1
|
Weng T, Chen G, Li N, Sirimanapong W, Huang T, Chen J, Xia L. Identifying the in vivo-induced antigenic genes is a strategy to develop DNA vaccine against Nocardia seriolae in hybrid snakehead (Channa maculata ♀ × Channa argus ♂). FISH & SHELLFISH IMMUNOLOGY 2024; 147:109410. [PMID: 38309489 DOI: 10.1016/j.fsi.2024.109410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/26/2023] [Accepted: 01/25/2024] [Indexed: 02/05/2024]
Abstract
Nocardia seriolae has been identified as the causative agent of fish nocardiosis, resulting in serious economic losses in aquaculture. With an aim to screen potential candidates for vaccine development against N. seriolae, the in vivo-induced genes of N. seriolae in hybrid snakehead (Channa maculate ♀ × Channa argus ♂) model were profiled via in vivo-induced antigen technology (IVIAT) in the present study, and 6 in vivo-induced genes were identified as follows: IS701 family transposase (is701), membrane protein insertase YidC (yidC), ergothioneine biosynthesis glutamate-cysteine ligase (egtA), molybdopterin respectively-dependent oxidoreductase (mol), phosphoketolase family protein (Ppl), hypothetical protein 6747 (hp6747). Additionally, the yidC was inserted into eukaryotic expression vector pcDNA3.1-myc-his-A to construct a DNA vaccine named as pcDNA-YidC to evaluate immunoprotection in hybrid snakehead after artificial challenge with N. serioale. Results showed that the transcription of yidC was detected in spleen, trunk kidney, muscle and liver in vaccinated fish, suggesting that this antigenic gene can be recombinantly expressed in fish. Meanwhile, indexes of humoral immunity were evaluated in the vaccinated fish through assessing specific-antibody IgM and serum enzyme activities, including lysozyme (LZM), superoxide dismutase (SOD), acid phosphatase (ACP) and alkaline phosphatase (AKP). Quantitative real-time PCR analysis indicated that pcDNA-YidC DNA vaccine could notably enhance the expression of immune-related genes (CD4、CD8α、MHCIIα、TNFα、IL-1β and MHCIα) in 4 tissues (spleen, trunk kidney, muscle and liver) of the vaccinated fish. Finally, an immuno-protection with a relative survival rate of 65.71 % was displayed in vaccinated fish in comparison to the control groups. Taken together, these results indicate that pcDNA-YidC DNA vaccine could boost strong immune responses in hybrid snakehead and show preferably protective efficacy against N. seriolae, indicating that IVIAT is a helpful strategy to screen the highly immunogenic antigens for vaccine development against fish nocardiosis.
Collapse
Affiliation(s)
- Tingting Weng
- Fisheries College of Guangdong Ocean University, Shenzhen Institute of Guangdong Ocean University, Guanedong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong, China
| | - Guoquan Chen
- Fisheries College of Guangdong Ocean University, Shenzhen Institute of Guangdong Ocean University, Guanedong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong, China
| | - Na Li
- Fisheries College of Guangdong Ocean University, Shenzhen Institute of Guangdong Ocean University, Guanedong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong, China
| | - Wanna Sirimanapong
- Veterinary Aquatic Animal Research & Health Care Unit, Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon-pathom, Thailand
| | - Ting Huang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Science, Nanning, 530021, Guangxi, China
| | - Jianlin Chen
- Fisheries College of Guangdong Ocean University, Shenzhen Institute of Guangdong Ocean University, Guanedong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong, China.
| | - Liqun Xia
- Fisheries College of Guangdong Ocean University, Shenzhen Institute of Guangdong Ocean University, Guanedong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Guangdong, China.
| |
Collapse
|
2
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
3
|
Filloux A. Bacterial protein secretion systems: Game of types. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35536734 DOI: 10.1099/mic.0.001193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.
