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Kaneda K, Takeuchi Y, Yamanaka K, Hasebe F, Maruyama C, Hamano Y. Cell-penetrating activity of a short-chain ε-poly-l-α-lysine. J Biosci Bioeng 2024:S1389-1723(24)00169-5. [PMID: 38991881 DOI: 10.1016/j.jbiosc.2024.06.006] [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: 05/28/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024]
Abstract
Bacteria produce polycationic homopoly(amino acid)s, which are characterized by isopeptide backbones. We previously demonstrated that two representative bacterial polycationic isopeptides, ε-poly-l-α-lysine consisting of 25-35 l-α-lysine residues (ε-PαL25-35) and ε-poly-l-β-lysine consisting of l-β-lysine residues (ε-PβL4-13), were internalized into mammalian cells by both energy-independent direct penetration and energy-dependent endocytosis/macropinocytosis, and then diffused throughout the cytosol. In this study, we investigated the cell-penetrating activity of an ε-PαL short-chain derivative consisting of 5-14 l-α-lysine residues (ε-PαL5-14) to gain insight into the relationship between the isopeptide-chain length and the manner of cellular internalization. We prepared a conjugate of ε-PαL5-14 and a fluorescent dye (FAM) by click chemistry, and incubated the resulting polymer, ε-PαL5-14-FAM, with HeLa cells. Unlike ε-PαL25-35-FAM, ε-PαL5-14-FAM was internalized into cells only by energy-dependent endocytosis/macropinocytosis. Furthermore, a high concentration (>50 μM) was required for the internalization events. ε-PαL5-14 has a chain length almost equal to that of the membrane permeable ε-PβL4-13, which can enter cells at low concentrations. Considering that the basicity of the β-amino group is higher than that of α-amino acid at physiological pH, ε-PβL is expected to have a greater cell-penetrating capacity than ε-PαL, provided their isopeptide-chain lengths are similar, suggesting that a more extended chain derivative of ε-PβL would be more advantageous for cellular internalization of cargo proteins than ε-PαL25-35.
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Affiliation(s)
- Kohei Kaneda
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui 910-1195, Japan
| | - Yamato Takeuchi
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui 910-1195, Japan
| | - Kazuya Yamanaka
- Department of Life Science & Technology, Kansai University, Suita, Osaka 564-8680, Japan
| | - Fumihito Hasebe
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui 910-1195, Japan; Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui 910-1195, Japan
| | - Chitose Maruyama
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui 910-1195, Japan; Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui 910-1195, Japan.
| | - Yoshimitsu Hamano
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui 910-1195, Japan; Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui 910-1195, Japan.
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Qiu Y, Xu D, Lei P, Li S, Xu H. Engineering functional homopolymeric amino acids: from biosynthesis to design. Trends Biotechnol 2024; 42:310-325. [PMID: 37775417 DOI: 10.1016/j.tibtech.2023.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/08/2023] [Accepted: 08/31/2023] [Indexed: 10/01/2023]
Abstract
Homopolymeric amino acids (HPAs) are a class of microbial polymers that can be classified into two categories: anionic and cationic HPAs. Notable examples include γ-poly-glutamic acid (γ-PGA) and ε-poly-L-lysine (ε-PL) that have wide-ranging applications in medicine, food, and agriculture. The primary method of manufacture is through microbial synthesis. In recent decades significant efforts have been made to enhance the production of HPAs, specifically focusing on γ-PGA and ε-PL. We comprehensively review current advances in understanding the synthetic mechanisms as well as metabolic engineering and fermentation process techniques to improve the production of HPAs. In addition, we discuss the major challenges and solutions associated with desired structure regulation of HPAs and the development of novel structures.
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Affiliation(s)
- Yibin Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Delei Xu
- College of Biological and Food Engineering, Changshu Institute of Technology, 99 South Third Ring Road, Changshu 215500, PR China
| | - Peng Lei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China.
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; Nanjing Shineking Biotech Co. Ltd., Nanjing 210061, PR China.
