Identification of Antimicrobial Peptides from Nibribacter radioresistens, a UV and Gamma Radiation Tolerant Bacterium
Abstract
:1. Introduction
2. Materials and Methods
2.1. Medium and Bacterial Strains Employed for This Study
2.2. N. radioresistens Genome Sequencing
2.3. Bioinformatic Analysis for Identification of AMPs from the N. radioresistens Genome
2.4. Exploration of AMPs Gene Expression Through Transcriptomic Analysis
2.5. N. radioresistens AMPs Gene Cloning and Peptide Synthesis
2.6. Evaluation of Antibacterial Activity of Cell-Free Supernatants and Synthetic Peptides
2.7. Statistical Analysis
3. Results and Discussion
3.1. The Nibribacter radioresistens Genome Includes Various AMP Genes
3.2. Transcriptomic Results of AMP Candidates from the N. radioresistens Genome
3.3. Antibacterial Activity of Cloned AMPs from the N. radioresistens Genome
3.4. Antibacterial Activity of Synthetic AMPs from the N. radioresistens Genome
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Forward | Reverse | ||
---|---|---|---|
Oligonucleotide Name | Nucleotide Seq | Oligonucleotide Name | Nucleotide Seq |
NB_AMP1-F | AAGTGGTGCGCGTCATAAAG | NB_AMP1-R | TCAAAGTCTGGCGTTTACGG |
NB_AMP2-F | AGTCCATGATGTGCGTGAAC | NB_AMP2-R | ATCAGGTTGCAACGGCCTAA |
NB_AMP3-F | GACGCCCAAAAAAGTTGACG | NB_AMP3-R | GCAAACATGATGGCTGCCTA |
NB_AMP4-F | AGCCCTGAAAGCTCTATCAAAG | NB_AMP4-R | CAGCAAAGCAAAGCTGCTCA |
NB_AMP5-F | GGCAACATAAGCTTCCTCTG | NB_AMP5-R | TGTATGAGATTGGAGCAGGA |
NB_AMP6-F | ACTGGAAGCCGATGATCATG | NB_AMP7-R | TGGCTCATGCCTTTGATTGG |
NB_AMP7-F | TTTACGACTACCTCACCACC | NB_AMP6-R | AGTTGGTGTATGTGGGCTTC |
NB_AMP8-F | TTACGACCTCTCTTAGCTCC | NB_AMP8-R | TAACAGAATTGGGGACGCAC |
NB_AMP9-F | CAGAGACGTGATTCCTTTCC | NB_AMP9-R | TTCATAGCGGTTGCGGTTAG |
NB_AMP10-F | ATCCCAAAGACCACAGTACC | NB_AMP10-R | AAGAGCCGATGATGGTAGAC |
NB_AMP11-F | AAGCTTATCATTACCCACCCTA | NB_AMP11-R | CTGACTGCAAATGCTGCAAC |
AMP Name | ORF Sequences * | Homologous AMPs | Synthesized AMPs | ||||
---|---|---|---|---|---|---|---|
Homolog Name | Identities/ Positives (%) | Amino Acid Sequences | Amino Acid Number | pI | MW | ||
NB_AMP1 | MENHTGNTSSNRMMTGMFKDRESAERAYNALHSRGYSKDDVNVIMSDDARKRHFSDSHNNDTELGDKALEGAGAGSAIGGTLGAIVGAIAAIGTSVALPGLGLVIAGPLAAGLAGAGAGGLTGGLLGALVGSGIPEDRAKVYESGVKEGNIVMG | Leptoglycin | 71/79 | - | - | - | - |