Collapse
Affiliation(s)
- Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| |
Collapse
|
4
|
Fujikawa K, Mori S, Nishiyama KI, Shimamoto K. A bacterial glycolipid essential for membrane protein integration. Adv Carbohydr Chem Biochem 2022; 81:95-129. [DOI: 10.1016/bs.accb.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
5
|
Mishra S, Brady LJ. The Cytoplasmic Domains of Streptococcus mutans Membrane Protein Insertases YidC1 and YidC2 Confer Unique Structural and Functional Attributes to Each Paralog. Front Microbiol 2021; 12:760873. [PMID: 34795653 PMCID: PMC8595059 DOI: 10.3389/fmicb.2021.760873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Integral and membrane-anchored proteins are pivotal to survival and virulence of the dental pathogen, Streptococcus mutans. The bacterial chaperone/insertase, YidC, contributes to membrane protein translocation. Unlike Escherichia coli, most Gram-positive bacteria contain two YidC paralogs. Herein, we evaluated structural features that functionally delineate S. mutans YidC1 and YidC2. Bacterial YidCs contain five transmembrane domains (TMD), two cytoplasmic loops, and a cytoplasmic tail. Because S. mutans YidC1 (SmYidC1) and YidC2 (SmYidC2) cytoplasmic domains (CD) are less well conserved than are TMD, we engineered ectopic expression of the 14 possible YidC1-YidC2 CD domain swap combinations. Growth and stress tolerance of each was compared to control strains ectopically expressing unmodified yidC1 or yidC2. Acid and osmotic stress sensitivity are associated with yidC2 deletion. Sensitivity to excess zinc was further identified as a ΔyidC1 phenotype. Overall, YidC1 tolerated CD substitutions better than YidC2. Preferences toward particular CD combinations suggested potential intramolecular interactions. In silico analysis predicted salt-bridges between C1 and C2 loops of YidC1, and C1 loop and C-terminal tail of YidC2, respectively. Mutation of contributing residues recapitulated ΔyidC1- and ΔyidC2-associated phenotypes. Taken together, this work revealed the importance of cytoplasmic domains in distinct functional attributes of YidC1 and YidC2, and identified key residues involved in interdomain interactions.
Collapse
Affiliation(s)
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
| |
Collapse
|
6
|
Wojciechowska N, Bagniewska-Zadworna A, Minicka J, Michalak KM, Kalemba EM. Localization and Dynamics of the Methionine Sulfoxide Reductases MsrB1 and MsrB2 in Beech Seeds. Int J Mol Sci 2021; 22:E402. [PMID: 33401671 PMCID: PMC7795007 DOI: 10.3390/ijms22010402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 11/24/2022] Open
Abstract
Beech seeds are produced irregularly, and there is a need for long-term storage of these seeds for forest management practices. Accumulated reactive oxygen species broadly oxidize molecules, including amino acids, such as methionine, thereby contributing to decreased seed viability. Methionine oxidation can be reversed by the activity of methionine sulfoxide reductases (Msrs), which are enzymes involved in the regulation of many developmental processes and stress responses. Two types of Msrs, MsrB1 and MsrB2, were investigated in beech seeds to determine their abundance and localization. MsrB1 and MsrB2 were detected in the cortical cells and the outer area of the vascular cylinder of the embryonic axes as well as in the epidermis and parenchyma cells of cotyledons. The abundances of MsrB1 and MsrB2 decreased during long-term storage. Ultrastructural analyses have demonstrated the accumulation of these proteins in protein storage vacuoles and in the cytoplasm, especially in close proximity to the cell membrane. In silico predictions of possible Msr interactions supported our findings. In this study, we investigate the contribution of MsrB1 and MsrB2 locations in the regulation of seed viability and suggest that MsrB2 is linked with the longevity of beech seeds via association with proper utilization of storage material.
Collapse
Affiliation(s)
- Natalia Wojciechowska
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.B.-Z.); (K.M.M.)
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.B.-Z.); (K.M.M.)
| | - Julia Minicka
- Department of Virology and Bacteriology, Institute of Plant Protection, Władysława Węgorka 20, 60-318 Poznań, Poland;
| | - Kornel M. Michalak
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.B.-Z.); (K.M.M.)
| | - Ewa M. Kalemba
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| |
Collapse
|