1
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Van Etten J, Stephens TG, Bhattacharya D. Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community. Environ Microbiol 2025; 27:e70048. [PMID: 39900484 PMCID: PMC11790422 DOI: 10.1111/1462-2920.70048] [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: 09/12/2024] [Revised: 01/15/2025] [Accepted: 01/18/2025] [Indexed: 02/05/2025]
Abstract
Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.
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Affiliation(s)
- Julia Van Etten
- Department of Biochemistry and Microbiology, RutgersThe State University of New JerseyNew BrunswickNew JerseyUSA
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, RutgersThe State University of New JerseyNew BrunswickNew JerseyUSA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, RutgersThe State University of New JerseyNew BrunswickNew JerseyUSA
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2
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Ngo KH, Distler ME, Evangelopoulos M, Ocampo TA, Ma Y, Minorik AJ, Mirkin CA. DNA Dendron Tagging as a Universal Way to Deliver Proteins to Cells. J Am Chem Soc 2025; 147:2129-2136. [PMID: 39812088 PMCID: PMC11755410 DOI: 10.1021/jacs.4c16205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2025]
Abstract
The use of proteins as intracellular probes and therapeutic tools is often limited by poor intracellular delivery. One approach to enabling intracellular protein delivery is to transform proteins into spherical nucleic acid (proSNA) nanoconstructs, with surfaces chemically modified with a dense shell of radially oriented DNA that can engage with cell-surface receptors that facilitate endocytosis. However, proteins often have a limited number of available reactive surface residues for DNA conjugation such that the extent of DNA loading and cellular uptake is restricted. Indeed, DNA surface density and sequence have been correlated with scavenger-receptor engagement, the first step of cellular internalization. Here, we report how branched DNA dendrons with dibenzocyclooctyne groups and proteins genetically engineered to include the noncanonical amino acid azido-phenylalanine for click chemistry can be used to synthesize hybrid DNA dendron-protein architectures that exhibit outstanding cellular internalization properties, without the need for extensive surface modification. In a head-to-head comparison, protein-DNA dendron structures (where DNA is concentrated in a local area) are taken up by cells more rapidly and to a greater extent than proSNAs (where the DNA is evenly distributed). Also, protein-G-rich dendron structures show enhanced uptake compared to protein-T-rich dendron structures, highlighting the importance of oligonucleotide sequence on nanoconjugate uptake. Finally, a generalizable method for chemically tagging proteins with dendrons that does not require mutagenesis is described. When a range of proteins, spanning 42 to 464 kDa, were modified through surface lysines with this method, a significant increase in their cellular uptake (up to 17-fold) compared to proteins that are not coupled to a DNA dendron was observed.
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Affiliation(s)
- Kathleen H. Ngo
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
| | - Max E. Distler
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
| | - Michael Evangelopoulos
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
| | - Tonatiuh A. Ocampo
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois, 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
| | - Yinglun Ma
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
| | - Andrew J. Minorik
- Department of Neurobiology, Northwestern University, Evanston, Illinois, 60208, United States
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
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3
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Wanarska M, Pawlak-Szukalska A, Rosińska A, Kozłowska-Tylingo K. Heterologous Production, Purification and Characterization of Two Cold-Active β-d-Galactosidases with Transglycosylation Activity from the Psychrotolerant Arctic Bacterium Arthrobacter sp. S3* Isolated from Spitsbergen Island Soil. Int J Mol Sci 2024; 25:13354. [PMID: 39769117 PMCID: PMC11677235 DOI: 10.3390/ijms252413354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 12/08/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025] Open
Abstract
Cold-adapted microorganisms possess cold-active enzymes with potential applications in different industries and research areas. In this study, two genes encoding β-d-galactosidases belonging to Glycoside Hydrolase families 2 and 42 from the psychrotolerant Arctic bacterium Arthrobacter sp. S3* were cloned, expressed in Escherichia coli and Komagataella phaffii, purified and characterized. The GH2 β-d-galactosidase is a tetramer with a molecular weight of 450 kDa, while the GH42 β-d-galactosidase is a 233 kDa trimer. The Bgal2 was optimally active at pH 7.5 and 22 °C and maintained 57% of maximum activity at 10 °C, whereas the Bgal42 was optimally active at pH 7.0 and 40 °C and exhibited 44% of maximum activity at 10 °C. Both enzymes hydrolyzed lactose and showed transglycosylation activity. We also found that 2 U/mL of the Bgal2 hydrolyzed 85% of lactose in milk within 10 h at 10 °C. The enzyme synthesized galactooligosaccharides, heterooligosaccharides, alkyl galactopyranosides and glycosylated salicin. The Bgal42 synthesized galactooligosaccharides and 20 U/mL of the enzyme hydrolyzed 72% of milk lactose within 24 h at 10 °C. The properties of Arthrobacter sp. S3* Bgal2 make it a candidate for lactose hydrolysis in the dairy industry and a promising tool for the glycosylation of various acceptors in the biomedical sector.
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Affiliation(s)
- Marta Wanarska
- Department of Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland; (A.P.-S.); (A.R.)
| | - Anna Pawlak-Szukalska
- Department of Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland; (A.P.-S.); (A.R.)
| | - Aleksandra Rosińska
- Department of Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland; (A.P.-S.); (A.R.)
| | - Katarzyna Kozłowska-Tylingo
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland;
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4
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Hu H, Peng Q, Tai J, Lu W, Liu J, Dan T. Unveiling the genetic basis and metabolic rewiring behind the galactose-positive phenotype in a Streptococcus thermophilus mutant. Microbiol Res 2024; 289:127894. [PMID: 39305781 DOI: 10.1016/j.micres.2024.127894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 09/01/2024] [Indexed: 11/02/2024]
Abstract
Streptococcus thermophilus (S. thermophilus) is a widely used starter culture in dairy fermentation, but most strains are galactose-negative and only metabolize glucose from lactose hydrolysis. In this study, we aimed to uncover the mechanisms underlying the acquisition of a stable galactose-positive (Gal+) phenotype in a mutant strain of S. thermophilus IMAU10636. By treating the wild-type strain with the mutagenic agent N-methyl-N-nitro-N-nitrosoguanidine, we successfully isolated a Gal+ mutant, S. thermophilus IMAU10636Y. Comparative enzyme activity assays revealed that the mutant exhibited higher β-galactosidase and galactokinase activities, but lower glucokinase and pyruvate kinase activities compared to the wild-type. High-performance liquid chromatography analysis confirmed the mutant's enhanced ability to utilize lactose and galactose, leading to increased glucose secretion. Integrated genome and transcriptomics analyses provided deeper insights into the underlying genetic and metabolic mechanisms. We found that the metabolism regulatory network of the glycolysis / Leloir pathway was altered in the mutant, possibly due to the upregulation of the gene expression in the galR-galK intergenic region. This likely led to increased RNA polymerase binding and transcription of the gal operon, ultimately promoting the Gal+ phenotype. Additionally, we identified a mutation in the scrR gene, encoding a LacI family transcriptional repressor, which also contributed to the Gal+ phenotype. These findings offer new perspectives on the metabolic rewiring and regulatory mechanisms that enable S. thermophilus to acquire the ability to metabolize galactose. This knowledge can inform strategies for engineering and selecting Gal+ strains with desirable fermentation characteristics for dairy applications.
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Affiliation(s)
- Haimin Hu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Qingting Peng
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Jiahui Tai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Wenhui Lu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Jinhui Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Tong Dan
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
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5
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Chang Y, Wang J, Guo H, Yao W, Xie H, Li L, Liu X. Temperature-dependent luminescent copper nanoclusters with noncovalent interactions for determination of β-galactosidase activity. Mikrochim Acta 2024; 191:768. [PMID: 39607597 DOI: 10.1007/s00604-024-06844-w] [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: 09/14/2024] [Accepted: 11/12/2024] [Indexed: 11/29/2024]
Abstract
The synthesis of a novel bidentate ligand-protected copper nanocluster via a solid-state strategy is reported. Single-crystal X-ray diffraction analysis result reveals that the copper nanocluster features an octahedral core (Cu6) coordinated by six ligands. Noncovalent interactions (C-H…π and π…π) exist between the copper nanoclusters. The copper nanocluster displays luminescence even at 250 °C. The luminescence intensity is linearly correlated with temperature changes. The copper nanocluster can assemble into luminescent nanosheets whose emission is quenched by 4-nitrophenol. Spectroscopic analysis and theoretical calculations results demonstrate that the inner filter effect and electron transfer cause the above quenching effect. A probe based on luminescent nanosheets was constructed for β-galactosidase activity determination. The linearity range is 3.3-91.8 U·L-1, and the limit of detection is 0.45 U·L-1. This probe was also evaluated for determination of the β-galactosidase activity in human serum via spiking experiments. The recoveries ranged from 96.2% to 101.8%.
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Affiliation(s)
- Yanping Chang
- Department of Chemistry and Environment, Jiaying University, Meisong Road 100, Meizhou, 514015, Guangdong, P. R. China
| | - Jingyi Wang
- Department of Chemistry and Environment, Jiaying University, Meisong Road 100, Meizhou, 514015, Guangdong, P. R. China
| | - Hongwei Guo
- Department of Chemistry and Environment, Jiaying University, Meisong Road 100, Meizhou, 514015, Guangdong, P. R. China
| | - Wanqing Yao
- Department of Chemistry and Environment, Jiaying University, Meisong Road 100, Meizhou, 514015, Guangdong, P. R. China
| | - Haijiao Xie
- Hangzhou Yanqu Information Technology Co., Ltd, Wen'er West Road 712, Hangzhou, 310003, Zhejiang, P. R. China
| | - Long Li
- Department of Chemistry and Environment, Jiaying University, Meisong Road 100, Meizhou, 514015, Guangdong, P. R. China.
| | - Xianhu Liu
- Department of Chemistry and Environment, Jiaying University, Meisong Road 100, Meizhou, 514015, Guangdong, P. R. China.
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6
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Wang H, Zhuang Y, Fu S, Shen Y, Qian H, Yan X, Ge J. Modular and Fast Assembly of Self-Immobilizing Fluorogenic Probes for β-Galactosidase Detection. Anal Chem 2024. [PMID: 39561279 DOI: 10.1021/acs.analchem.4c02307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2024]
Abstract
β-Galactosidase (β-gal) has emerged as a pivotal biomarker in primary ovarian cancer. Despite the existence of numerous fluorescent probes for β-gal activity detection, quinone methide-based immobilizing probes were shown to avoid rapid diffusion of the activated fluorophore and improve the resolution. However, the synthesis of these fluorophores, particularly near-infrared fluorophores, still exhibits lower efficiency. In this study, we introduce modular and rapidly assembled self-immobilizing fluorogenic probes, capitalizing on the proximity labeling properties of quinone methide (QM). Compared to conventional fluorescent probes, these new probes not only exhibit a fluorogenic response but also achieve permanent retention, demonstrating improved detection sensitivity, particularly after cell fixation and in vivo animal model studies. This straightforward synthesis approach holds promise for broader applications in detecting other analytes.
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Affiliation(s)
- Hongfeng Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yuli Zhuang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Siyi Fu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yuxuan Shen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huijuan Qian
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiaoqiao Yan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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7
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Hovorková M, Kaščáková B, Petrásková L, Havlíčková P, Nováček J, Pinkas D, Gardian Z, Křen V, Bojarová P, Smatanová IK. The variable structural flexibility of the Bacillus circulans β-galactosidase isoforms determines their unique functionalities. Structure 2024; 32:2023-2037.e5. [PMID: 39353423 DOI: 10.1016/j.str.2024.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/29/2024] [Accepted: 09/04/2024] [Indexed: 10/04/2024]
Abstract
β-Galactosidase from Bacillus circulans ATCC 31382 (BgaD) is a biotechnologically important enzyme for the synthesis of β-galactooligosaccharides (GOS). Among its four isoforms, isoform A (BgaD-A) has distinct synthetic properties. Here, we present cryoelectron microscopy (cryo-EM) structures of BgaD-A and compare them with the known X-ray crystal structure of isoform D (BgaD-D), revealing substantial structural divergences between the two isoforms. In contrast to BgaD-D, BgaD-A features a flexible Big-4 domain and another enigmatic domain. The newly identified flexible region in BgaD-A is termed as "barrier domain 8," and serves as a barricade, obstructing the access of longer oligosaccharide substrates into the active site of BgaD-A. The transgalactosylation reactions catalyzed by both isoforms revealed that BgaD-A has a higher selectivity than BgaD-D in the earlier stages of the reaction and is prevailingly directed to shorter galactooligosaccharides. This study improves our understanding of the structural determinants governing β-galactosidase catalysis, with implications for tailored GOS production.
