, is abundantly expressed on the surface of gametocytes. However, none of the seven novel TBV candidates expressed here induced an antibody response that reduced parasite development in the mosquito midgut as assessed in the standard membrane feeding assay. Altogether, the antigen fragments used in this study did not prove to be promising transmission blocking vaccine constructs, but led to the identification of two gametocyte surface proteins that may provide new leads for studying gametocyte biology.
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Affiliation(s)
- Roos M. de Jong
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Susheel K. Singh
- Centre for Medical Parasitology at Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Karina Teelen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Geert-Jan van Gemert
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Will J. R. Stone
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Emily Locke
- PATH‘s Malaria Vaccine Initiative, Washington, DC, United States
| | - Jordan Plieskatt
- PATH‘s Malaria Vaccine Initiative, Washington, DC, United States
| | - Michael Theisen
- Centre for Medical Parasitology at Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Teun Bousema
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Matthijs M. Jore
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
- *Correspondence: Matthijs M. Jore,
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88
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Wang B, Wang M, Zhang H, Xu J, Hou J, Zhu Y. Canine Adenovirus 1 Isolation Bioinformatics Analysis of the Fiber. Front Cell Infect Microbiol 2022; 12:879360. [PMID: 35770071 PMCID: PMC9235841 DOI: 10.3389/fcimb.2022.879360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Canine adenovirus type 1 (CAdV-1) is a double-stranded DNA virus, which is the causative agent of fox encephalitis. The Fiber protein is one of the structural proteins in CAdV-1, which mediates virion binding to the coxsackievirus and adenovirus receptor on host cells. The suspected virus was cultured in the MDCK cells, and it was determined through the cytopathic effects, sequencing and electron microscopy. The informatics analysis of the Fiber was done using online bioinformatics servers. The CAdV-1-JL2021 strain was isolated successfully, and were most similar to the CAdV-1 strain circulating in Italy. The occurrence of negative selection and recombination were found in the CAdV-1-JL2021 and CAdV-2-AC_000020.1. Host cell membrane was its subcellular localization. The CAdV-1-JL2021 Fiber (ON164651) had 6 glycosylation sites and 107 phosphorylation sites, exerted adhesion receptor-mediated virion attachment to host cell, which was the same as CAdV-2-AC_000020.1 Fiber. The Fiber tertiary structure of the CAdV-1-JL2021 and CAdV-2-AC_000020.1 was different, but they had the same coxsackievirus and adenovirus receptor. “VATTSPTLTFAYPLIKNNNH” were predicted to be the potential CAdV-1 B cell linear epitope. The MHC-I binding peptide “KLGVKPTTY” were both presented in the CAdV-1-JL2021 and CAdV-2-AC_000020.1 Fiber and it is useful to design the canine adenovirus vaccine.
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Affiliation(s)
- Ben Wang
- Animal Science and Technology College, Jilin Agriculture Science and Technology University, Jilin, China
| | - Minchun Wang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Hongling Zhang
- Animal Science and Technology College, Jilin Agriculture Science and Technology University, Jilin, China
| | - Jinfeng Xu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jinyu Hou
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Yanzhu Zhu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- *Correspondence: Yanzhu Zhu,
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89
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Nakai K, Wei L. Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics. FRONTIERS IN BIOINFORMATICS 2022; 2:910531. [PMID: 36304291 PMCID: PMC9580943 DOI: 10.3389/fbinf.2022.910531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Prediction of subcellular localization of proteins from their amino acid sequences has a long history in bioinformatics and is still actively developing, incorporating the latest advances in machine learning and proteomics. Notably, deep learning-based methods for natural language processing have made great contributions. Here, we review recent advances in the field as well as its related fields, such as subcellular proteomics and the prediction/recognition of subcellular localization from image data.
