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Zhou Y, Zhang Y, Rosi NL. Imparting Stability to Chiral Helical Gold Nanoparticle Superstructures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40. [PMID: 39018267 PMCID: PMC11295200 DOI: 10.1021/acs.langmuir.4c01531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/13/2024] [Accepted: 07/01/2024] [Indexed: 07/19/2024]
Abstract
Realizing the promise of chiral inorganic nanomaterials hinges on improving their structural stability under various chemical and environmental conditions. Here, we examine the stability of 1-D gold nanoparticle (Au NP) single helices prepared using the amphiphilic peptide conjugate Cx-(PEPAuM-ox)2 (PEPAuM-ox = AYSSGAPPMoxPPF; x = 16-22). We present a general template-independent strategy of tuning helix stability that relies on controlling the dimensions of constituent NPs. As NP dimensions increase, Au NP single helices become both more thermally stable and more stable in the presence of chemical denaturants and protein digestion agents (e.g., urea and proteinase K, respectively). We use this strategy for imparting helix stability to create colloidal suspensions of thermally robust Au NP single helices which maintain their plasmonic chiroptical activity up to ∼80 °C.
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Affiliation(s)
- Yicheng Zhou
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yuyu Zhang
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Nathaniel L. Rosi
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemical and Petroleum Engineering, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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2
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Lv B, Wang X, Li J, Xu Y, Jiang B, Zhao D, Li C. Proteomics analysis of the influence of proteolysis on the subsequent glycation of myofibrillar protein. Food Chem 2024; 431:137084. [PMID: 37579610 DOI: 10.1016/j.foodchem.2023.137084] [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: 12/21/2022] [Revised: 07/09/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
Proteomics was used to study the influence of proteolysis on the glycation of myofibrillar proteins (MPs). Proteolysis by papain and proteinase K generated the highest level of amino acids (AAs) and peptides, respectively. Both the glycation degree (A value increased from 0.173 to 0.202-0.348) and speed (k value increased from 0.0099 to 0.0132-0.0145) were enhanced by proteolysis using papain and proteinase K. Proteomics analysis revealed that proteolysis largely enhanced the glycation site number in Lys, Arg and N-terminal residues (eg. Leu, Gly, Thr, Ala, Met, Ile, Phe and Val residues in myosin light chain). Proteolysis by papain preferentially acted on actin and therefore specifically increased the glycation sites from actin. Proteolysis reduced the level of aldehydes but enhanced the aromatic E-nose signals, possibly due to the combination of aldehydes with released AAs/peptides. The proteomics analysis helped to detail the relationship between proteolysis and subsequent glycation/flavour formation.
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Affiliation(s)
- Bowen Lv
- Key Laboratory of Meat Processing and Quality Control, MOE, Nanjing 210095, PR China; Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Nanjing 210095, PR China; Key Laboratory of Meat Products Processing, MOA, Nanjing 210095, PR China; Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaoqing Wang
- Key Laboratory of Meat Processing and Quality Control, MOE, Nanjing 210095, PR China; Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Nanjing 210095, PR China; Key Laboratory of Meat Products Processing, MOA, Nanjing 210095, PR China; Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiaxin Li
- Key Laboratory of Meat Processing and Quality Control, MOE, Nanjing 210095, PR China; Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Nanjing 210095, PR China; Key Laboratory of Meat Products Processing, MOA, Nanjing 210095, PR China; Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yao Xu
- Key Laboratory of Meat Processing and Quality Control, MOE, Nanjing 210095, PR China; Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Nanjing 210095, PR China; Key Laboratory of Meat Products Processing, MOA, Nanjing 210095, PR China; Nanjing Agricultural University, Nanjing 210095, PR China
| | - Boya Jiang
- Key Laboratory of Meat Processing and Quality Control, MOE, Nanjing 210095, PR China; Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Nanjing 210095, PR China; Key Laboratory of Meat Products Processing, MOA, Nanjing 210095, PR China; Nanjing Agricultural University, Nanjing 210095, PR China
| | - Di Zhao
- Key Laboratory of Meat Processing and Quality Control, MOE, Nanjing 210095, PR China; Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Nanjing 210095, PR China; Key Laboratory of Meat Products Processing, MOA, Nanjing 210095, PR China; Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Chunbao Li
- Key Laboratory of Meat Processing and Quality Control, MOE, Nanjing 210095, PR China; Jiangsu Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Nanjing 210095, PR China; Key Laboratory of Meat Products Processing, MOA, Nanjing 210095, PR China; Nanjing Agricultural University, Nanjing 210095, PR China
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3
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Dhar R, Bowman AM, Hatungimana B, Sg Slusky J. Evolutionary Engineering a Larger Porin Using a Loop-to-Hairpin Mechanism. J Mol Biol 2023; 435:168292. [PMID: 37769963 PMCID: PMC11215794 DOI: 10.1016/j.jmb.2023.168292] [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: 06/14/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
In protein evolution, diversification is generally driven by genetic duplication. The hallmarks of this mechanism are visible in the repeating topology of various proteins. In outer membrane β-barrels, duplication is visible with β-hairpins as the repeating unit of the barrel. In contrast to the overall use of duplication in diversification, a computational study hypothesized evolutionary mechanisms other than hairpin duplications leading to increases in the number of strands in outer membrane β-barrels. Specifically, the topology of some 16- and 18-stranded β-barrels appear to have evolved through a loop to β-hairpin transition. Here we test this novel evolutionary mechanism by creating a chimeric protein from an 18-stranded β-barrel and an evolutionarily related 16-stranded β-barrel. The chimeric combination of the two was created by replacing loop L3 of the 16-stranded barrel with the sequentially matched transmembrane β-hairpin region of the 18-stranded barrel. We find the resulting chimeric protein is stable and has characteristics of increased strand number. This study provides the first experimental evidence supporting the evolution through a loop to β-hairpin transition.