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Affiliation(s)
- Michaela Hovorková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14200 Praha4, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, CZ-12843 Praha2, Czech Republic
| | - Barbora Kaščáková
- Department of Chemistry, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, CZ-37005 České Budějovice, Czech Republic
| | - Lucie Petrásková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14200 Praha4, Czech Republic
| | - Petra Havlíčková
- Department of Chemistry, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, CZ-37005 České Budějovice, Czech Republic
| | - Jiří Nováček
- Cryo-Electron Microscopy Core Facility, CEITEC, CZ-62500 Brno, Czech Republic
| | - Daniel Pinkas
- Cryo-Electron Microscopy Core Facility, CEITEC, CZ-62500 Brno, Czech Republic
| | - Zdenko Gardian
- Department of Chemistry, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, CZ-37005 České Budějovice, Czech Republic; Laboratory of Electron Microscopy, Biology Centre of the Czech Academy of Sciences, CZ-37005 České Budějovice, Czech Republic
| | - Vladimír Křen
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14200 Praha4, Czech Republic
| | - Pavla Bojarová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14200 Praha4, Czech Republic.
| | - Ivana Kutá Smatanová
- Department of Chemistry, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, CZ-37005 České Budějovice, Czech Republic.
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8
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Sassù F, Vomáčková Kykalová B, Vieira CS, Volf P, Loza Telleria E. Stability and suitability of housekeeping genes in phlebotomine sand flies. Sci Rep 2024; 14:23353. [PMID: 39375431 PMCID: PMC11458623 DOI: 10.1038/s41598-024-74776-9] [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: 08/07/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024] Open
Abstract
We investigated gene expression patterns in Lutzomyia and Phlebotomus sand fly vectors of leishmaniases. Using quantitative PCR, we assessed the expression stability of potential endogenous control genes commonly used in dipterans. We analyzed Lutzomyia longipalpis and Phlebotomus papatasi samples from L3 and L4 larval stages, adult sand flies of different sexes, diets, dsRNA injection, and Leishmania infection. Six genes were evaluated: actin, α-tubulin, GAPDH, 60 S ribosomal proteins L8 and L32 (RiboL8 and RiboL32), and elongation factor 1-α (EF1-α). EF1-α was among the most stably expressed along with RiboL8 in L. longipalpis larvae and RiboL32 in adults. In P. papatasi, EF1-α and RiboL32 were the top in larvae, while EF1-α and actin were the most stable in adults. RiboL8 and actin were the most stable genes in dissected tissues and infected guts. Additionally, five primer pairs designed for L. longipalpis or P. papatasi were effective in PCR with Lutzomyia migonei, Phlebotomus duboscqi, Phlebotomus perniciosus, and Sergentomyia schwetzi cDNA. Furthermore, L. longipalpis RiboL32 and P. papatasi α-tubulin primers were suitable for qPCR with cDNA from the other four species. Our research provides tools to enhance relative gene expression studies in sand flies, facilitating the selection of endogenous control for qPCR.
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Affiliation(s)
- Fabiana Sassù
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, 128 00, Czech Republic
| | - Barbora Vomáčková Kykalová
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, 128 00, Czech Republic
| | - Cecilia Stahl Vieira
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, 128 00, Czech Republic
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, 128 00, Czech Republic
| | - Erich Loza Telleria
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, 128 00, Czech Republic.
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9
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Patiño-Ruiz MF, Anshari ZR, Gaastra B, Slotboom DJ, Poolman B. Chemiosmotic nutrient transport in synthetic cells powered by electrogenic antiport coupled to decarboxylation. Nat Commun 2024; 15:7976. [PMID: 39266519 PMCID: PMC11392934 DOI: 10.1038/s41467-024-52085-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 08/27/2024] [Indexed: 09/14/2024] Open
Abstract
Cellular homeostasis depends on the supply of metabolic energy in the form of ATP and electrochemical ion gradients. The construction of synthetic cells requires a constant supply of energy to drive membrane transport and metabolism. Here, we provide synthetic cells with long-lasting metabolic energy in the form of an electrochemical proton gradient. Leveraging the L-malate decarboxylation pathway we generate a stable proton gradient and electrical potential in lipid vesicles by electrogenic L-malate/L-lactate exchange coupled to L-malate decarboxylation. By co-reconstitution with the transporters GltP and LacY, the synthetic cells maintain accumulation of L-glutamate and lactose over periods of hours, mimicking nutrient feeding in living cells. We couple the accumulation of lactose to a metabolic network for the generation of intermediates of the glycolytic and pentose phosphate pathways. This study underscores the potential of harnessing a proton motive force via a simple metabolic network, paving the way for the development of more complex synthetic systems.
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Affiliation(s)
- Miyer F Patiño-Ruiz
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Zaid Ramdhan Anshari
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bauke Gaastra
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dirk J Slotboom
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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10
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Luo W, Diao Q, Lv L, Li T, Ma P, Song D. A novel NIR fluorescent probe for enhanced β-galactosidase detection and tumor imaging in ovarian cancer models. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 317:124411. [PMID: 38728851 DOI: 10.1016/j.saa.2024.124411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
The advancement of biological imaging techniques critically depends on the development of novel near-infrared (NIR) fluorescent probes. In this study, we introduce a designed NIR fluorescent probe, NRO-βgal, which exhibits a unique off-on response mechanism to β-galactosidase (β-gal). Emitting a fluorescence peak at a wavelength of 670 nm, NRO-βgal showcases a significant Stokes shift of 85 nm, which is indicative of its efficient energy transfer and minimized background interference. The probe achieves a remarkably low in vitro detection limit of 0.2 U/L and demonstrates a rapid response within 10 min, thereby underscoring its exceptional sensitivity, selectivity, and operational swiftness. Such superior analytical performance broadens the horizon for its application in intricate biological imaging studies. To validate the practical utility of NRO-βgal in bio-imaging, we employed ovarian cancer cell and mouse models, where the probe's efficacy in accurately delineating tumor cells was examined. The results affirm NRO-βgal's capability to provide sharp, high-contrast images of tumor regions, thereby significantly enhancing the precision of surgical tumor resection. Furthermore, the probe's potential for real-time monitoring of enzymatic activity in living tissues underscores its utility as a powerful tool for diagnostics in oncology and beyond.
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Affiliation(s)
- Weiwei Luo
- Liaoning Key Laboratory of Development and Utilization for Natural Products Active Molecules, School of Chemistry and Life Science, Anshan Normal University, Anshan, China
| | - Quanping Diao
- Liaoning Key Laboratory of Development and Utilization for Natural Products Active Molecules, School of Chemistry and Life Science, Anshan Normal University, Anshan, China.
| | - Linlin Lv
- Liaoning Key Laboratory of Development and Utilization for Natural Products Active Molecules, School of Chemistry and Life Science, Anshan Normal University, Anshan, China
| | - Tiechun Li
- Liaoning Key Laboratory of Development and Utilization for Natural Products Active Molecules, School of Chemistry and Life Science, Anshan Normal University, Anshan, China
| | - Pinyi Ma
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun, China
| | - Daqian Song
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun, China
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11
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Rs N, Sinha SK, Batra S, Regatti PR, Syal K. Promoter characterization of relZ-bifunctional (pp)pGpp synthetase in mycobacteria. Genes Cells 2024; 29:710-721. [PMID: 38923083 DOI: 10.1111/gtc.13135] [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: 03/19/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
The second messenger guanosine 3',5'-bis(diphosphate)/guanosine tetraphosphate (ppGpp) and guanosine 3'-diphosphate 5'-triphosphate/guanosine pentaphosphate (pppGpp) ((p)ppGpp) has been shown to be crucial for the survival of mycobacteria under hostile conditions. Unexpectedly, deletion of primary (p)ppGpp synthetase-Rel did not completely diminish (p)ppGpp levels leading to the discovery of novel bifunctional enzyme-RelZ, which displayed guanosine 5'-monophosphate,3'-diphosphate (pGpp), ppGpp, and pppGpp ((pp)pGpp) synthesis and RNAseHII activity. What conditions does it express itself under, and does it work in concert with Rel? The regulation of its transcription and whether the Rel enzyme plays a role in such regulation remain unclear. In this article, we have studied relZ promoter and compared its activity with rel promoter in different growth conditions. We observed that the promoter activity of relZ was constitutive; it is weaker than rel promoter, lies within 200 bp upstream of translation-start site, and it increased under carbon starvation. Furthermore, the promoter activity of relZ was compromised in the rel-knockout strain in the stationary phase. Our study unveils the dynamic regulation of relZ promoter activity by SigA and SigB sigma factors in different growth phases in mycobacteria. Importantly, elucidating the regulatory network of RelZ would enable the development of the targeted interventions for treating mycobacterial infections.
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Affiliation(s)
- Neethu Rs
- Genetics and Molecular Microbiology Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, Telangana, India
| | - Shubham Kumar Sinha
- Genetics and Molecular Microbiology Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, Telangana, India
| | - Sakshi Batra
- Genetics and Molecular Microbiology Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, Telangana, India
- Department of Pulmonary Medicine, Malla Reddy Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Pavan Reddy Regatti
- Genetics and Molecular Microbiology Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, Telangana, India
| | - Kirtimaan Syal
- Genetics and Molecular Microbiology Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, Telangana, India
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12
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Kil Y, Pichkur EB, Sergeev VR, Zabrodskaya Y, Myasnikov A, Konevega AL, Shtam T, Samygina VR, Rychkov GN. The archaeal highly thermostable GH35 family β-galactosidase DaβGal has a unique seven domain protein fold. FEBS J 2024; 291:3686-3705. [PMID: 38825733 DOI: 10.1111/febs.17166] [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: 10/11/2023] [Revised: 04/29/2024] [Accepted: 05/17/2024] [Indexed: 06/04/2024]
Abstract
The most extensively studied β-d-galactosidases (EC3.2.1.23) belonging to four glycoside hydrolase (GH) families 1, 2, 35, and 42 are widely distributed among Bacteria, Archaea and Eukaryotes. Here, we report a novel GH35 family β-galactosidase from the hyperthermophilic Thermoprotei archaeon Desulfurococcus amylolyticus (DaβGal). Unlike fungal monomeric six-domain β-galactosidases, the DaβGal enzyme is a dimer; it has an extra jelly roll domain D7 and three composite domains (D4, D5, and D6) that are formed by the distantly located polypeptide chain regions. The enzyme possesses a high specificity for β-d-galactopyranosides, and its distinguishing feature is the ability to cleave pNP-β-d-fucopyranoside. DaβGal efficiently catalyzes the hydrolysis of lactose at high temperatures, remains stable and active at 65 °С, and retains activity at 95 °С with a half-life time value equal to 73 min. These properties make archaeal DaβGal a more attractive candidate for biotechnology than the widely used fungal β-galactosidases.