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Affiliation(s)
- Kenta Nakai
- Institute of Medical Science, The University of Tokyo, Minato-Ku, Japan
- *Correspondence: Kenta Nakai,
| | - Leyi Wei
- School of Software, Shandong University, Jinan, China
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90
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Liu Y, Bao Z, Lin Z, Xue Q. Genome-wide identification and characterization of superoxide dismutases in four oyster species reveals functional differentiation in response to biotic and abiotic stress. BMC Genomics 2022; 23:378. [PMID: 35585505 PMCID: PMC9118643 DOI: 10.1186/s12864-022-08610-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/05/2022] [Indexed: 11/11/2022] Open
Abstract
Background Oysters inhabit in the intertidal zone and may be suffered from environmental stresses, which can increase the production of reactive oxygen species (ROS), resulting in mass mortality. Superoxide dismutases (SODs) protect oysters from ROS damage through different mechanisms compared with vertebrates. However, the molecular and functional differentiation in oyster SODs were rarely analyzed. Result In this study, a total of 13, 13, 10, and 8 candidate SODs were identified in the genome of Crassostrea gigas, Crassostrea virginica, Crassostrea hongkongensis, and Saccostrea glomerata respectively. The domain composition, gene structure, subcellular locations, conserved ligands, and cis-elements elucidated the SODs into five groups (Mn-SODs, Cu-only-SODs, Cu/Zn ion ligand Cu/Zn-SOD with enzyme activity, Zn-only-SODs, and no ligand metal ions Cu/Zn-SODs). For single domain Cu/Zn-SODs, only one cytosolic Cu/Zn-SOD (cg_XM_034479061.1) may conserve enzymatic activity while most extracellular Cu/Zn-SOD proteins appeared to lose SOD enzyme activity according to conserved ligand amino acid analysis and expression pattern under biotic and abiotic stress in C. gigas. Further, multi-domain-SODs were identified and some of them were expressed in response to biotic and abiotic stressors in C. gigas. Moreover, the expression patterns of these genes varied in response to different stressors, which may be due to the cis-elements in the gene promoter. Conclusion These findings revealed the most extracellular Cu/Zn-SOD proteins appeared to lose SOD enzyme activity in oysters. Further, our study revealed that only one cytosolic Cu/Zn-SOD (cg_XM_034479061.1) may conserve enzymatic activity of SOD. Moreover, the expression patterns of these genes varied in response to different stressors, which may be due to the cis-elements in the promoter. This study provides important insights into the mechanisms through which oysters adapt to harsh intertidal conditions, as well as potential biomarkers of stress response in related species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08610-9.
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Affiliation(s)
- Youli Liu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China.,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, 315100, China.,College of Marine life Sciences, Ocean University of China, Qingdao, 266100, China
| | - Zhenmin Bao
- College of Marine life Sciences, Ocean University of China, Qingdao, 266100, China
| | - Zhihua Lin
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China. .,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, 315100, China.
| | - Qinggang Xue
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China. .,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, 315100, China.
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91
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Park JH, Lee HM, Jin EJ, Lee EJ, Kang YJ, Kim S, Yoo SS, Lee GM, Kim YG. Development of an in vitro screening system for synthetic signal peptide in mammalian cell-based protein production. Appl Microbiol Biotechnol 2022; 106:3571-3582. [PMID: 35581431 DOI: 10.1007/s00253-022-11955-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 11/27/2022]
Abstract
Optimizing appropriate signal peptides in mammalian cell-based protein production is crucial given that most recombinant proteins produced in mammalian cells are thought to be secreted proteins. Until now, most studies on signal peptide in mammalian cells have replaced native signal peptides with well-known heterologous signal peptides and bioinformatics-based signal peptides. In the present study, we successfully established an in vitro screening system for synthetic signal peptide in CHO cells by combining a degenerate codon-based oligonucleotides library, a site-specific integration system, and a FACS-based antibody detection assay. Three new signal peptides were screened using this new screening system, confirming to have structural properties as signal peptides by the SignalP web server, a neural network-based algorithm that quantifies the signal peptide-ness of amino acid sequences. The novel signal peptides selected in this study increased Fc-fusion protein production in CHO cells by increasing specific protein productivity, whereas they did not negatively affect cell growth. Particularly, the SP-#149 clone showed the highest qp, 0.73 ± 0.01 pg/cell/day from day 1 to day 4, representing a 1.47-fold increase over the native signal peptide in a serum-free suspension culture mode. In addition, replacing native signal peptide with the novel signal peptides did not significantly affect sialylated N-glycan formation, N-terminal cleavage pattern, and biological function of Fc-fusion protein produced in CHO cells. The overall results indicate the utility of a novel in vitro screening system for synthetic signal peptide for mammalian cell-based protein production. KEY POINTS: • An in vitro screening system for synthetic signal peptide in mammalian cells was established • This system combined a degenerate codon-based library, site-specific integration, and a FACS-based detection assay • The novel signal peptides selected in this study could increase Fc-fusion protein production in mammalian cells.
