Genomics, Proteomics, and Antifungal Activity of Chitinase from the Antarctic Marine Bacterium Curtobacterium sp. CBMAI 2942
Abstract
:1. Introduction
2. Results
2.1. Sequencing, Assembly, and Taxonomic Affiliation of Marine Curtobacterium sp. CBMAI 2942 Genome
2.2. Genomic Potential for Chitin Degradation
2.3. Production of Chitinase in Liquid Medium
2.4. Optimization of Chitinase Production
2.5. Isolation and Proteomic Analysis of Chitinase
2.6. Antifungal Activity of Chitinase Produced by Curtobacterium sp. CBMAI 2942
3. Discussion
4. Materials and Methods
4.1. Bacterial Strain
4.2. Sequencing, Assembly, and Annotation of the Curtobacterium sp. CBMAI 2942 Genome
4.2.1. Genomic DNA Extraction and Sequencing
4.2.2. Assembly and Annotation
4.2.3. Phylogenomic Identification
4.3. Production of Chitinase in Liquid Medium
4.3.1. Cultivation Conditions
4.3.2. Determination of Biomass
4.3.3. Quantification of Total Proteins
4.3.4. Chitinase Enzyme Activity
- CGlc = concentration of N-acetylglucosamine (GlcNAc) determined by the standard curve.
- Vt = total volume in the enzymatic reaction (2 mL).
- PM = N-acetylglucosamine (GlcNAc) molecular mass (221.208 mg/mmol).
- Ve = volume of enzyme preparation used (1 mL).
- T = reaction time (6 h).
- Dil = dilution applied to the enzyme preparation.
4.3.5. Evaluation of the Optimal Growth Temperature
4.4. Statistical Optimization Design for Chitinase Production
4.4.1. Screening of Variables by Plackett–Burman Design
4.4.2. Central Composite Design
4.5. Separation by SDS-PAGE and Identification of Chitinases via Mass Spectrometry
4.6. Antifungal Activity of Chitinases
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sequence Data | Curtobacterium sp. CBMAI 2942 |
---|---|
Coverage (X) | 350 |
# Contigs | 1 |
Total compression | 3,685,083 |
Largest contig | 3,679,616 |
Smallest contig | 5467 |
N50 | 3,679,616 |
% CG | 71.48 |
% Completeness | 99.44 |
% Contamination | 0.76 |
Marine Bacterial Strain | Related Bacteria | ANIb (%) | dDDH (%) | Difference in G + C Content (%) |
---|---|---|---|---|
Curtobacterium sp. CBMAI 2942 | Curtobacterium luteum DSM 20542T | 87.71 | 33.60 | 0.22 |
Curtobacterium oceanosedimentum NS359 | 82.66 | 26.10 | 0.26 | |
Curtobacterium citreum DSM 20528T | 82.79 | 26.60 | 0.46 | |
Curtobacterium pusillum ATCC 19096T | 83.52 | 27.00 | 0.63 |
Bacterium | Gene ID | Gene Name | Start | Final | Size (pb) | COG ID | Function COG |
---|---|---|---|---|---|---|---|
Curtobacterium sp. CBMAI 2942 | >NODE_1_length_3679616_cov_83.786059_76 | Chitin binding | 91,936 | 93,246 | 1310 | COG3979 | ChBD of chitin binding (Chi C) |
>NODE_1_length_3679616_cov_83.786059_3152 | Chitin binding | 3,317,000 | 3,318,553 | 1553 | COG3979 | ChBD of chitin binding (Chi C) |
Assay | Colloidal Chitin (%) | Yeast Extract (g/L) | Peptone (g/L) | K2HPO4 (g/L) | KH2PO4 (g/L) | MgSO4·7H2O (g/L) | NH4NO3 (g/L) | NaCl (g/L) | pH | U/L (96 h) | U/L (120 h) |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 1 (3) | −1 (0.1) | −1 (0.1) | −1(0.2) | 1 (0.5) | −1 (0.1) | −1 (0.2) | 1 (1.8) | 1(8) | 28.18 | 28.96 |
2 | 1 (3) | 1 (0.5) | −1 (0.1) | −1(0.2) | −1 (0.1) | 1 (0.9) | −1 (0.2) | −1 (0.2) | 1(8) | 31.89 | 38.54 |
3 | 1 (3) | 1 (0.5) | 1 (0.5) | −1(0.2) | −1 (0.1) | −1 (0.1) | 1 (3.8) | −1 (0.2) | −1 (6) | 30.72 | 32.67 |
4 | 1 (3) | 1 (0.5) | 1 (0.5) | 1 (1.2) | −1 (0.1) | −1 (0.1) | −1 (0.2) | 1 (1.8) | −1 (6) | 28.18 | 29.15 |
5 | −1 (1) | 1 (0.5) | 1 (0.5) | 1 (1.2) | 1 (0.5) | −1 (0.1) | −1 (0.2) | −1 (0.2) | 1(8) | 28.96 | 30.52 |
6 | 1 (3) | −1 (0.1) | 1 (0.5) | 1 (1.2 | 1 (0.5) | 1 (0.9) | −1 (0.2) | −1 (0.2) | −1 (6) | 39.33 | 39.72 |