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Affiliation(s)
- Yury Kil
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
| | - Evgeny B Pichkur
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
- Structural Biology Department, Kurchatov Complex of NBICS Nature-Like Technologies, National Research Center "Kurchatov Institute", Moscow, Russia
- Laboratory of X-ray Analysis and Synchrotron Radiation, Federal Scientific Research Center "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, Russia
| | - Vladimir R Sergeev
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
- Institute of Biomedical Systems and Biotechnology, Peter the Great Saint-Petersburg Polytechnic University, Russia
| | - Yana Zabrodskaya
- Institute of Biomedical Systems and Biotechnology, Peter the Great Saint-Petersburg Polytechnic University, Russia
- Department of Molecular Biology of Viruses, Smorodintsev Research Institute of Influenza, St. Petersburg, Russia
| | - Alexander Myasnikov
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
| | - Andrey L Konevega
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
- Structural Biology Department, Kurchatov Complex of NBICS Nature-Like Technologies, National Research Center "Kurchatov Institute", Moscow, Russia
- Institute of Biomedical Systems and Biotechnology, Peter the Great Saint-Petersburg Polytechnic University, Russia
| | - Tatiana Shtam
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
- Structural Biology Department, Kurchatov Complex of NBICS Nature-Like Technologies, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Valeriya R Samygina
- Structural Biology Department, Kurchatov Complex of NBICS Nature-Like Technologies, National Research Center "Kurchatov Institute", Moscow, Russia
- Laboratory of X-ray Analysis and Synchrotron Radiation, Federal Scientific Research Center "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, Russia
| | - Georgy N Rychkov
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
- Institute of Biomedical Systems and Biotechnology, Peter the Great Saint-Petersburg Polytechnic University, Russia
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13
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Miki K, Oe M, Suzuki K, Miki K, Mu H, Kato Y, Iwatake M, Yukawa H, Baba Y, Ueda Y, Mori Y, Ohe K. Dual-responsive near-infrared turn-on fluorescent probe for cancer stem cell-specific visualization. J Mater Chem B 2024; 12:6959-6967. [PMID: 38913327 DOI: 10.1039/d4tb00897a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Aldehyde dehydrogenase 1A1 (ALDH1A1) stands out as one of the most reliable intracellular biomarkers for stem cells because it is expressed in both cancer stem cells (CSCs) and normal somatic stem cells (NSCs). Although several turn-on fluorescent probes for ALDH1A1 have been developed to visualize CSCs in cancer cells, the discrimination of CSCs from NSCs is difficult. We here report an AND-type dual-responsive fluorescent probe, CHO_βgal, the near-infrared fluorescence of which can be turned on after responding to both ALDH1A1 and β-galactosidase. The AND-type dual responsiveness enables CSCs to be clearly visualized, whereas NSCs are non-emissive in microscopy. CSC-positive metastasis model lungs were successfully discriminated from normal lungs in ex vivo staining experiments using CHO_βgal, whereas the single-input ALDH1A1-responsive probe failed to achieve this discrimination owing to pronounced false-positive fluorescence output from lung NSCs. In tissue slice staining experiments, even in the presence of adjacent normal tissues, the peripheral region-specific localization of CSCs was clear. The versatility of CHO_βgal holds promise not only as a fundamental in vitro research tool for visualizing CSCs but also as a valuable asset in practical tissue staining diagnosis, significantly contributing to the assessment of cancer malignancy.
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Affiliation(s)
- Koji Miki
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Masahiro Oe
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Kanae Suzuki
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Koki Miki
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Huiying Mu
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Yoshimi Kato
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Mayumi Iwatake
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroshi Yukawa
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology (QST), Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, Chiba 265-8522, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology (QST), Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
| | - Yoshifumi Ueda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kouichi Ohe
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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14
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Tetz V, Kardava K, Vecherkovskaya M, Khodadadi-Jamayran A, Tsirigos A, Tetz G. Previously unknown regulatory role of extracellular RNA on bacterial directional migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603110. [PMID: 39026763 PMCID: PMC11257571 DOI: 10.1101/2024.07.11.603110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Bacterial directional migration plays a significant role in bacterial adaptation. However, the regulation of this process, particularly in young biofilms, remains unclear. Here, we demonstrated the critical role of extracellular RNA as part of the Universal Receptive System in bacterial directional migration using a multidisciplinary approach, including bacterial culture, biochemistry, and genetics. We found that the destruction or inactivation of extracellular RNA with RNase or RNA-specific antibodies in the presence of the chemoattractant triggered the formation of bacterial "runner cells» in what we call a "panic state" capable of directional migration. These cells quickly migrated even on the surface of 1.5% agar and formed evolved colonies that were transcriptionally and biochemically different from the ancestral cells. We have also shown that cell-free DNA from blood plasma can act as a potent bacterial chemoattractant. Our data revealed a previously unknown role of bacterial extracellular RNA in the regulation of bacterial migration and have shown that its destruction or inhibition triggered the directional migration of developing and mature biofilms towards the chemoattractant.
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15
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Yadav S, Vinothkumar KR. Factors affecting macromolecule orientations in thin films formed in cryo-EM. Acta Crystallogr D Struct Biol 2024; 80:535-550. [PMID: 38935342 PMCID: PMC11220838 DOI: 10.1107/s2059798324005229] [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: 11/20/2023] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour.
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Affiliation(s)
- Swati Yadav
- National Centre for Biological SciencesTata Institute of Fundamental ResearchGKVK Post, Bellary RoadBengaluru560 065India
| | - Kutti R. Vinothkumar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchGKVK Post, Bellary RoadBengaluru560 065India
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16
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Chau CC, Maffeo CM, Aksimentiev A, Radford SE, Hewitt EW, Actis P. Single molecule delivery into living cells. Nat Commun 2024; 15:4403. [PMID: 38782907 PMCID: PMC11116494 DOI: 10.1038/s41467-024-48608-3] [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: 02/12/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Controlled manipulation of cultured cells by delivery of exogenous macromolecules is a cornerstone of experimental biology. Here we describe a platform that uses nanopipettes to deliver defined numbers of macromolecules into cultured cell lines and primary cells at single molecule resolution. In the nanoinjection platform, the nanopipette is used as both a scanning ion conductance microscope (SICM) probe and an injection probe. The SICM is used to position the nanopipette above the cell surface before the nanopipette is inserted into the cell into a defined location and to a predefined depth. We demonstrate that the nanoinjection platform enables the quantitative delivery of DNA, globular proteins, and protein fibrils into cells with single molecule resolution and that delivery results in a phenotypic change in the cell that depends on the identity of the molecules introduced. Using experiments and computational modeling, we also show that macromolecular crowding in the cell increases the signal-to-noise ratio for the detection of translocation events, thus the cell itself enhances the detection of the molecules delivered.
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Affiliation(s)
- Chalmers C Chau
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK
| | - Christopher M Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sheena E Radford
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Eric W Hewitt
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, LS2 9JT, UK.
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK.
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17
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Yu K, Zhou P, Wang M, Zou P, Wang H, Liu Y, Xie M. β-Galactosidase-guided self-assembled 68Ga nanofibers probe for micro-PET tumor imaging. Bioorg Med Chem Lett 2024; 104:129727. [PMID: 38582132 DOI: 10.1016/j.bmcl.2024.129727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/12/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
β-galactosidase (β-gal) has high activity in various malignancies, which is suitable for targeted positron emission tomography (PET) imaging. Meanwhile, β-gal can successfully guide the formation of nanofibers, which enhances the intensity of imaging and extends the imaging time. Herein, we designed a β-galactosidase-guided self-assembled PET imaging probe [68Ga]Nap-NOTA-1Gal. We envisage that β-gal could recognize and cleave the target site, bringing about self-assembling to form nanofibers, thereby enhancing the PET imaging effect. The targeting specificity of [68Ga]Nap-NOTA-1Gal for detecting β-gal activity was examined using the control probe [68Ga]Nap-NOTA-1. Micro-PET imaging showed that tumor regions of [68Ga]Nap-NOTA-1Gal were visible after injection. And the tumor uptake of [68Ga]Nap-NOTA-1Gal was higher than [68Ga]Nap-NOTA-1 at all-time points. Our results demonstrated that the [68Ga]Nap-NOTA-1Gal can be used for the purpose of a new promising PET probe for helping diagnose cancer with high levels of β-gal activity.
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Affiliation(s)
- Kangxia Yu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Peng Zhou
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Meimei Wang
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Pei Zou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Hongyong Wang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Yaling Liu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
| | - Minhao Xie
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China; NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
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18
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Pollack D, Nozoe T, Kussell E. Proteolytic stability and aggregation in a key metabolic enzyme of bacteria. Proc Natl Acad Sci U S A 2024; 121:e2301458121. [PMID: 38683989 PMCID: PMC11087809 DOI: 10.1073/pnas.2301458121] [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: 01/31/2023] [Accepted: 03/07/2024] [Indexed: 05/02/2024] Open
Abstract
Proteins that are kinetically stable are thought to be less prone to both aggregation and proteolysis. We demonstrate that the classical lac system of Escherichia coli can be leveraged as a model system to study this relation. β-galactosidase (LacZ) plays a critical role in lactose metabolism and is an extremely stable protein that can persist in growing cells for multiple generations after expression has stopped. By attaching degradation tags to the LacZ protein, we find that LacZ can be transiently degraded during lac operon expression but once expression has stopped functional LacZ is protected from degradation. We reversibly destabilize its tetrameric assembly using α-complementation, and show that unassembled LacZ monomers and dimers can either be degraded or lead to formation of aggregates within cells, while the tetrameric state protects against proteolysis and aggregation. We show that the presence of aggregates is associated with cell death, and that these proteotoxic stress phenotypes can be alleviated by attaching an ssrA tag to LacZ monomers which leads to their degradation. We unify our findings using a biophysical model that enables the interplay of protein assembly, degradation, and aggregation to be studied quantitatively in vivo. This work may yield approaches to reversing and preventing protein-misfolding disease states, while elucidating the functions of proteolytic stability in constant and fluctuating environments.
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Affiliation(s)
- Dan Pollack
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY10003
| | - Takashi Nozoe
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo153-8902, Japan
- Research Center for Complex Systems Biology, The University of Tokyo, Tokyo153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo113-0033, Japan
| | - Edo Kussell
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY10003
- Department of Physics, New York University, New York, NY10003
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19
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Dolan M, Shi Y, Mastri M, Long MD, McKenery A, Hill JW, Vaghi C, Benzekry S, Barbi J, Ebos JM. A senescence-mimicking (senomimetic) VEGFR TKI side-effect primes tumor immune responses via IFN/STING signaling. Mol Cancer Ther 2024; 23:745113. [PMID: 38690835 PMCID: PMC11527799 DOI: 10.1158/1535-7163.mct-24-0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024]
Abstract
Tyrosine kinase inhibitors (TKIs) that block the vascular endothelial growth factor receptors (VEGFRs) disrupt tumor angiogenesis but also have many unexpected side-effects that impact tumor cells directly. This includes the induction of molecular markers associated with senescence, a form of cellular aging that typically involves growth arrest. We have shown that VEGFR TKIs can hijack these aging programs by transiently inducting senescence-markers (SMs) in tumor cells to activate senescence-associated secretory programs that fuel drug resistance. Here we show that these same senescence-mimicking ('senomimetic') VEGFR TKI effects drive an enhanced immunogenic signaling that, in turn, can alter tumor response to immunotherapy. Using a live-cell sorting method to detect beta-galactosidase, a commonly used SM, we found that subpopulations of SM-expressing (SM+) tumor cells have heightened interferon (IFN) signaling and increased expression of IFN-stimulated genes (ISGs). These ISG increases were under the control of the STimulator of INterferon Gene (STING) signaling pathway, which we found could be directly activated by several VEGFR TKIs. TKI-induced SM+ cells could stimulate or suppress CD8 T-cell activation depending on host:tumor cell contact while tumors grown from SM+ cells were more sensitive to PD-L1 inhibition in vivo, suggesting that offsetting immune-suppressive functions of SM+ cells can improve TKI efficacy overall. Our findings may explain why some (but not all) VEGFR TKIs improve outcomes when combined with immunotherapy and suggest that exploiting senomimetic drug side-effects may help identify TKIs that uniquely 'prime' tumors for enhanced sensitivity to PD-L1 targeted agents.