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Affiliation(s)
- Jong-Ho Park
- Department of Biological Sciences, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, Korea
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
| | - Hoon-Min Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea
| | - Eun-Ju Jin
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea
| | - Eun-Ji Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea
| | - Yeon-Ju Kang
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea
| | - Sungkyun Kim
- Choong Ang Vaccine Laboratory Co., Ltd. (CAVAC), 1476-37 Yuseong-daero, Yuseong-gu, Daejeon, Korea
| | - Sung-Sick Yoo
- Choong Ang Vaccine Laboratory Co., Ltd. (CAVAC), 1476-37 Yuseong-daero, Yuseong-gu, Daejeon, Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, Korea.
| | - Yeon-Gu Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea.
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea.
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Liu Z, Yu W, Zhang X, Huang J, Wang W, Miao M, Hu L, Wan C, Yuan Y, Wu B, Lyu M. Genome-Wide Identification and Expression Analysis of Chitinase-like Genes in Petunia axillaris. PLANTS (BASEL, SWITZERLAND) 2022; 11:1269. [PMID: 35567270 PMCID: PMC9100346 DOI: 10.3390/plants11091269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Chitinase (EC 3.2.1.14) is a kind of chitin-degrading glycosidase, which plays important roles in the abiotic and biotic defense of plants. In this study, we conducted whole-genome annotation, molecular evolution, and gene expression analyses on the chitinase-like (CTL) gene family members of Petunia axillaris. Thirty-three Petunia axillarischitinase-like genes (PaCTLs) were identified from the latest Petunia genome database. According to the phylogenetic analyses, these genes were divided into GH18 and GH19 subgroups and further subdivided into five classes (Class I to Class V). Conserved motif arrangements indicated their functional relevance within each group. The expansion and homeology analyses showed that gene replication events played an important role in the evolution of PaCTLs and the increase of the GH18 subgroup members was the main reason for the expansion of the PaCTL gene family in the evolution progress. By qRT-PCR analysis, we found that most of the PaCTLs showed a very low expression level in the normal growing plants. But lots of PaCTLs showed upregulated expression profiles when the plants suffered different abiotic stress conditions. Among them, five PaCTLs responded to high temperature and exhibited significantly upregulate expression level. Correspondingly, many hormone responses, as well as biotic and abiotic stress elements were found in the promoters of PaCTLs by using cis-acting element analysis. These results provide a foundation for the exploration of PaCTLs' function and enrich the evolutionary process of the CTL gene family.
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Affiliation(s)
- Zhuoyi Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
- College of Horticulture, South China Agriculture University, Guangzhou 510642, China
| | - Wenfei Yu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Xiaowen Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Jinfeng Huang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Wei Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Miao Miao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Li Hu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Chao Wan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Yuan Yuan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Binghua Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
| | - Meiling Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (W.Y.); (X.Z.); (J.H.); (W.W.); (M.M.); (L.H.); (C.W.); (Y.Y.); (B.W.)