7 | −1 (1) | 1 (0.5) | −1 (0.1) | 1 (1.2) | 1 (0.5) | 1 (0.9) | 1 (3.8) | −1 (0.2) | −1 (6) | 30.52 | 32.09 |
8 | 1 (3) | −1 (0.1) | 1 (0.5) | −1(0.2) | 1 (0.5) | 1 (0.9) | 1 (3.8) | 1 (1.8) | −1 (6) | 44.22 | 46.76 |
9 | 1 (3) | 1 (0.5) | −1 (0.1) | 1 (1.2) | −1 (0.1) | 1 (0.9) | 1 (3.8) | 1 (1.8) | 1(8) | 27.98 | 28.18 |
10 | −1 (1) | 1 (0.5) | 1 (0.5) | −1(0.2) | 1 (0.5) | −1 (0.1) | 1 (3.8) | 1 (1.8) | 1(8) | 30.72 | 32.09 |
11 | −1 (1) | −1 (0.1) | 1 (0.5) | 1 (1.2) | −1 (0.1) | 1 (0.9) | −1 (0.2) | 1 (1.8) | 1(8) | 30.52 | 32.28 |
12 | 1 (3) | −1 (0.1) | −1 (0.1) | 1 (1.2) | 1 (0.5) | −1 (0.1) | 1 (3.8) | −1 (0.2) | 1(8) | 28.18 | 30.33 |
13 | −1 (1) | 1 (0.5) | −1 (0.1) | −1(0.2) | 1 (0.5) | 1 (0.9) | −1 (0.2) | 1 (1.8) | −1 (6) | 25.83 | 26.22 |
14 | −1 (1) | −1 (0.1) | 1 (0.5) | −1(0.2) | −1 (0.1) | 1 (0.9) | 1 (3.8) | −1 (0.2) | 1(8) | 26.81 | 32.09 |
15 | −1 (1) | −1 (0.1) | −1 (0.1) | 1 (1.2) | −1 (0.1) | −1 (0.1) | 1 (3.8) | 1 (1.8) | −1 (6) | 25.24 | 26.22 |
16 | −1 (1) | −1 (0.1) | −1 (0.1) | −1(0.2) | −1 (0.1) | −1 (0.1) | −1 (0.2) | −1 (0.2) | −1 (6) | 26.02 | 28.57 |
17 | 0 (2) | 0 (0.3) | 0 (0.3) | 0 (0.7) | 0 (0.3) | 0 (0.5) | 0 (2.0) | 0 (1.0) | 0 (7) | 27.20 | 27.98 |
18 | 0 (2) | 0 (0.3) | 0 (0.3) | 0 (0.7) | 0 (0.3) | 0 (0.5) | 0 (2.0) | 0 (1.0) | 0 (7) | 27.78 | 28.18 |
19 | 0 (2) | 0 (0.3) | 0 (0.3) | 0 (0.7) | 0 (0.3) | 0 (0.5) | 0 (2.0) | 0 (1.0) | 0 (7) | 27.00 | 28.96 |
Assay | Colloidal Chitin (%) | Peptone (g/L) | KH2PO4 (g/L) | U/L (96 h) | U/L (120 h) |
---|---|---|---|---|---|
1 | (1.50) | (0.20) | (0.20) | 32.09 | 35.41 |
2 | (5.00) | (0.20) | (0.20) | 58.50 | 71.80 |
3 | (1.50) | (0.60) | (0.20) | 30.33 | 32.28 |
4 | (5.00) | (0.60) | (0.20) | 60.26 | 80.01 |
5 | (1.50) | (0.20) | (0.50) | 31.70 | 34.83 |
6 | (5.00) | (0.20) | (0.50) | 54.00 | 71.21 |
7 | (1.50) | (0.60) | (0.50) | 30.13 | 31.50 |
8 | (5.00) | (0.60) | (0.50) | 61.82 | 75.91 |
9 | (0.31) | (0.40) | (0.35) | 23.28 | 24.46 |
10 | (6.19) | (0.40) | (0.35) | 86.27 | 99.19 |
11 | (3.25) | (0.06) | (0.35) | 36.78 | 42.26 |
12 | (3.25) | (0.74) | (0.35) | 38.74 | 39.72 |
13 | (3.25) | (0.40) | (0.10) | 39.52 | 41.09 |
14 | (3.25) | (0.40) | (0.60) | 58.69 | 59.28 |
15 | (3.25) | (0.40) | (0.35) | 57.32 | 58.69 |
16 | (3.25) | (0.40) | (0.35) | 57.13 | 61.04 |
17 | (3.25) | (0.40) | (0.35) | 56.54 | 58.89 |
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Vasquez, Y.M.S.-C.; Cueva-Yesquen, L.G.; Duarte, A.W.F.; Rosa, L.H.; Valladão, R.; Lopes, A.R.; Costa Bonugli-Santos, R.; Oliveira, V.M.d. Genomics, Proteomics, and Antifungal Activity of Chitinase from the Antarctic Marine Bacterium Curtobacterium sp. CBMAI 2942. Int. J. Mol. Sci. 2024, 25, 9250. https://doi.org/10.3390/ijms25179250
Vasquez YMS-C, Cueva-Yesquen LG, Duarte AWF, Rosa LH, Valladão R, Lopes AR, Costa Bonugli-Santos R, Oliveira VMd. Genomics, Proteomics, and Antifungal Activity of Chitinase from the Antarctic Marine Bacterium Curtobacterium sp. CBMAI 2942. International Journal of Molecular Sciences. 2024; 25(17):9250. https://doi.org/10.3390/ijms25179250
Chicago/Turabian StyleVasquez, Yesenia Melissa Santa-Cruz, Luis Gabriel Cueva-Yesquen, Alysson Wagner Fernandes Duarte, Luiz Henrique Rosa, Rodrigo Valladão, Adriana Rios Lopes, Rafaella Costa Bonugli-Santos, and Valéria Maia de Oliveira. 2024. "Genomics, Proteomics, and Antifungal Activity of Chitinase from the Antarctic Marine Bacterium Curtobacterium sp. CBMAI 2942" International Journal of Molecular Sciences 25, no. 17: 9250. https://doi.org/10.3390/ijms25179250