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Affiliation(s)
- Melissa Dolan
- Department of Experimental Therapeutics, Roswell Park Comprehensive Cancer Center Buffalo, NY, 14263. USA
| | - Yuhao Shi
- Department of Experimental Therapeutics, Roswell Park Comprehensive Cancer Center Buffalo, NY, 14263. USA
| | - Michalis Mastri
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263. USA
| | - Mark D. Long
- Department of Bioinformatics and Statistics, Roswell Park Comprehensive Cancer Center Buffalo, NY, 14263. USA
| | - Amber McKenery
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263. USA
| | - James W. Hill
- Jacobs School of Medicine and Biomedical Sciences, SUNY at Buffalo, Buffalo, New York, 14263. USA
| | - Cristina Vaghi
- Inria Team MONC, Inria Bordeaux Sud-Ouest, Talence, France
- Computational Pharmacology and Clinical Oncology (COMPO), Inria Sophia Antipolis–Méditerranée, Cancer Research Center of Marseille, Inserm UMR1068, CNRS UMR7258, Aix Marseille University UM105, 13385 Marseille, France
| | - Sebastien Benzekry
- Inria Team MONC, Inria Bordeaux Sud-Ouest, Talence, France
- Computational Pharmacology and Clinical Oncology (COMPO), Inria Sophia Antipolis–Méditerranée, Cancer Research Center of Marseille, Inserm UMR1068, CNRS UMR7258, Aix Marseille University UM105, 13385 Marseille, France
| | - Joseph Barbi
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263. USA
| | - John M.L. Ebos
- Department of Experimental Therapeutics, Roswell Park Comprehensive Cancer Center Buffalo, NY, 14263. USA
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263. USA
- Department of Medicine, Roswell Park Comprehensive Cancer Center Buffalo, NY, 14263. USA
- Lead Contact
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20
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Tong Y, Lu X, Shen D, Rao L, Zou L, Lyu S, Hou L, Sun G, Chen L. Identification and characterization of emGalaseE, a β-1,4 galactosidase from Elizabethkingia meningoseptica, and its application on living cell surface. Int J Biol Macromol 2024; 268:131766. [PMID: 38657932 DOI: 10.1016/j.ijbiomac.2024.131766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/18/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
The biological function of terminal galactose on glycoprotein is an open field of research. Although progress had being made on enzymes that can remove the terminal galactose on glycoproteins, there is a lack of report on galactosidases that can work directly on living cells. In this study, a unique beta 1,4 galactosidase was isolated from Elizabethkingia meningoseptica (Em). It exhibited favorable stability at various temperatures (4-37 °C) and pH (5-8) levels and can remove β-1, 4 linked galactoses directly from glycoproteins. Using Alanine scanning, we found that two acidic residues (Glu-468, and Glu-531) in the predicted active pocket are critical for galactosidase activity. In addition, we also demonstrated that it could cleave galactose residues present on living cell surface. As this enzyme has a potential application for living cell glycan editing, we named it emGalaseE or glycan-editing galactosidase I (csgeGalaseI). In summary, our findings lay the groundwork for further investigation by presenting a simple and effective approach for the removal of galactose moieties from cell surface.
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Affiliation(s)
- Yongliang Tong
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xinrong Lu
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Danfeng Shen
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lin Rao
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lin Zou
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Shaoxian Lyu
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Linlin Hou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China.
| | - Guiqin Sun
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang Province, China.
| | - Li Chen
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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21
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Jiang J, Zhao Y, Chen A, Sun J, Zhou M, Hu J, Cao X, Dai N, Liang Z, Feng S. Efficient markerless genetic manipulation of Pasteurella multocida using lacZ and pheSm as selection markers. Appl Environ Microbiol 2024; 90:e0204323. [PMID: 38547470 PMCID: PMC11022533 DOI: 10.1128/aem.02043-23] [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: 11/14/2023] [Accepted: 03/07/2024] [Indexed: 04/18/2024] Open
Abstract
Pasteurella multocida is a zoonotic conditional pathogen that infects multiple livestock species, causing substantial economic losses in the animal husbandry industry. An efficient markerless method for gene manipulation may facilitate the investigations of P. multocida gene function and pathogenesis of P. multocida. Herein, a temperature-sensitive shuttle vector was constructed using lacZ as a selection marker, and markerless glgB, opa, and hyaE mutants of P. multocida were subsequently constructed through blue-white colony screening. The screening efficiency of markerless deletion strains was improved by the lacZ system, and the method could be used for multiple gene deletions. However, the fur mutant was unavailable via this method. Therefore, we constructed a pheSm screening system based on mutated phenylalanine tRNA synthetase as a counterselection marker to achieve fur deletion mutant. The transformed strain was sensitive to 20 mM p-chloro-phenylalanine, demonstrating the feasibility of pheSm as a counter-selective marker. The pheSm system was used for markerless deletions of glgB, opa, and hyaE as well as fur that could not be screened by the lacZ system. A comparison of screening efficiencies of the system showed that the pheSm counterselection system was more efficient than the lacZ system and broadly applicable for mutant screening. The methods developed herein may provide valuable tools for genetic manipulation of P. multocida.IMPORTANCEPasteurella multocida is a highly contagious zoonotic pathogen. An understanding of its underlying pathogenic mechanisms is of considerable importance and requires efficient species-specific genetic tools. Herein, we propose a screening system for P. multocida mutants using lacZ or pheSm screening markers. We evaluated the efficiencies of both systems, which were used to achieve markerless deletion of multiple genes. The results of this study support the use of lacZ or pheSm as counterselection markers to improve counterselection efficiency in P. multocida. This study provides an effective genetic tool for investigations of the virulence gene functions and pathogenic mechanisms of P. multocida.
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Affiliation(s)
- Jinfei Jiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yishan Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Aihua Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Juan Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mengruo Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jialian Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuewei Cao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ning Dai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhaoping Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
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22
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Nomura K, Onda K, Murase H, Hashiya F, Ono Y, Terai G, Oka N, Asai K, Suzuki D, Takahashi N, Hiraoka H, Inagaki M, Kimura Y, Shimizu Y, Abe N, Abe H. Development of PCR primers enabling the design of flexible sticky ends for efficient concatenation of long DNA fragments. RSC Chem Biol 2024; 5:360-371. [PMID: 38576723 PMCID: PMC10989509 DOI: 10.1039/d3cb00212h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/19/2024] [Indexed: 04/06/2024] Open
Abstract
We developed chemically modified PCR primers that allow the design of flexible sticky ends by introducing a photo-cleavable group at the phosphate moiety. Nucleic acid derivatives containing o-nitrobenzyl photo-cleavable groups with a tert-butyl group at the benzyl position were stable during strong base treatment for oligonucleotide synthesis and thermal cycling in PCR reactions. PCR using primers incorporating these nucleic acid derivatives confirmed that chain extension reactions completely stopped at position 1 before and after the site of the photo-cleavable group was introduced. DNA fragments of 2 and 3 kbp, with sticky ends of 50 bases, were successfully concatenated with a high yield of 77%. A plasmid was constructed using this method. Finally, we applied this approach to construct a 48.5 kbp lambda phage DNA, which is difficult to achieve using restriction enzyme-based methods. After 7 days, we were able to confirm the generation of DNA of the desired length. Although the efficiency is yet to be improved, the chemically modified PCR primer offers potential to complement enzymatic methods and serve as a DNA concatenation technique.
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Affiliation(s)
- Kohei Nomura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Kaoru Onda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Hirotaka Murase
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- CREST, Japan Science and Technology Agency 7 Gobancho Chiyoda-ku Tokyo 102-0076 Japan
| | - Yukiteru Ono
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo Kashiwanoha, Kashiwa Chiba 277-8561 Japan
| | - Goro Terai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo Kashiwanoha, Kashiwa Chiba 277-8561 Japan
| | - Natsuhisa Oka
- Department of Chemistry and Biomolecular Science Faculty of Engineering, Gifu University Gifu 501-1193 Japan
| | - Kiyoshi Asai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo Kashiwanoha, Kashiwa Chiba 277-8561 Japan
| | - Daisuke Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Naho Takahashi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Haruka Hiraoka
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research Suita Osaka 565-0874 Japan
| | - Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- Research Center for Materials Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- CREST, Japan Science and Technology Agency 7 Gobancho Chiyoda-ku Tokyo 102-0076 Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8601 Japan
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23
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Lan PD, Nissley DA, Sitarik I, Vu QV, Jiang Y, To P, Xia Y, Fried SD, Li MS, O'Brien EP. Synonymous Mutations Can Alter Protein Dimerization Through Localized Interface Misfolding Involving Self-entanglements. J Mol Biol 2024; 436:168487. [PMID: 38341172 PMCID: PMC11260358 DOI: 10.1016/j.jmb.2024.168487] [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: 09/07/2023] [Revised: 01/10/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Synonymous mutations in messenger RNAs (mRNAs) can reduce protein-protein binding substantially without changing the protein's amino acid sequence. Here, we use coarse-grain simulations of protein synthesis, post-translational dynamics, and dimerization to understand how synonymous mutations can influence the dimerization of two E. coli homodimers, oligoribonuclease and ribonuclease T. We synthesize each protein from its wildtype, fastest- and slowest-translating synonymous mRNAs in silico and calculate the ensemble-averaged interaction energy between the resulting dimers. We find synonymous mutations alter oligoribonuclease's dimer properties. Relative to wildtype, the dimer interaction energy becomes 4% and 10% stronger, respectively, when translated from its fastest- and slowest-translating mRNAs. Ribonuclease T dimerization, however, is insensitive to synonymous mutations. The structural and kinetic origin of these changes are misfolded states containing non-covalent lasso-entanglements, many of which structurally perturb the dimer interface, and whose probability of occurrence depends on translation speed. These entangled states are kinetic traps that persist for long time scales. Entanglements cause altered dimerization energies for oligoribonuclease, as there is a large association (odds ratio: 52) between the co-occurrence of non-native self-entanglements and weak-binding dimer conformations. Simulated at all-atom resolution, these entangled structures persist for long timescales, indicating the conclusions are independent of model resolution. Finally, we show that regions of the protein we predict to have changes in entanglement are also structurally perturbed during refolding, as detected by limited-proteolysis mass spectrometry. Thus, non-native changes in entanglement at dimer interfaces is a mechanism through which oligomer structure and stability can be altered.
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Affiliation(s)
- Pham Dang Lan
- Institute for Computational Sciences and Technology, Ho Chi Minh City, Viet Nam; Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, Ho Chi Minh City, Viet Nam
| | - Daniel Allen Nissley
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Quyen V Vu
- Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip To
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yingzi Xia
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA; Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mai Suan Li
- Institute for Computational Sciences and Technology, Ho Chi Minh City, Viet Nam; Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA; Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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24
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Sharma A, Verwilst P, Li M, Ma D, Singh N, Yoo J, Kim Y, Yang Y, Zhu JH, Huang H, Hu XL, He XP, Zeng L, James TD, Peng X, Sessler JL, Kim JS. Theranostic Fluorescent Probes. Chem Rev 2024; 124:2699-2804. [PMID: 38422393 PMCID: PMC11132561 DOI: 10.1021/acs.chemrev.3c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
The ability to gain spatiotemporal information, and in some cases achieve spatiotemporal control, in the context of drug delivery makes theranostic fluorescent probes an attractive and intensely investigated research topic. This interest is reflected in the steep rise in publications on the topic that have appeared over the past decade. Theranostic fluorescent probes, in their various incarnations, generally comprise a fluorophore linked to a masked drug, in which the drug is released as the result of certain stimuli, with both intrinsic and extrinsic stimuli being reported. This release is then signaled by the emergence of a fluorescent signal. Importantly, the use of appropriate fluorophores has enabled not only this emerging fluorescence as a spatiotemporal marker for drug delivery but also has provided modalities useful in photodynamic, photothermal, and sonodynamic therapeutic applications. In this review we highlight recent work on theranostic fluorescent probes with a particular focus on probes that are activated in tumor microenvironments. We also summarize efforts to develop probes for other applications, such as neurodegenerative diseases and antibacterials. This review celebrates the diversity of designs reported to date, from discrete small-molecule systems to nanomaterials. Our aim is to provide insights into the potential clinical impact of this still-emerging research direction.