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Tran VHN, Nguyen TT, Meier S, Holck J, Cao HTT, Van TTT, Meyer AS, Mikkelsen MD. The Endo-α(1,3)-Fucoidanase Mef2 Releases Uniquely Branched Oligosaccharides from Saccharina latissima Fucoidans. Mar Drugs 2022; 20:305. [PMID: 35621956 PMCID: PMC9147238 DOI: 10.3390/md20050305] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 02/05/2023] Open
Abstract
Fucoidans are complex bioactive sulfated fucosyl-polysaccharides primarily found in brown macroalgae. Endo-fucoidanases catalyze the specific hydrolysis of α-L-fucosyl linkages in fucoidans and can be utilized to tailor-make fucoidan oligosaccharides and elucidate new structural details of fucoidans. In this study, an endo-α(1,3)-fucoidanase encoding gene, Mef2, from the marine bacterium Muricauda eckloniae, was cloned, and the Mef2 protein was functionally characterized. Based on the primary sequence, Mef2 was suggested to belong to the glycosyl hydrolase family 107 (GH107) in the Carbohydrate Active enZyme database (CAZy). The Mef2 fucoidanase showed maximal activity at pH 8 and 35 °C, although it could tolerate temperatures up to 50 °C. Ca2+ was shown to increase the melting temperature from 38 to 44 °C and was furthermore required for optimal activity of Mef2. The substrate specificity of Mef2 was investigated, and Fourier transform infrared spectroscopy (FTIR) was used to determine the enzymatic activity (Units per μM enzyme: Uf/μM) of Mef2 on two structurally different fucoidans, showing an activity of 1.2 × 10-3 Uf/μM and 3.6 × 10-3 Uf/μM on fucoidans from Fucus evanescens and Saccharina latissima, respectively. Interestingly, Mef2 was identified as the first described fucoidanase active on fucoidans from S. latissima. The fucoidan oligosaccharides released by Mef2 consisted of a backbone of α(1,3)-linked fucosyl residues with unique and novel α(1,4)-linked fucosyl branches, not previously identified in fucoidans from S. latissima.
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Affiliation(s)
- Vy Ha Nguyen Tran
- Section for Protein Chemistry and Enzyme Technology, DTU Bioengineering-Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (V.H.N.T.); (T.T.N.); (J.H.)
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam; (H.T.T.C.); (T.T.T.V.)
| | - Thuan Thi Nguyen
- Section for Protein Chemistry and Enzyme Technology, DTU Bioengineering-Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (V.H.N.T.); (T.T.N.); (J.H.)
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam; (H.T.T.C.); (T.T.T.V.)
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Jesper Holck
- Section for Protein Chemistry and Enzyme Technology, DTU Bioengineering-Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (V.H.N.T.); (T.T.N.); (J.H.)
| | - Hang Thi Thuy Cao
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam; (H.T.T.C.); (T.T.T.V.)
| | - Tran Thi Thanh Van
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam; (H.T.T.C.); (T.T.T.V.)
| | - Anne S. Meyer
- Section for Protein Chemistry and Enzyme Technology, DTU Bioengineering-Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (V.H.N.T.); (T.T.N.); (J.H.)
| | - Maria Dalgaard Mikkelsen
- Section for Protein Chemistry and Enzyme Technology, DTU Bioengineering-Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (V.H.N.T.); (T.T.N.); (J.H.)
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94
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Tenea GN, Ascanta P. Bioprospecting of Ribosomally Synthesized and Post-translationally Modified Peptides Through Genome Characterization of a Novel Probiotic Lactiplantibacillus plantarum UTNGt21A Strain: A Promising Natural Antimicrobials Factory. Front Microbiol 2022; 13:868025. [PMID: 35464932 PMCID: PMC9020862 DOI: 10.3389/fmicb.2022.868025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
The present work describes the genome sequencing and characterization of a novel Lactiplantibacillus plantarum strain assigned UTNGt21A isolated from wild Solanum quitoense (L.) fruits. In silico analysis has led to identifying a wide range of biosynthetic gene clusters (BGCs) and metabolic compounds. The genome had a total of 3,558,611 bp with GC of 43.96%, harboring 3,449 protein-coding genes, among which 3,209 were assigned by the EggNOG database, and 240 hypothetical proteins have no match in the BLASTN database. It also contains 68 tRNAs, 1 23S rRNA, 1 16S rRNA, 6 5S rRNA, and 1 tmRNA. In addition, no acquired resistance genes nor virulence and pathogenic factors were predicted, indicating that UTNGt21A is a safe strain. Three areas of interest (AOI) consisting of multiple genes encoding for bacteriocins and ABC transporters were predicted with BAGEL4, while eight secondary metabolite regions were predicted with the antiSMASH web tool. GutSMASH analysis predicted one metabolic gene cluster (MGC) type pyruvate to acetate-formate, a primary metabolite region essential for anaerobe growth. Several lanthipeptides and non-ribosomal peptide synthetase (NRPS) clusters were detected in the UTNGt21A but not the reference genomes, suggesting that their genome diversity might be linked to its niche-specific lineage and adaptation to a specific environment. Moreover, the application of a targeted genome mining tool (RiPPMiner) uncovered a diverse arsenal of important antimicrobial molecules such as lanthipeptides. Furthermore, in vitro analysis indicated that the crude extract (CE) of UTNGt21A exerted a wide spectrum of inhibition against several pathogens. The results indicated that the possible peptide-protein extract (PC) from UTNGt21A induces morphological and ultrastructural changes of Salmonella enterica subsp. enterica ATCC51741, compatible with its inhibitory potential. Genome characterization is the basis for further in vitro and in vivo studies to explore their use as antimicrobial producers or probiotic strains.