NB_AMP2 | MAKRNKKYLESADPVCGLCEREVGFTTLHHLIPREEGGKHGPTVPLCQPCHSTIHLTYTNKELAVLYNNVHALRASEGLQKYLSWVKNKRLDKITNRRGKGNRKR | Melittin | 57/71 | GLQKYLSWVKNKRL | 14 | 10.46 | 1733.09 |
NB_AMP3 | MKKITSIWLAAAFGFCMITSPLAAQDTTKVQETNKEKAKHGTHQVGHGTKEVGKGTKKVVVAGAKATGKGAKKAGKAVKKTVKKGVDKVD | Cecropin-B1 | 50/64 | KGAKKAGKAVKKTVKK | 16 | 10.85 | 1670.12 |
NB_AMP4 | MDTYNLKPENMRAPEHLNEAEARKSLEELDAKIKVLQGRAHATAADSHHTYHEHIAALEAKRALIAQKLENSTTATDSTWQEIKNSLEDLSDSIKKLF | Caerin-4.3 | 53/73 | WQEIKNSLEDLSDSI | 15 | 3.92 | 1776.92 |
NB_AMP5 | MTSNTLSSIASLLKKLISRLTGPTLQPIPVPVRQQPNR | H/V-peptide | 67/83 | NTLSSIASLLKK | 12 | 10.00 | 1274.52 |
NB_AMP6 | MKDNQKDQQSSNLGSTTGGSMGNTGASGSTGSGMGSSSSSSGMSSGSSGMSGSTGSMGSGTSGSGLSGGTSGSGMSGSSSGMSGSTGSTSKKGSSSLTSSKGTSGSSSTLSAGSTDKKSSTSKSSTPKASTSKSGSTSKSGKSSSSKSGSSASNSSKMGQDNDSMMGGQSDSMRNMGGGQYNQGGYGSQGGDYGQGGYGQGSMGGGYG | NLP-30 | 49/60 | GQYNQGGYGSQGGDYGQGGYGQGSMGGGYG | 30 | 3.80 | 2864.87 |
NB_AMP7 | MKDNQKDQQSSNLGSTTGGSMGNTGASGSTGSGMGSSSSSSGMSSGSSGMSGSTGSMGSGTSGSGLSGGTSGSGMSGSSSGMSGSTGSTSKKGSSSLTSSKGTSGSSSTLSAGSTDKKSSTSKSSTPKASTSKSGSTSKSGKSSSSKSGSSASNSSKMGQDNDSMMGGQSDSMRNMGGGQYNQGGYGSQGGDYGQGGYGQGSMGGGYGQQHGESWGQGGSNYGQGGYGSSMGGNMGGSNYGQGGYGGQGSMG | NLP-29 | 51/55 | - | - | - | - |
NB_AMP8 | MQIASVYTHQLVSNYKLLSNSLNILLKIEGICI | Hemoglobin subunit alpha | 62/85 | NYKLLSNSLNILL | 13 | 8.59 | 1504.79 |
NB_AMP9 | MLKKYATSLLLVLALFVGSAQAQSSQDKEKEKKELAKQKAAEKKAEGLAKAQAAKEKEKAKAAAIKEKEAAKKAADKEKAAAAKAKEQQKKEAAKQKALAAKEKEKAKAAEAKQKAAAKKLAAKEKAAAAKEKEAAKKAAAKEKKKA | DBAASP_471 | 56/67 | KKLAAKEKAAAAKEKEAAKKAAAKEKK | 27 | 10.08 | 2839.42 |
NB_AMP10 | MSDRFRDTYRIPSARLQDWDYGWNAAYFVTICTKDKQHFFGRFKKEKWSCLRLDNWLKDFGKRFQPISHLFY | DBAASP_6715 | 78/100 | FFGRFKKEK | 9 | 10.29 | 1186.42 |
NB_AMP11 | MTEETTLLKNYSDQEKGAYLGALATIASADGTVTEDELTFLRLLGEAAELPASLEQEVESIAKNPSQISLQKCLDVLKASDLRFSFVTDLISFAKSDGEYSPEEQQRIGEIGQYLGIDQKQFSILDQFVDKANQAQQQGEDPTSQSFLNKSGFGDMFKKSGISPGMVTGMLGILAPMVISGMMRRKGGRSMGMGGGMMGGMGGGLGGLLGGLLGGGMMSRGGMYGGGRTGGLGSMASILGGLAGRSRYGGMGSGGLGGLLGGILGGGRRGGGTGW | Acanthoscurrin-1 | 54/60 | - | - | - | - |
Sample | Total Reads | Mapped_Reads | Mapping_Rate% | Count (>0) | Exp (>1) |
---|---|---|---|---|---|
Nibribacter_1 | 69,515,047 | 11,295,952 | 16.25 | 3797 | 3797 |
Nibribacter_2 | 59,667,108 | 2,588,387 | 4.34 | 3797 | 3797 |