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Affiliation(s)
- Amit Sharma
- Amity
School of Chemical Sciences, Amity University
Punjab, Sector 82A, Mohali 140 306, India
| | - Peter Verwilst
- Rega
Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Mingle Li
- College
of Materials Science and Engineering, Shenzhen
University, Shenzhen 518060, China
| | - Dandan Ma
- College
of Materials Science and Engineering, Shenzhen
University, Shenzhen 518060, China
- College
of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Nem Singh
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Jiyoung Yoo
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Yujin Kim
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Ying Yang
- School of
Light Industry and Food Engineering, Guangxi
University, Nanning, Guangxi 530004, China
| | - Jing-Hui Zhu
- College
of Materials Science and Engineering, Shenzhen
University, Shenzhen 518060, China
- College
of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Haiqiao Huang
- College
of Materials Science and Engineering, Shenzhen
University, Shenzhen 518060, China
- College
of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Xi-Le Hu
- Key
Laboratory for Advanced Materials and Joint International Research
Laboratory of Precision Chemistry and Molecular Engineering, Feringa
Nobel Prize Scientist Joint Research Center, School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiao-Peng He
- Key
Laboratory for Advanced Materials and Joint International Research
Laboratory of Precision Chemistry and Molecular Engineering, Feringa
Nobel Prize Scientist Joint Research Center, School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- National
Center for Liver Cancer, the International Cooperation Laboratory
on Signal Transduction, Eastern Hepatobiliary
Surgery Hospital, Shanghai 200438, China
| | - Lintao Zeng
- School of
Light Industry and Food Engineering, Guangxi
University, Nanning, Guangxi 530004, China
| | - Tony D. James
- Department
of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
- School
of Chemistry and Chemical Engineering, Henan
Normal University, Xinxiang 453007, China
| | - Xiaojun Peng
- College
of Materials Science and Engineering, Shenzhen
University, Shenzhen 518060, China
- State
Key Laboratory of Fine Chemicals, Dalian
University of Technology, Dalian 116024, China
| | - Jonathan L. Sessler
- Department
of Chemistry, The University of Texas at
Austin, Texas 78712-1224, United
States
| | - Jong Seung Kim
- Department
of Chemistry, Korea University, Seoul 02841, Korea
- TheranoChem Incorporation, Seongbuk-gu, Seoul 02841, Korea
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25
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Hu Y, Luo H, Zhao L, Guo X, Wang S, Hu R, Yang G. A chalcone-based ESIPT and AIE fluorophore for β-gal imaging in living cells. Org Biomol Chem 2024; 22:1850-1858. [PMID: 38345427 DOI: 10.1039/d3ob01953e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
β-Galactosidase (β-gal), which is responsible for the hydrolysis of the glycosidic bond of lactose to galactose, has been recognized as an important biomarker of cell or organism status, especially cell senescence and primary ovarian cancer. Extensive efforts have been devoted to develop probes for detecting and visualizing β-gal in cells. Herein, a fluorescent probe gal-HCA which possesses both excited-state intramolecular proton transfer (ESIPT) and aggregation-induced emission (AIE) properties was prepared to monitor β-gal in living cells. The probe consists of 2-hydroxy-4'-dimethylamino-chalcone (HCA) capped with a D-galactose group. The cleavage of the glycosidic bond in gal-HCA triggered by β-gal releases HCA, which results in a significant bathochromic shift in fluorescence from 532 to 615 nm. The probe exhibited high selectivity and sensitivity toward β-gal with a detection limit as low as 0.0122 U mL-1. The confocal imaging investigation demonstrated the potential of gal-HCA in monitoring the endocellular overexpressed β-gal in senescent cells and ovarian cancer cells. This study provides a straightforward approach for the development of fluorescent probes to monitor β-gal and detection of β-gal-associated diseases.
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Affiliation(s)
- Yiran Hu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China.
| | - Haiyan Luo
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China.
| | - Luyao Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China.
| | - Xudong Guo
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China.
| | - Shuangqing Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China.
| | - Rui Hu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China.
| | - Guoqiang Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry, Institute of Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, China.
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26
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Juretić D, Bonačić Lošić Ž. Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation. ENTROPY (BASEL, SWITZERLAND) 2024; 26:151. [PMID: 38392406 PMCID: PMC10888251 DOI: 10.3390/e26020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni-uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production-the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics.
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Affiliation(s)
- Davor Juretić
- Mediterranean Institute for Life Sciences, Šetalište Ivana Meštrovića 45, 21000 Split, Croatia
- Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
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27
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Kapse N, Pisu V, Dhakephalkar T, Margale P, Shetty D, Wagh S, Dagar S, Dhakephalkar PK. Unveiling the Probiotic Potential of Streptococcus thermophilus MCC0200: Insights from In Vitro Studies Corroborated with Genome Analysis. Microorganisms 2024; 12:347. [PMID: 38399752 PMCID: PMC10891967 DOI: 10.3390/microorganisms12020347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Streptococcus thermophilus is widely used as a starter culture in the dairy industry and has garnered attention as a beneficial bacterium owing to its health-promoting functionalities in humans. In this study, the probiotic potential of S. thermophilus MCC0200 isolated from a dairy product was investigated through a combinatorial approach of in vitro and in silico studies. MCC0200 demonstrated the ability to survive harsh gastrointestinal (GI) transit, adhere to intestinal mucosa and exert health-promoting traits in in vitro studies. These findings were corroborated with in silico evidence, wherein, MCC0200 genome harboured genes associated with tolerance to GI conditions, intestinal adhesion and colonization. Genome mapping also highlighted the ability of MCC0200 to produce compounds advantageous for the host (folate, bacteriocins), to release antioxidant enzymes that can quench the free radicals (superoxide dismutase, NADH peroxidase), and to metabolize food components that can be harmful to sensitive people (lactose). MCC0200 also demonstrated a positive effect on reducing cholesterol levels, proving to be a potential candidate for food and pharmaceutical applications. The absence of transmissible antibiotic resistance genes and virulence genes underscored the generally regarded as safe (GRAS) nature of MCC0200. This study explored the potential of Streptococcus thermophilus for its probable applications as a probiotic beyond the dairy industry.
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Affiliation(s)
- Neelam Kapse
- Bioenergy Group, MACS-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune 411004, Maharashtra, India; (N.K.); (V.P.); (D.S.)
| | - Vaidehi Pisu
- Bioenergy Group, MACS-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune 411004, Maharashtra, India; (N.K.); (V.P.); (D.S.)
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind Rd., Aundh, Pune 411007, Maharashtra, India
| | - Tanisha Dhakephalkar
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind Rd., Aundh, Pune 411007, Maharashtra, India
- Hi Tech BioSciences India Ltd., Research & Development Centre, Plot No. 6 & 8, Ambadvet Industrial Estate, PO Paud, Pune 412108, Maharashtra, India
| | - Prajakta Margale
- Bioenergy Group, MACS-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune 411004, Maharashtra, India; (N.K.); (V.P.); (D.S.)
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind Rd., Aundh, Pune 411007, Maharashtra, India
| | - Deepa Shetty
- Bioenergy Group, MACS-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune 411004, Maharashtra, India; (N.K.); (V.P.); (D.S.)
| | - Shilpa Wagh
- Hi Tech BioSciences India Ltd., Research & Development Centre, Plot No. 6 & 8, Ambadvet Industrial Estate, PO Paud, Pune 412108, Maharashtra, India
| | - Sumit Dagar
- Bioenergy Group, MACS-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune 411004, Maharashtra, India; (N.K.); (V.P.); (D.S.)
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind Rd., Aundh, Pune 411007, Maharashtra, India
| | - Prashant K. Dhakephalkar
- Bioenergy Group, MACS-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune 411004, Maharashtra, India; (N.K.); (V.P.); (D.S.)
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind Rd., Aundh, Pune 411007, Maharashtra, India
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28
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Kocherlakota S, Baes M. Benefits and Caveats in the Use of Retinal Pigment Epithelium-Specific Cre Mice. Int J Mol Sci 2024; 25:1293. [PMID: 38279294 PMCID: PMC10816505 DOI: 10.3390/ijms25021293] [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: 12/18/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
The retinal pigment epithelium (RPE) is an important monolayer of cells present in the outer retina, forming a major part of the blood-retina barrier (BRB). It performs many tasks essential for the maintenance of retinal integrity and function. With increasing knowledge of the retina, it is becoming clear that both common retinal disorders, like age-related macular degeneration, and rare genetic disorders originate in the RPE. This calls for a better understanding of the functions of various proteins within the RPE. In this regard, mice enabling an RPE-specific gene deletion are a powerful tool to study the role of a particular protein within the RPE cells in their native environment, simultaneously negating any potential influences of systemic changes. Moreover, since RPE cells interact closely with adjacent photoreceptors, these mice also provide an excellent avenue to study the importance of a particular gene function within the RPE to the retina as a whole. In this review, we outline and compare the features of various Cre mice created for this purpose, which allow for inducible or non-inducible RPE-specific knockout of a gene of interest. We summarize the various benefits and caveats involved in the use of such mouse lines, allowing researchers to make a well-informed decision on the choice of Cre mouse to use in relation to their research needs.
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Affiliation(s)
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
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29
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Li L, Jia F, Li Y, Peng Y. Design strategies and biological applications of β-galactosidase fluorescent sensor in ovarian cancer research and beyond. RSC Adv 2024; 14:3010-3023. [PMID: 38239445 PMCID: PMC10795002 DOI: 10.1039/d3ra07968f] [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: 11/21/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024] Open
Abstract
Beta-galactosidase (β-galactosidase), a lysosomal hydrolytic enzyme, plays a critical role in the catalytic hydrolysis of glycosidic bonds, leading to the conversion of lactose into galactose. This hydrolytic enzyme is used as a biomarker in various applications, including enzyme-linked immunosorbent assays (ELISAs), gene expression studies, tuberculosis classification, and in situ hybridization. β-Galactosidase abnormalities are linked to various diseases, such as ganglioside deposition, primary ovarian cancer, and cell senescence. Thus, effective detection of β-galactosidase activity may aid disease diagnoses and treatment. Activatable optical probes with high sensitivity, specificity, and spatiotemporal resolution imaging capabilities have become powerful tools for visualization and real time tracking in vivo in the past decade. This manuscript reviews the sensing mechanism, molecular design strategies, and advances of fluorescence probes in the biological application of β-galactosidase, particularly in the field of ovarian cancer research. Current challenges in tracking β-galactosidase and future directions are also discussed.
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Affiliation(s)
- Liangliang Li
- Shenzhen Longhua District Central Hospital Guangzhou 518000 People's Republic of China
| | - Feifei Jia
- Shenzhen Longhua District Central Hospital Guangzhou 518000 People's Republic of China
| | - Yunxiu Li
- Shenzhen Longhua District Central Hospital Guangzhou 518000 People's Republic of China
| | - Yan Peng
- Shenzhen Longhua District Central Hospital Guangzhou 518000 People's Republic of China
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30
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Navarro MX, Brennan CK, Love AC, Prescher JA. Caged luciferins enable rapid multicomponent bioluminescence imaging. Photochem Photobiol 2024; 100:67-74. [PMID: 37259257 PMCID: PMC10687313 DOI: 10.1111/php.13814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/21/2023] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
Bioluminescence is a sensitive technique for imaging biological features over time. Historically, though, the modality has been challenging to employ for multiplexed tracking due to a lack of resolvable luciferase-luciferin pairs. Recent years have seen the development of numerous orthogonal probes for multi-parameter imaging. While successful, generating such tools often requires complex syntheses and lengthy enzyme evolution campaigns. This work showcases an alternative strategy for multiplexed bioluminescence that takes advantage of already-orthogonal caged luciferins and established uncaging enzymes. These probes generate unique bioluminescent signals that can be distinguished via a linear unmixing algorithm. Caged luciferins enabled two- and three-component imaging on the minutes time scale. We further showed that the tools can be used in conjunction with endogenous enzymes for multiplexed studies. Collectively, this approach lowers the barrier to multicomponent bioluminescence imaging and can be readily adopted by the broader community.