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Patel KD, Gulick AM. Structural and functional insights into δ-poly-L-ornithine polymer biosynthesis from Acinetobacter baumannii. Commun Biol 2023; 6:982. [PMID: 37752201 PMCID: PMC10522769 DOI: 10.1038/s42003-023-05362-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Cationic homo-polyamino acid (CHPA) peptides containing isopeptide bonds of diamino acids have been identified from Actinomycetes strains. However, none has been reported from other bacteria. Here, we report a δ-poly-L-ornithine synthetase from Acinetobacter baumannii, which we name PosA. Surprisingly, structural analysis of the adenylation domain and biochemical assay shows L-ornithine as the substrate for PosA. The product from the enzymatic reaction was purified and identified as poly-L-ornithine composed of 7-12 amino acid units. Chemical labeling of the polymer confirmed the isopeptide linkage of δ-poly-L-ornithine. We examine the biological activity of chemically synthesized 12-mer δ-poly-L-ornithine, illustrating that the polymer may act as an anti-fungal agent. Structures of the isolated adenylation domain from PosA are presented with several diamino acids and biochemical assays identify important substrate binding residues. Structurally-guided genome-mining led to the identification of homologs with different substrate binding residues that could activate additional substrates. A homolog from Bdellovibrionales sp. shows modest activity with L-arginine but not with any diamino acids observed to be substrates for previously examined CHPA synthetases. Our study indicates the possibility that additional CHPAs may be produced by various microbes, supporting the further exploration of uncharacterized natural products.
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Affiliation(s)
- Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, 14203, USA
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, 14203, USA.
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First direct evidence for direct cell-membrane penetrations of polycationic homopoly(amino acid)s produced by bacteria. Commun Biol 2022; 5:1132. [PMID: 36289442 PMCID: PMC9606270 DOI: 10.1038/s42003-022-04110-4] [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: 06/03/2022] [Accepted: 10/13/2022] [Indexed: 11/08/2022] Open
Abstract
Bacteria produce polycationic homopoly(amino acid)s, which are characterized by isopeptide backbones. Although the biological significance of polycationic homopoly(amino acid)s remains unclear, increasing attention has recently been focused on their potential use to achieve cellular internalization. Here, for the first time, we provide direct evidence that two representative bacterial polycationic isopeptides, ε-poly-L-α-lysine (ε-PαL) and ε-oligo-L-β-lysine (ε-OβL), were internalized into mammalian cells by direct cell-membrane penetration and then diffused throughout the cytosol. In this study, we used clickable ε-PαL and ε-OβL derivatives carrying a C-terminal azide group, which were enzymatically produced and then conjugated with a fluorescent dye to analyze subcellular localization. Interestingly, fluorescent proteins conjugated with the clickable ε-PαL or ε-OβL were also internalized into cells and diffused throughout the cytosol. Notably, a Cre recombinase conjugate with ε-PαL entered cells and mediated the Cre/loxP recombination, and ε-PαL was found to deliver a full-length IgG antibody to the cytosol and nucleus.
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Yamanaka K, Fukumoto H, Yoshimura N, Arakawa K, Kato Y, Hamano Y, Oikawa T. Discovery of a Polyamino Acid Antibiotic Solely Comprising l-β-Lysine by Potential Producer Prioritization-Guided Genome Mining. ACS Chem Biol 2022; 17:171-180. [PMID: 34886659 DOI: 10.1021/acschembio.1c00832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While the genome mining approach has enabled the rational exploration of untapped bioactive natural products, in silico identifications of their biosynthetic genes are often unconnected to the actual production of the corresponding molecules in native strains due to the genetic dormancy. We report here the rational discovery of an unexplored cationic homo polyamino acid (CHPA) antibiotic by potential producer prioritization-guided genome mining. Mining the genome of γ-poly-d-diaminobutyric acid (poly-d-Dab)-producing Streptoalloteichus hindustanus NBRC 15115, which was selected based on the finding that the known CHPAs are universally co-produced in pairs, identified a putative CHPA synthetase, PblA, as a potential candidate being expressed actively. Bioinformatic and biochemical analyses of PblA provided the critical clue that its polymer product could be an unusual CHPA consisting of l-β-lysine. Instrumental analyses of the metabolites from S. hindastanus indeed revealed the production of an unprecedented linear CHPA, ε-poly-l-β-lysine, concomitantly with poly-d-Dab. The CHPA we discovered exerted excellent antimicrobial activity against a broad spectrum of microorganisms, including bacteria and fungi, and was revealed to show resistance against nonspecific proteolytic enzymes. This study marks the first report of the efficacy of the strain prioritization-guided genome mining strategy for the discovery of bioactive CHPAs.
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Affiliation(s)
- Kazuya Yamanaka
- Department of Life Science & Technology, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan
- Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan
| | - Hibiki Fukumoto
- Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan
| | - Naoki Yoshimura
- Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan
| | - Kenji Arakawa
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Yasuo Kato
- Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa,
Imizu, Toyama 939-0398, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Tadao Oikawa
- Department of Life Science & Technology, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan
- Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan
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