SeqName | AMP Name | Nibribacter_1.c | Nibribacter_2.c | Nibribacter_1.e | Nibribacter_2.e |
---|---|---|---|---|---|
>MLDJCCKF_00064 | NB_AMP1 | 14,665.99 | 1832.39 | 2491.731 | 368.873 |
>MLDJCCKF_00258 | NB_AMP2 | 838 | 828.57 | 142.375 | 166.797 |
>MLDJCCKF_00361 | NB_AMP3 | 4062.06 | 1139.23 | 690.138 | 229.334 |
>MLDJCCKF_00464 | NB_AMP4 | 2212.92 | 1031.13 | 375.972 | 207.572 |
>MLDJCCKF_01600 | NB_AMP5 | 39,418.47 | 10,317.65 | 6697.144 | 2077.011 |
>MLDJCCKF_01708 | NB_AMP6 | 1738.38 | 877.3 | 295.348 | 176.606 |
>MLDJCCKF_01884 | NB_AMP7 | 6896.51 | 3234.09 | 1171.707 | 651.043 |
>MLDJCCKF_02400 | NB_AMP8 | 136,561.28 | 4190.21 | 23,201.575 | 843.517 |
>MLDJCCKF_02565 | NB_AMP9 | 1294.13 | 1079.39 | 219.871 | 217.289 |
>MLDJCCKF_02663 | NB_AMP10 | 1105.5 | 542.04 | 187.824 | 109.116 |
>MLDJCCKF_02732 | NB_AMP11 | 546.7 | 472.2 | 92.884 | 95.058 |
Synthetic Peptides | NB_AMP2 | NB_AMP3 | NB_AMP4 | NB_AMP5 | NB_AMP6 | NB_AMP8 | NB_AMP9 | NB_AMP10 |
---|---|---|---|---|---|---|---|---|
E. coli | 0.17 mg/mL (0.10 mmol/mL) | 3.43 mg/mL (2.05 mmol/mL) | 4.96 mg/mL (2.79 mmol/mL) | 10.21 mg/mL (8.01 mmol/mL) | 9.43 mg/mL (3.29 mmol/mL) | - | - | 2.60 mg/mL (2.19 mmol/mL) |
S. aureus | 0.23 mg/mL (0.13 mmol/mL) | 2.88 mg/mL (1.73 mmol/mL) | 2.95 mg/mL (1.66 mmol/mL) | 3.24 mg/mL (2.55 mmol/mL) | 5.83 mg/mL (2.04 mmol/mL) | 8.36 mg/mL (5.55 mmol/mL) | 5.05 mg/mL (1.78 mmol/mL) | 2.11 mg/mL (1.78 mmol/mL) |
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Kim, S.W.; Bang, W.Y. Identification of Antimicrobial Peptides from Nibribacter radioresistens, a UV and Gamma Radiation Tolerant Bacterium. Genes 2025, 16, 353. https://doi.org/10.3390/genes16030353
Kim SW, Bang WY. Identification of Antimicrobial Peptides from Nibribacter radioresistens, a UV and Gamma Radiation Tolerant Bacterium. Genes. 2025; 16(3):353. https://doi.org/10.3390/genes16030353
Chicago/Turabian StyleKim, Sam Woong, and Woo Young Bang. 2025. "Identification of Antimicrobial Peptides from Nibribacter radioresistens, a UV and Gamma Radiation Tolerant Bacterium" Genes 16, no. 3: 353. https://doi.org/10.3390/genes16030353
APA StyleKim, S. W., & Bang, W. Y. (2025). Identification of Antimicrobial Peptides from Nibribacter radioresistens, a UV and Gamma Radiation Tolerant Bacterium. Genes, 16(3), 353. https://doi.org/10.3390/genes16030353