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Affiliation(s)
- Mariana X. Navarro
- Department of Chemistry, University of California, Irvine 1120 Natural Science II, Irvine, CA 92617 (USA)
| | - Caroline K. Brennan
- Department of Chemistry, University of California, Irvine 1120 Natural Science II, Irvine, CA 92617 (USA)
| | - Anna C. Love
- Department of Chemistry, University of California, Irvine 1120 Natural Science II, Irvine, CA 92617 (USA)
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine 1120 Natural Science II, Irvine, CA 92617 (USA)
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 3205 McGaugh Hall, Irvine, CA 92716 (USA)
- Department of Pharmaceutical Sciences, University of California, Irvine, 101 Theory, Suite 100, Irvine, CA 92617 (USA)
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31
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Song BPC, Ch'ng ACW, Lim TS. Review of phage display: A jack-of-all-trades and master of most biomolecule display. Int J Biol Macromol 2024; 256:128455. [PMID: 38013083 DOI: 10.1016/j.ijbiomac.2023.128455] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Phage display was first described by George P. Smith when it was shown that virus particles were capable of presenting foreign proteins on their surface. The technology has paved the way for the evolution of various biomolecules presentation and diverse selection strategies. This unique feature has been applied as a versatile platform for numerous applications in drug discovery, protein engineering, diagnostics, and vaccine development. Over the decades, the limits of biomolecules displayed on phage particles have expanded from peptides to proteomes and even alternative scaffolds. This has allowed phage display to be viewed as a versatile display platform to accommodate various biomolecules ranging from small peptides to larger proteomes which has significantly impacted advancements in the biomedical industry. This review will explore the vast array of biomolecules that have been successfully employed in phage display technology in biomedical research.
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Affiliation(s)
- Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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32
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Liu P, Chen Y, Ma C, Ouyang J, Zheng Z. β-Galactosidase: a traditional enzyme given multiple roles through protein engineering. Crit Rev Food Sci Nutr 2023:1-20. [PMID: 38108277 DOI: 10.1080/10408398.2023.2292282] [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: 12/19/2023]
Abstract
β-Galactosidases are crucial carbohydrate-active enzymes that naturally catalyze the hydrolysis of galactoside bonds in oligo- and disaccharides. These enzymes are commonly used to degrade lactose and produce low-lactose and lactose-free dairy products that are beneficial for lactose-intolerant people. β-galactosidases exhibit transgalactosylation activity, and they have been employed in the synthesis of galactose-containing compounds such as galactooligosaccharides. However, most β-galactosidases have intrinsic limitations, such as low transglycosylation efficiency, significant product inhibition effects, weak thermal stability, and a narrow substrate spectrum, which greatly hinder their applications. Enzyme engineering offers a solution for optimizing their catalytic performance. The study of the enzyme's structure paves the way toward explaining catalytic mechanisms and increasing the efficiency of enzyme engineering. In this review, the structure features of β-galactosidases from different glycosyl hydrolase families and the catalytic mechanisms are summarized in detail to offer guidance for protein engineering. The properties and applications of β-galactosidases are discussed. Additionally, the latest progress in β-galactosidase engineering and the strategies employed are highlighted. Based on the combined analysis of structure information and catalytic mechanisms, the ultimate goal of this review is to furnish a thorough direction for β-galactosidases engineering and promote their application in the food and dairy industries.
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Affiliation(s)
- Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, People's Republic of China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Yuehua Chen
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Jia Ouyang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Zhaojuan Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
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33
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Beal MA, Meier MJ, Dykes A, Yauk CL, Lambert IB, Marchetti F. The functional mutational landscape of the lacZ gene. iScience 2023; 26:108407. [PMID: 38058303 PMCID: PMC10696112 DOI: 10.1016/j.isci.2023.108407] [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: 05/11/2023] [Revised: 09/23/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023] Open
Abstract
The lacZ gene of Escherichia coli encodes β-galactosidase (β-gal), a lactose metabolism enzyme of the lactose operon. Previous chemical modification or site-directed mutagenesis experiments have identified 21 amino acids that are essential for β-gal catalytic activity. We have assembled over 10,000 lacZ mutations from published studies that were collected using a positive selection assay to identify mutations in lacZ that disrupted β-gal function. We analyzed 6,465 independent lacZ mutations that resulted in 2,732 missense mutations that impaired β-gal function. Those mutations affected 492 of the 1,023 lacZ codons, including most of the 21 previously known residues critical for catalytic activity. Most missense mutations occurred near the catalytic site and in regions important for subunit tetramerization. Overall, our work provides a comprehensive and detailed map of the amino acid residues affecting the structure and catalytic activity of the β-gal enzyme.
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Affiliation(s)
- Marc A. Beal
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Matthew J. Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Angela Dykes
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Iain B. Lambert
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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Feng B, Chu F, Bi A, Huang X, Fang Y, Liu M, Chen F, Li Y, Zeng W. Fidelity-oriented fluorescence imaging probes for beta-galactosidase: From accurate diagnosis to precise treatment. Biotechnol Adv 2023; 68:108244. [PMID: 37652143 DOI: 10.1016/j.biotechadv.2023.108244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/11/2023] [Accepted: 08/27/2023] [Indexed: 09/02/2023]
Abstract
Beta-galactosidase (β-gal), a typical glycosidase catalyzing the hydrolysis of glycosidic bonds, is regarded as a vital biomarker for cell senescence and cancer occurrence. Given the advantages of high spatiotemporal resolution, high sensitivity, non-invasiveness, and being free of ionizing radiations, fluorescent imaging technology provides an excellent choice for in vivo imaging of β-gal. In this review, we detail the representative biotech advances of fluorescence imaging probes for β-gal bearing diverse fidelity-oriented improvements to elucidate their future potential in preclinical research and clinical application. Next, we propose the comprehensive design strategies of imaging probes for β-gal with respect of high fidelity. Considering the systematic implementation approaches, a range of high-fidelity imaging-guided theragnostic are adopted for the individual β-gal-associated biological scenarios. Finally, current challenges and future trends are proposed to promote the next development of imaging agents for individual and specific application scenarios.
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Affiliation(s)
- Bin Feng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, PR China
| | - Feiyi Chu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, PR China
| | - Anyao Bi
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, PR China; Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha 410078, China
| | - Xueyan Huang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, PR China
| | - Yanpeng Fang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, PR China
| | - Meihui Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, PR China
| | - Fei Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, PR China
| | - Yanbing Li
- Department of Clinical Laboratory Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wenbin Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, PR China.
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35
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Merritt J, Kreth J. Illuminating the oral microbiome and its host interactions: tools and approaches for molecular microbiology studies. FEMS Microbiol Rev 2023; 47:fuac050. [PMID: 36549660 PMCID: PMC10719069 DOI: 10.1093/femsre/fuac050] [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: 08/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Advancements in DNA sequencing technologies within the last decade have stimulated an unprecedented interest in the human microbiome, largely due the broad diversity of human diseases found to correlate with microbiome dysbiosis. As a direct consequence of these studies, a vast number of understudied and uncharacterized microbes have been identified as potential drivers of mucosal health and disease. The looming challenge in the field is to transition these observations into defined molecular mechanistic studies of symbiosis and dysbiosis. In order to meet this challenge, many of these newly identified microbes will need to be adapted for use in experimental models. Consequently, this review presents a comprehensive overview of the molecular microbiology tools and techniques that have played crucial roles in genetic studies of the bacteria found within the human oral microbiota. Here, we will use specific examples from the oral microbiome literature to illustrate the biology supporting these techniques, why they are needed in the field, and how such technologies have been implemented. It is hoped that this information can serve as a useful reference guide to help catalyze molecular microbiology studies of the many new understudied and uncharacterized species identified at different mucosal sites in the body.
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Affiliation(s)
- Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, United States
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, United States
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36
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R G, Kar S, Nagai M, Mahapatra PS, Santra TS. Massively Parallel High-Throughput Single-Cell Patterning and Large Biomolecular Delivery in Mammalian Cells Using Light Pulses. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303053. [PMID: 37548122 DOI: 10.1002/smll.202303053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/21/2023] [Indexed: 08/08/2023]
Abstract
The recent advancements of single-cell analysis have significantly enhanced the ability to understand cellular physiology when compared to bulk cellular analysis. Here a massively parallel single-cell patterning and very large biomolecular delivery is reported. Micro-pillar polydimethyl siloxane stamp with different diameters (40-100 µm with 1 cm × 1 cm patterning area) is fabricated and then imprint distinct proteins and finally pattern single-cell to small clusters of cells depending on the micro-pillar diameters. The maximum patterning efficiency is achieved 99.7% for SiHa, 96.75% for L929, and 98.6% for MG63 cells, for the 100 µm micro-pillar stamp. For intracellular delivery of biomolecules into the patterned cells, a titanium micro-dish device is aligned on top of the cells and exposed by infrared light pulses. The platform successfully delivers small to very large biomolecules such as PI dyes (668 Da), dextran 3000 Da, siRNA (20-24 bp), and large size enzymes (464 KDa) in SiHa, L929 and MG63 cells. The delivery efficiency for PI dye, Dextran 3000, siRNA, and enzyme for patterned cells are ≈95 ± 3%, 97 ± 1%, 96 ± 1% and 94 ± 3%, with cell viability of 98 ± 1%. Thus, the platform is compact, robust, easy for printing, and potentially applicable for single-cell therapy and diagnostics.
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Affiliation(s)
- Gayathri R
- Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai, 600036, India
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Srabani Kar
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai, 600036, India
- Department of Physics, Indian Institute of Science Education and Research, Tirupati, 517507, India
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi, 441-8580, Japan
| | - Pallab Sinha Mahapatra
- Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Tuhin Subhra Santra
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai, 600036, India
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37
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Rawi MH, Tan HY, Sarbini SR. Identification of acacia gum fermenting bacteria from pooled human feces using anaerobic enrichment culture. Front Microbiol 2023; 14:1245042. [PMID: 37881253 PMCID: PMC10597704 DOI: 10.3389/fmicb.2023.1245042] [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: 06/23/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
Commercial acacia gum (AG) used in this study is a premium-grade free-flowing powder. It is a gummy exudate composed of arabinogalactan branched polysaccharide, a biopolymer of arabinose and galactose. Also known as food additive, acacia gum (E414), which is presently marketed as a functional dietary fiber to improve overall human gut health. The health effects may be related to the luminal pH regulation from the short-chain fatty acids (SCFA) production. Studies suggested that amylolytic and butyrogenic pathways are the major factors determining the SCFA outcome of AG in the lower gut. However, the primary bacteria involved in the fermentation have not been studied. This study aimed to investigate the putative primary degraders of acacia gum in the gut ecosystem. Isolation and identification of gum-fermenting bacteria were performed through enrichment culture fermentation. The experiment was conducted in an anaerobic chamber for 144 h in three stages. The study was conducted in triplicate using an anaerobic chamber system. This culture system allows specific responses to support only bacteria that are responsible for gum fermentation among the gut microbiota. Five bacterial strains were isolated and found to be gum-fermenting bacteria. Based on the 16s RNA sequence, the isolates matched to butyrate-producing Escherichia fergusonii, ATCC 35469.