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Affiliation(s)
- Gabriela N Tenea
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Technical University of the North, Ibarra, Ecuador
| | - Pamela Ascanta
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Technical University of the North, Ibarra, Ecuador
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95
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Mining the Proteome of Toxoplasma Parasites Seeking Vaccine and Diagnostic Candidates. Animals (Basel) 2022; 12:ani12091098. [PMID: 35565525 PMCID: PMC9099775 DOI: 10.3390/ani12091098] [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: 02/25/2022] [Revised: 04/16/2022] [Accepted: 04/20/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary The One Health concept to toxoplasmosis highlights that the health of humans is closely related to the health of animals and our common environment. Toxoplasmosis outcomes might be severe and fatal in patients with immunodeficiency, diabetes, and pregnant women and infants. Consequently, the development of effective vaccine and diagnostic strategies is urgent for the elimination of this disease. Proteomics analysis has allowed the identification of key proteins that can be utilized in the development of novel disease diagnostics and vaccines. This work presents relevant proteins found in the proteome of the life cycle-specific stages of Toxoplasma parasites. In fact, it brings together the main functionality key proteins from Toxoplasma parasites coming from proteomic approaches that are most likely to be useful in improving the disease management, and critically proposes innovative directions to finally develop promising vaccines and diagnostics tools. Abstract Toxoplasma gondii is a pathogenic protozoan parasite that infects the nucleated cells of warm-blooded hosts leading to an infectious zoonotic disease known as toxoplasmosis. The infection outcomes might be severe and fatal in patients with immunodeficiency, diabetes, and pregnant women and infants. The One Health approach to toxoplasmosis highlights that the health of humans is closely related to the health of animals and our common environment. The presence of drug resistance and side effects, the further improvement of sensitivity and specificity of serodiagnostic tools and the potentiality of vaccine candidates to induce the host immune response are considered as justifiable reasons for the identification of novel targets for the better management of toxoplasmosis. Thus, the identification of new critical proteins in the proteome of Toxoplasma parasites can also be helpful in designing and test more effective drugs, vaccines, and diagnostic tools. Accordingly, in this study we present important proteins found in the proteome of the life cycle-specific stages of Toxoplasma parasites that are potential diagnostic or vaccine candidates. The current study might help to understand the complexity of these parasites and provide a possible source of strategies and biomolecules that can be further evaluated in the pathobiology of Toxoplasma parasites and for diagnostics and vaccine trials against this disease.
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96
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Fang H, Zhong C, Tang C. Predicting protein–protein interactions between banana and Fusarium oxysporum f. sp. cubense race 4 integrating sequence and domain homologous alignment and neural network verification. Proteome Sci 2022; 20:4. [PMID: 35351140 PMCID: PMC8962045 DOI: 10.1186/s12953-022-00186-2] [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: 10/30/2021] [Accepted: 03/06/2022] [Indexed: 11/18/2022] Open
Abstract
Background The pathogen of banana Fusarium oxysporum f. sp. cubense race 4(Foc4) infects almost all banana species, and it is the most destructive. The molecular mechanism of the interactions between Fusarium oxysporum and banana still needs to be further investigated. Methods We use both the interolog and domain-domain method to predict the protein–protein interactions (PPIs) between banana and Foc4. The predicted protein interaction sequences are encoded by the conjoint triad and autocovariance method respectively to obtain continuous and discontinuous information of protein sequences. This information is used as the input data of the neural network model. The Long Short-Term Memory (LSTM) neural network five-fold cross-validation and independent test methods are used to verify the predicted protein interaction sequences. To further confirm the PPIs between banana and Foc4, the GO (Gene Ontology) and KEGG (Kyoto Encylopedia of Genes and Genomics) functional annotation and interaction network analysis are carried out. Results The experimental results show that the PPIs for banana and foc4 predicted by our proposed method may interact with each other in terms of sequence structure, GO and KEGG functional annotation, and Foc4 protein plays a more active role in the process of Foc4 infecting banana. Conclusions This study obtained the PPIs between banana and Foc4 by using computing means for the first time, which will provide data support for molecular biology experiments. Supplementary Information The online version contains supplementary material available at 10.1186/s12953-022-00186-2.