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Affiliation(s)
- Muhamad Hanif Rawi
- Innovative Food Processing and Ingredients Research Group, Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Hui Yan Tan
- Department of Crop Science, Faculty of Agricultural Science and Forestry, Universiti Putra Malaysia Bintulu Campus, Bintulu, Sarawak, Malaysia
| | - Shahrul Razid Sarbini
- Department of Crop Science, Faculty of Agricultural Science and Forestry, Universiti Putra Malaysia Bintulu Campus, Bintulu, Sarawak, Malaysia
- Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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38
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Hunt JP, Free TJ, Galiardi J, Watt KM, Wood DW, Bundy BC. Streamlining the Detection of Human Thyroid Receptor Ligand Interactions with XL1-Blue Cell-Free Protein Synthesis and Beta-Galactosidase Fusion Protein Biosensors. Life (Basel) 2023; 13:1972. [PMID: 37895354 PMCID: PMC10608756 DOI: 10.3390/life13101972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Thyroid receptor signaling controls major physiological processes and disrupted signaling can cause severe disorders that negatively impact human life. Consequently, methods to detect thyroid receptor ligands are of great toxicologic and pharmacologic importance. Previously, we reported thyroid receptor ligand detection with cell-free protein synthesis of a chimeric fusion protein composed of the human thyroid receptor beta (hTRβ) receptor activator and a β-lactamase reporter. Here, we report a 60% reduction in sensing cost by reengineering the chimeric fusion protein biosensor to include a reporter system composed of either the full-length beta galactosidase (β-gal), the alpha fragment of β-gal (β-gal-α), or a split alpha fragment of the β-gal (split β-gal-α). These biosensor constructs are deployed using E. coli XL1-Blue cell extract to (1) avoid the β-gal background activity abundant in BL21 cell extract and (2) facilitate β-gal complementation reporter activity to detect human thyroid receptor ligands. These results constitute a promising platform for high throughput screening and potentially the portable detection of human thyroid receptor ligands.
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Affiliation(s)
- J. Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Tyler J. Free
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Jackelyn Galiardi
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Kevin M. Watt
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84108, USA
| | - David W. Wood
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
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39
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Belkova M, Janegova T, Hrabarova E, Nahalka J. Physiologically Aggregated LacZ Applied in Trehalose Galactosylation in a Recycled Batch Mode. Life (Basel) 2023; 13:1619. [PMID: 37629477 PMCID: PMC10455999 DOI: 10.3390/life13081619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/27/2023] Open
Abstract
Galactooligosaccharides obtained via β-galactosidase transgalactosylation have health-promoting properties and are widely recognized as effective prebiotics. Trehalose-based galactooligosaccharides could be introduced into food and pharmaceutical industries similarly to trehalose. In light of this, new technological approaches are needed. Recently, in vivo enzyme immobilizations for recombinant proteins have been introduced, and physiological aggregation into active inclusion bodies (aIBs) has emerged as one such method of in vivo immobilization. To prepare LacZ β-galactosidase in the form of aIBs, we used a short 10 amino acid aggregation-prone tag. These native protein particles were simply washed from the cell lysate and applied in trehalose galactosylation in a recycled batch mode. In this study, aIBs entrapped in alginate beads, encapsulated in alginate/cellulose sulfate/poly(methylene-co-guanidine) capsules and magnetized were compared with free aIBs. Alginate/cellulose sulfate/PMCG capsules showed more suitable properties and applicability for biotransformation of trehalose at its high concentration (25%, w/v) and elevated temperature (50 °C).
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Affiliation(s)
- Martina Belkova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska Cesta 9, SK-84538 Bratislava, Slovakia; (M.B.)
- Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovakia
| | - Tatiana Janegova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska Cesta 9, SK-84538 Bratislava, Slovakia; (M.B.)
- Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovakia
| | - Eva Hrabarova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska Cesta 9, SK-84538 Bratislava, Slovakia; (M.B.)
- Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovakia
| | - Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska Cesta 9, SK-84538 Bratislava, Slovakia; (M.B.)
- Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovakia
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40
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Hashim PK, Dokainish HM, Tamaoki N. Chaperonin GroEL hydrolyses ortho-nitrophenyl β-galactoside. Org Biomol Chem 2023. [PMID: 37464895 DOI: 10.1039/d3ob00989k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
We serendipitously found that chaperonin GroEL can hydrolyze ortho-nitrophenyl β-galactoside (ONPG), a well-known substrate of the enzyme β-galactosidase. The ONPG hydrolysis by GroEL follows typical enzyme kinetics. Our experiments and molecular docking studies suggest ONPG binding at the ATP binding site of GroEL.
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Affiliation(s)
- P K Hashim
- Research Institute for Electronic Science, Hokkaido University, Kita20, Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Hisham M Dokainish
- Center of Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, Hokkaido 060-0812, Japan
| | - Nobuyuki Tamaoki
- Research Institute for Electronic Science, Hokkaido University, Kita20, Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.
- Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
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41
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Zhang X, Tang Q, Sun J, Guo Y, Zhang S, Liang S, Dai P, Chen X. Cellular-scale proximity labeling for recording cell spatial organization in mouse tissues. SCIENCE ADVANCES 2023; 9:eadg6388. [PMID: 37235653 DOI: 10.1126/sciadv.adg6388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Proximity labeling has emerged as a powerful strategy for interrogating cell-cell interactions. However, the nanometer-scale labeling radius impedes the use of current methods for indirect cell communications and makes recording cell spatial organization in tissue samples difficult. Here, we develop quinone methide-assisted identification of cell spatial organization (QMID), a chemical strategy with the labeling radius matching the cell dimension. The activating enzyme is installed on the surface of bait cells, which produces QM electrophiles that can diffuse across micrometers and label proximal prey cells independent of cell-cell contacts. In cell coculture, QMID reveals gene expression of macrophages that are regulated by spatial proximity to tumor cells. Furthermore, QMID enables labeling and isolation of proximal cells of CD4+ and CD8+ T cells in the mouse spleen, and subsequent single-cell RNA sequencing uncovers distinctive cell populations and gene expression patterns within the immune niches of specific T cell subtypes. QMID should facilitate dissecting cell spatial organization in various tissues.
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Affiliation(s)
- Xu Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Qi Tang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Jiayu Sun
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Yilan Guo
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Shaoran Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shuyu Liang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Peng Dai
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
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42
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Jiang D, Tan Q, Shen Y, Ye M, Li J, Zhou Y. NIR-excited imaging and in vivo visualization of β-galactosidase activity using a pyranonitrile-modified upconversion nanoprobe. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 292:122411. [PMID: 36731306 DOI: 10.1016/j.saa.2023.122411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
β-galactosidase (β-gal) is a diagnostic biomarker of primary ovarian cancers. The development of effective fluorescent probes for investigating the activity of β-gal will be beneficial to cancer diagnosis. Herein, a near-infrared (NIR) excited ratiometric nanoprobe (DCM-β-gal-UCNPs) by assembling pyranonitrile dye (DCM-β-gal) on the surface of upconversion nanophosphors (UCNPs) was designed for the evaluation of β-gal activity in vivo. Upon the interaction with β-gal, a marked decrease of upconversion luminescence (UCL) signal in the green channel was observed owing to the luminescence resonance energy transfer from the UCNPs to pyranonitrile chromophore, whereas the NIR UCL emission at 800 nm was almost no influence. Thus, the β-gal activity could be quantitatively detected by the UCL intensity ratio of UCL543 nm/UCL800 nm with the limit of detection of 3.1 × 10-4 U/mL. Moreover, DCM-β-gal-UCNPs was effectively applied for monitoring β-gal fluctuation in living cells and zebrafish by a ratiometric UCL signal excited by 980 nm laser. We envision that nanoprobe DCM-β-gal-UCNPs might be used as a potential bioimaging tool to disclose more biological information of β-gal in β-gal-associated diseases in the future.
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Affiliation(s)
- Detao Jiang
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Qi Tan
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yuhan Shen
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Minan Ye
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Jingyun Li
- Department of Plastic&Cosmetic Surgery, Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, PR China
| | - Yi Zhou
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, PR China.
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43
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Zhao Y, Sun S, Lyu Y, Gao M, Lin H, Yang C. A near-infrared fluorescent nanoprobe for senescence-associated β-galactosidase sensing in living cells. Chem Commun (Camb) 2023; 59:2974-2977. [PMID: 36807350 DOI: 10.1039/d2cc05550c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
A near-infrared fluorescent nanoprobe based on semiconducting polymer nanoparticles (SPNs) for the detection of senescence-associated β-gal (SA-β-gal) is developed. Benefiting from the intrinsic lysosome-locating feature, this probe can be successfully used for the visualization of SA-β-gal in living cells.
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Affiliation(s)
- Ye Zhao
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
| | - Shan Sun
- International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
| | - Yan Lyu
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
| | - Mengyao Gao
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
| | - Hengwei Lin
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China. .,International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
| | - Cheng Yang
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
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44
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Xu L, Chu H, Gao D, Wu Q, Sun Y, Wang Z, Ma P, Song D. Chemosensor with Ultra-High Fluorescence Enhancement for Assisting in Diagnosis and Resection of Ovarian Cancer. Anal Chem 2023; 95:2949-2957. [PMID: 36695319 DOI: 10.1021/acs.analchem.2c04705] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fluorescence imaging-guided diagnostics is one of the most promising approaches for facile detection of tumors in situ owing to its simple operation and non-invasiveness. As a crucial biomarker for primary ovarian cancers, β-galactosidase (β-gal) has been demonstrated to be the significant molecular target for visualization of ovarian tumors. Herein, a membrane-permeable fluorescent chemosensor (namely, LAN-βgal) was synthesized for β-gal-specific detection using the d-galactose residue as a specific recognition unit and LAN-OH (ΦF = 0.47) as a fluorophore. After β-gal was digested, the fluorescence of the initially quenched LAN-βgal (ΦF < 0.001) was enhanced by up to more than 2000-fold, which exceeded the fluorescence enhancement of other previously reported probes. We also demonstrated that the chemosensor LAN-βgal could visualize endogenous β-gal and distinguish ovarian cancer cells from normal ovarian cells. Further, the chemosensor LAN-βgal was successfully applied to visualize the back tumor-bearing mouse model and peritoneal metastatic ovarian cancer model in vivo. More importantly, through in situ spraying, the proposed chemosensor was successfully employed to assist in the surgical resection of ovarian cancer tumors due to its high tumor-to-normal (T/N) tissue fluorescence ratio of 218. To the best of our knowledge, this is the highest T/N tissue fluorescence ratio ever reported. We believe that the LAN-βgal chemosensor can be utilized as a new tool for the clinical diagnosis and treatment of ovarian cancer.
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Affiliation(s)
- Lanlan Xu
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Hongyu Chu
- Nanomedicine and Translational Research Center, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Dejiang Gao
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Qiong Wu
- Nanomedicine and Translational Research Center, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Ying Sun
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Renmin Street 5625, Changchun 130022, China
| | - Pinyi Ma
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Daqian Song
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
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45
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Videira-Quintela D, Guillén F, Prazeres SF, Montalvo G. Immobilization of Kluyveromyces lactis β-Galactosidase on Meso-macroporous Silica: Use of Infrared Spectroscopy to Rationalize the Catalytic Efficiency. Chempluschem 2022; 87:e202200340. [PMID: 36515233 PMCID: PMC10369856 DOI: 10.1002/cplu.202200340] [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: 10/04/2022] [Revised: 11/16/2022] [Indexed: 11/20/2022]
Abstract
Enzyme immobilization on adequate carriers is a challenging strategy. Understanding the enzyme-carrier interactions and their effects on enzyme conformation and bioactivity is critical. In this study, a meso-macropores silica (MMS) was used to immobilize β-galactosidase from the yeast Kluyveromyces lactis (β-gal-KL) by physical adsorption. The bioactivity of the immobilized β-gal-KL was altered, evidenced by the increased Km , decreased Vmax and kcat , and increased activity at alkaline values. By performing infrared spectroscopy analysis and subsequent secondary structure assessment from the amide I band, the immobilized β-gal-KL suffered a β-sheet (∼31-35 %) to α-helix (∼15-19 %) transition with increased turns (∼21-22 %) with respect to the free β-gal-KL having ∼12 % α-helix, ∼42 % β-sheet, and ∼17 % turns. These findings led us to correlate the observed bioactivity performance to structural alterations to a non-native conformation. The presented line of thought can lead to a better understanding of the reasons causing bioactivity alterations upon enzyme immobilization.
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Affiliation(s)
- Diogo Videira-Quintela
- Facultad de Farmacia, Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Francisco Guillén
- Facultad de Farmacia, Departamento de Biomedicina y Biotecnología, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Sofia F Prazeres
- Facultad de Farmacia, Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Gemma Montalvo
- Facultad de Farmacia, Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain.,Instituto Universitario de Investigación en Ciencias Policiales, Universidad de Alcalá, Libreros 27, 28801, Madrid, Spain
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46
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A Review on Psychrophilic β-D-Galactosidases and Their Potential Applications. Appl Biochem Biotechnol 2022; 195:2743-2766. [PMID: 36422804 DOI: 10.1007/s12010-022-04215-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 11/25/2022]
Abstract
The majority of the Earth's ecosystem is frigid and frozen, which permits a vast range of microbial life forms to thrive by triggering physiological responses that allow them to survive in cold and frozen settings. The apparent biotechnology value of these cold-adapted enzymes has been targeted. Enzymes' market size was around USD 6.3 billion in 2017 and will witness growth at around 6.8% CAGR up to 2024 owing to shifting consumer preferences towards packaged and processed foods due to the rising awareness pertaining to food safety and security reported by Global Market Insights (Report ID-GMI 743). Various firms are looking for innovative psychrophilic enzymes in order to construct more effective biochemical pathways with shorter reaction times, use less energy, and are ecologically acceptable. D-Galactosidase catalyzes the hydrolysis of the glycosidic oxygen link between the terminal non-reducing D-galactoside unit and the glycoside molecule. At refrigerated temperature, the stable structure of psychrophile enzymes adjusts for the reduced kinetic energy. It may be beneficial in a wide variety of activities such as pasteurization of food, conversion of biomass, biological role of biomolecules, ambient biosensors, and phytoremediation. Recently, psychrophile enzymes are also used in claning the contact lens. β-D-Galactosidases have been identified and extracted from yeasts, fungi, bacteria, and plants. Conventional (hydrolyzing activity) and nonconventional (non-hydrolytic activity) applications are available for these enzymes due to its transgalactosylation activity which produce high value-added oligosaccharides. This review content will offer new perspectives on cold-active β-galactosidases, their source, structure, stability, and application.
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47
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Guo H, Ryan JC, Song X, Mallet A, Zhang M, Pabst V, Decrulle AL, Ejsmont P, Wintermute EH, Lindner AB. Spatial engineering of E. coli with addressable phase-separated RNAs. Cell 2022; 185:3823-3837.e23. [PMID: 36179672 DOI: 10.1016/j.cell.2022.09.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 04/25/2022] [Accepted: 09/06/2022] [Indexed: 01/26/2023]
Abstract
Biochemical processes often require spatial regulation and specific microenvironments. The general lack of organelles in bacteria limits the potential of bioengineering complex intracellular reactions. Here, we demonstrate synthetic membraneless organelles in Escherichia coli termed transcriptionally engineered addressable RNA solvent droplets (TEARS). TEARS are assembled from RNA-binding protein recruiting domains fused to poly-CAG repeats that spontaneously drive liquid-liquid phase separation from the bulk cytoplasm. Targeting TEARS with fluorescent proteins revealed multilayered structures with composition and reaction robustness governed by non-equilibrium dynamics. We show that TEARS provide organelle-like bioprocess isolation for sequestering biochemical pathways, controlling metabolic branch points, buffering mRNA translation rates, and scaffolding protein-protein interactions. We anticipate TEARS to be a simple and versatile tool for spatially controlling E. coli biochemistry. Particularly, the modular design of TEARS enables applications without expression fine-tuning, simplifying the design-build-test cycle of bioengineering.
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Affiliation(s)
- Haotian Guo
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France.
| | - Joseph C Ryan
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Xiaohu Song
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Adeline Mallet
- Ultrastructural BioImaging UTechS, C2RT, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France
| | - Mengmeng Zhang
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Science, Shenzhen, China
| | - Victor Pabst
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Antoine L Decrulle
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Paulina Ejsmont
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Edwin H Wintermute
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France.
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48
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Kang JTL, Teo JJY, Bertrand D, Ng A, Ravikrishnan A, Yong M, Ng OT, Marimuthu K, Chen SL, Chng KR, Gan YH, Nagarajan N. Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects. Nat Microbiol 2022; 7:1516-1524. [PMID: 36109646 PMCID: PMC9519440 DOI: 10.1038/s41564-022-01221-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 07/29/2022] [Indexed: 11/09/2022]
Abstract
AbstractLong-term colonization of the gut microbiome by carbapenemase-producing Enterobacteriaceae (CPE) is a growing area of public health concern as it can lead to community transmission and rapid increase in cases of life-threatening CPE infections. Here, leveraging the observation that many subjects are decolonized without interventions within a year, we used longitudinal shotgun metagenomics (up to 12 timepoints) for detailed characterization of ecological and evolutionary dynamics in the gut microbiome of a cohort of CPE-colonized subjects and family members (n = 46; 361 samples). Subjects who underwent decolonization exhibited a distinct ecological shift marked by recovery of microbial diversity, key commensals and anti-inflammatory pathways. In addition, colonization was marked by elevated but unstable Enterobacteriaceae abundances, which exhibited distinct strain-level dynamics for different species (Escherichia coli and Klebsiella pneumoniae). Finally, comparative analysis with whole-genome sequencing data from CPE isolates (n = 159) helped identify substrain variation in key functional genes and the presence of highly similar E. coli and K. pneumoniae strains with variable resistance profiles and plasmid sharing. These results provide an enhanced view into how colonization by multi-drug-resistant bacteria associates with altered gut ecology and can enable transfer of resistance genes, even in the absence of overt infection and antibiotic usage.
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49
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Mofokeng MM, Prinsloo G, Araya HT, Amoo SO, du Plooy CP, Mashela PW. NADES Compounds Identified in Hypoxis hemerocallidea Corms during Dormancy. PLANTS 2022; 11:plants11182387. [PMID: 36145788 PMCID: PMC9503605 DOI: 10.3390/plants11182387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 12/01/2022]
Abstract
Soaking Hypoxis hemerocallidea corms in distilled water improved the propagation and development of cormlets, suggesting the potential leaching-out of inhibitory chemical compounds. To investigate the presence of inhibitory compounds, nuclear magnetic resonance (NMR) spectral data of the leachate from dormant H. hemerocallidea corms were obtained using a 600 MHz 1H-NMR spectrometer. The 1H-NMR analysis led to the identification of choline, succinate, propylene glycol, and lactose, as inhibitory compounds. These four chemical compounds are part of the “Natural Deep Eutectic Solvents” (NADES) that protect plant cells during stress periods, each of which has the potential to inhibit bud growth and development. These compounds are supposedly leached out of the corms during the first rain under natural conditions, possibly accompanied by changes in the ratios of dormancy-breaking phytohormones and inhibitory compounds, to release bud dormancy. The identified chemical compounds heralded a novel frontier in the vegetative propagation of H. hemerocallidea as a medicinal plant, and for its enhanced sustainable uses.
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Affiliation(s)
- Motiki M. Mofokeng
- Agricultural Research Council—Vegetable, Industrial and Medicinal Plants (ARC-VIMP), Private Bag X293, Pretoria 0001, South Africa
- Green Technologies Research Centre, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
- Correspondence: (M.M.M.); (H.T.A.); (S.O.A.); Tel.: +27-12-808-8000 (M.M.M. & H.T.A. & S.O.A)
| | - Gerhard Prinsloo
- Department of Agriculture and Animal Health, University of South Africa, Private Bag X6, Johannesburg 1710, South Africa
| | - Hintsa T. Araya
- Agricultural Research Council—Vegetable, Industrial and Medicinal Plants (ARC-VIMP), Private Bag X293, Pretoria 0001, South Africa
- Correspondence: (M.M.M.); (H.T.A.); (S.O.A.); Tel.: +27-12-808-8000 (M.M.M. & H.T.A. & S.O.A)
| | - Stephen O. Amoo
- Agricultural Research Council—Vegetable, Industrial and Medicinal Plants (ARC-VIMP), Private Bag X293, Pretoria 0001, South Africa
- Department of Botany and Plant Biotechnology, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
- Correspondence: (M.M.M.); (H.T.A.); (S.O.A.); Tel.: +27-12-808-8000 (M.M.M. & H.T.A. & S.O.A)
| | - Christian P. du Plooy
- Agricultural Research Council—Vegetable, Industrial and Medicinal Plants (ARC-VIMP), Private Bag X293, Pretoria 0001, South Africa
| | - Phatu W. Mashela
- Green Technologies Research Centre, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
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50
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Almammadov T, Elmazoglu Z, Atakan G, Kepil D, Aykent G, Kolemen S, Gunbas G. Locked and Loaded: β-Galactosidase Activated Photodynamic Therapy Agent Enables Selective Imaging and Targeted Treatment of Glioblastoma Multiforme Cancer Cells. ACS APPLIED BIO MATERIALS 2022; 5:4284-4293. [PMID: 36043987 PMCID: PMC9490748 DOI: 10.1021/acsabm.2c00484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022]
Abstract
Selective detection and effective therapy of brain cancer, specifically, the very aggressive glioblastoma multiforme (GBM), remains one of the paramount challenges in clinical settings. While radiotherapy combined surgery is proposed as the main treatment course, it has several drawbacks such as complexity of the operation and common development of recurrent tumors in this course of patient care. Unique opportunities presented by photodynamic therapy (PDT) offer promising, effective, and precise therapy against GBM cells along with simultaneous imaging opportunities. However, activatable, theranostic molecular systems in PDT modality for GBM remained scarce. Specifically, even though elevated β-galactosidase (β-gal) activity in glioblastoma cells is well-documented, targeted, activatable therapeutic PDT agents have not been realized. Herein, we report a β-galactosidase (β-gal) activatable phototheranostic agent based on an iodinated resorufin core (RB-1) which was realized in only three steps with commercial reagents in 29% overall yield. RB-1 showed very high singlet oxygen (1O2) quantum yield (54%) accompanied by a remarkable turn-on response in fluorescence upon enzymatic activation. RB-1 was tested in different cell lines and revealed selective photocytotoxicity in U-87MG glioblastoma cells. Additionally, thanks to almost 7% fluorescence quantum yield (ΦF) despite extremely high 1O2 generation yield, RB-1 was also demonstrated as a successful agent for fluorescence imaging of U-87MG cells. Due to significantly lower (β-gal) activity in healthy cells (NIH/3T3), RB-1 stayed in a passive state and showed minimal photo and dark toxicity. RB-1 marks the first example of a β-gal activatable phototheranostic agent toward effective treatment of glioblastoma.
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Affiliation(s)
- Toghrul Almammadov
- Department
of Chemistry, Koç University, Rumelifeneri Yolu, 34450 Istanbul, Turkey
| | - Zubeyir Elmazoglu
- Department
of Chemistry, Middle East Technical University
(METU), 06800 Ankara, Turkey
| | - Gizem Atakan
- Department
of Chemistry, Middle East Technical University
(METU), 06800 Ankara, Turkey
| | - Dilay Kepil
- Department
of Chemistry, Middle East Technical University
(METU), 06800 Ankara, Turkey
| | - Guzide Aykent
- Department
of Chemistry, Middle East Technical University
(METU), 06800 Ankara, Turkey
| | - Safacan Kolemen
- Department
of Chemistry, Koç University, Rumelifeneri Yolu, 34450 Istanbul, Turkey
- Surface
Science and Technology Center (KUYTAM), Koç University, 34450 Istanbul, Turkey
- Boron
and Advanced Materials Application and Research Center, Koç University, 34450 Istanbul, Turkey
| | - Gorkem Gunbas
- Department
of Chemistry, Middle East Technical University
(METU), 06800 Ankara, Turkey
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