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97
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Altimira F, Arias-Aravena M, Jian L, Real N, Correa P, González C, Godoy S, Castro JF, Zamora O, Vergara C, Vitta N, Tapia E. Genomic and Experimental Analysis of the Insecticidal Factors Secreted by the Entomopathogenic Fungus Beauveria pseudobassiana RGM 2184. J Fungi (Basel) 2022; 8:253. [PMID: 35330256 PMCID: PMC8952764 DOI: 10.3390/jof8030253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
The entomopathogenic fungus Beauveria pseudobassiana strain RGM 2184 can reach a maximum efficacy of 80% against the quarantine pest Lobesia botrana in field assays. In this study, the RGM 2184 genome was sequenced, and genome mining analyses were performed to predict the factors involved in its insecticidal activity. Additionally, the metabolic profiling of the RMG 2184 culture's supernatants was analyzed by mass spectrometry, and the insecticidal activity from one of these extracts was evaluated in Galleria mellonella larvae. The genome analysis resulted in 114 genes encoding for extracellular enzymes, four biosynthetic gene clusters reported as producers of insecticidal and bactericidal factors (oosporein, beauvericin, desmethylbassianin, and beauveriolide), 20 toxins, and at least 40 undescribed potential biocontrol factors (polyketides and nonribosomal peptides). Comparative genomic analysis revealed that 65-95% of these genes are Beauveria genus-specific. Metabolic profiling of supernatant extracts from RGM 2184 cultures exhibited secondary metabolites such as beauveriolide, oosporein, inflatin C, and bassiatin. However, a number of detected metabolites still remain undescribed. The metabolite extract caused 79% mortality of Galleria mellonella larvae at 28 days. The results of this research lay the groundwork for the study of new insecticidal molecules.
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Affiliation(s)
- Fabiola Altimira
- Laboratorio de Entomología y Biotecnología, Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, Chile; (M.A.-A.); (N.R.); (P.C.); (S.G.); (N.V.); (E.T.)
| | - Matias Arias-Aravena
- Laboratorio de Entomología y Biotecnología, Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, Chile; (M.A.-A.); (N.R.); (P.C.); (S.G.); (N.V.); (E.T.)
| | - Ling Jian
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Nicolas Real
- Laboratorio de Entomología y Biotecnología, Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, Chile; (M.A.-A.); (N.R.); (P.C.); (S.G.); (N.V.); (E.T.)
| | - Pablo Correa
- Laboratorio de Entomología y Biotecnología, Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, Chile; (M.A.-A.); (N.R.); (P.C.); (S.G.); (N.V.); (E.T.)
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile;
| | - Sebastián Godoy
- Laboratorio de Entomología y Biotecnología, Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, Chile; (M.A.-A.); (N.R.); (P.C.); (S.G.); (N.V.); (E.T.)
| | - Jean Franco Castro
- Banco de Recursos Genéticos Microbianos, Instituto de Investigaciones Agropecuarias, INIA, Chillán 3800062, Chile;
| | - Olga Zamora
- Laboratorio de Materias Primas y Alimentos, Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, Chile; (O.Z.); (C.V.)
| | - Cristina Vergara
- Laboratorio de Materias Primas y Alimentos, Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, Chile; (O.Z.); (C.V.)
| | - Nancy Vitta
- Laboratorio de Entomología y Biotecnología, Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, Chile; (M.A.-A.); (N.R.); (P.C.); (S.G.); (N.V.); (E.T.)
| | - Eduardo Tapia
- Laboratorio de Entomología y Biotecnología, Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, Chile; (M.A.-A.); (N.R.); (P.C.); (S.G.); (N.V.); (E.T.)
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98
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Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI, Tsirigos KD, Winther O, Brunak S, von Heijne G, Nielsen H. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat Biotechnol 2022; 40:1023-1025. [PMID: 34980915 PMCID: PMC9287161 DOI: 10.1038/s41587-021-01156-3] [Citation(s) in RCA: 828] [Impact Index Per Article: 414.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/08/2021] [Indexed: 11/09/2022]
Abstract
Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects all five SP types and is applicable to metagenomic data. A new version of SignalP predicts all types of signal peptides.
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Affiliation(s)
- Felix Teufel
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - José Juan Almagro Armenteros
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Magnús Halldór Gíslason
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen, Denmark
| | - Silas Irby Pihl
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Ole Winther
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen, Denmark.,Department of Biology, Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.,Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Henrik Nielsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
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99
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Abstract
Strawberry species (Fragaria spp.) are known as the “queen of fruits” and are cultivated around the world. Over the past few years, eight strawberry genome sequences have been released. The reuse of these large amount of genomic data, and the more large-scale comparative analyses are very challenging to both plant biologists and strawberry breeders. To promote the reuse and exploration of strawberry genomic data and enable extensive analyses using various bioinformatics tools, we have developed the Genome Database for Strawberry (GDS). This platform integrates the genome collection, storage, integration, analysis, and dissemination of large amounts of data for researchers engaged in the study of strawberry. We collected and formatted the eight published strawberry genomes. We constructed the GDS based on Linux, Apache, PHP and MySQL. Different bioinformatic software were integrated. The GDS contains data from eight strawberry species, as well as multiple tools such as BLAST, JBrowse, synteny analysis, and gene search. It has a designed interface and user-friendly tools that perform a variety of query tasks with a few simple operations. In the future, we hope that the GDS will serve as a community resource for the study of strawberries.
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100
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Schlachter CR, O’Malley A, Grimes LL, Tomashek JJ, Chruszcz M, Lee LA. Purification, Characterization, and Structural Studies of a Sulfatase from Pedobacter yulinensis. Molecules 2021; 27:87. [PMID: 35011319 PMCID: PMC8746622 DOI: 10.3390/molecules27010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Sulfatases are ubiquitous enzymes that hydrolyze sulfate from sulfated organic substrates such as carbohydrates, steroids, and flavones. These enzymes can be exploited in the field of biotechnology to analyze sulfated metabolites in humans, such as steroids and drugs of abuse. Because genomic data far outstrip biochemical characterization, the analysis of sulfatases from published sequences can lead to the discovery of new and unique activities advantageous for biotechnological applications. We expressed and characterized a putative sulfatase (PyuS) from the bacterium Pedobacter yulinensis. PyuS contains the (C/S)XPXR sulfatase motif, where the Cys or Ser is post-translationally converted into a formylglycine residue (FGly). His-tagged PyuS was co-expressed in Escherichia coli with a formylglycine-generating enzyme (FGE) from Mycobacterium tuberculosis and purified. We obtained several crystal structures of PyuS, and the FGly modification was detected at the active site. The enzyme has sulfatase activity on aromatic sulfated substrates as well as phosphatase activity on some aromatic phosphates; however, PyuS did not have detectable activity on 17α-estradiol sulfate, cortisol 21-sulfate, or boldenone sulfate.
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Affiliation(s)
- Caleb R. Schlachter
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC 29063, USA; (C.R.S.); (L.L.G.); (J.J.T.)
| | - Andrea O’Malley
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA;
| | - Linda L. Grimes
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC 29063, USA; (C.R.S.); (L.L.G.); (J.J.T.)
| | - John J. Tomashek
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC 29063, USA; (C.R.S.); (L.L.G.); (J.J.T.)
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA;
| | - L. Andrew Lee
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC 29063, USA; (C.R.S.); (L.L.G.); (J.J.T.)
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