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Affiliation(s)
- Rik Dhar
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA. https://twitter.com/Rik_Skywalker
| | - Alexander M Bowman
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Brunojoel Hatungimana
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Joanna Sg Slusky
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA; Computational Biology Program, The University of Kansas, Lawrence, KS 66047, USA.
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4
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Falkenberg F, Bott M, Bongaerts J, Siegert P. Phylogenetic survey of the subtilase family and a data-mining-based search for new subtilisins from Bacillaceae. Front Microbiol 2022; 13:1017978. [PMID: 36225363 PMCID: PMC9549277 DOI: 10.3389/fmicb.2022.1017978] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
The subtilase family (S8), a member of the clan SB of serine proteases are ubiquitous in all kingdoms of life and fulfil different physiological functions. Subtilases are divided in several groups and especially subtilisins are of interest as they are used in various industrial sectors. Therefore, we searched for new subtilisin sequences of the family Bacillaceae using a data mining approach. The obtained 1,400 sequences were phylogenetically classified in the context of the subtilase family. This required an updated comprehensive overview of the different groups within this family. To fill this gap, we conducted a phylogenetic survey of the S8 family with characterised holotypes derived from the MEROPS database. The analysis revealed the presence of eight previously uncharacterised groups and 13 subgroups within the S8 family. The sequences that emerged from the data mining with the set filter parameters were mainly assigned to the subtilisin subgroups of true subtilisins, high-alkaline subtilisins, and phylogenetically intermediate subtilisins and represent an excellent source for new subtilisin candidates.
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Affiliation(s)
- Fabian Falkenberg
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
- *Correspondence: Petra Siegert,
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5
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Reher R, Aron AT, Fajtová P, Stincone P, Wagner B, Pérez-Lorente AI, Liu C, Shalom IYB, Bittremieux W, Wang M, Jeong K, Matos-Hernandez ML, Alexander KL, Caro-Diaz EJ, Naman CB, Scanlan JHW, Hochban PMM, Diederich WE, Molina-Santiago C, Romero D, Selim KA, Sass P, Brötz-Oesterhelt H, Hughes CC, Dorrestein PC, O'Donoghue AJ, Gerwick WH, Petras D. Native metabolomics identifies the rivulariapeptolide family of protease inhibitors. Nat Commun 2022; 13:4619. [PMID: 35941113 PMCID: PMC9358669 DOI: 10.1038/s41467-022-32016-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 07/12/2022] [Indexed: 11/15/2022] Open
Abstract
The identity and biological activity of most metabolites still remain unknown. A bottleneck in the exploration of metabolite structures and pharmaceutical activities is the compound purification needed for bioactivity assignments and downstream structure elucidation. To enable bioactivity-focused compound identification from complex mixtures, we develop a scalable native metabolomics approach that integrates non-targeted liquid chromatography tandem mass spectrometry and detection of protein binding via native mass spectrometry. A native metabolomics screen for protease inhibitors from an environmental cyanobacteria community reveals 30 chymotrypsin-binding cyclodepsipeptides. Guided by the native metabolomics results, we select and purify five of these compounds for full structure elucidation via tandem mass spectrometry, chemical derivatization, and nuclear magnetic resonance spectroscopy as well as evaluation of their biological activities. These results identify rivulariapeptolides as a family of serine protease inhibitors with nanomolar potency, highlighting native metabolomics as a promising approach for drug discovery, chemical ecology, and chemical biology studies. Bioactivity-guided isolation of specialized metabolites is an iterative process. Here, the authors demonstrate a native metabolomics approach that allows for fast screening of complex metabolite extracts against a protein of interest and simultaneous structure annotation.
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Affiliation(s)
- Raphael Reher
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany.,Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, Marburg, Germany
| | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Paolo Stincone
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Berenike Wagner
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Alicia I Pérez-Lorente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Chenxi Liu
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Ido Y Ben Shalom
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Kyowon Jeong
- Applied Bioinformatics, Computer Science Department, University of Tuebingen, Tuebingen, Germany
| | - Marie L Matos-Hernandez
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico
| | - Kelsey L Alexander
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Eduardo J Caro-Diaz
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico
| | - C Benjamin Naman
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - J H William Scanlan
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology (ZTI), University of Marburg, Marburg, Germany
| | - Phil M M Hochban
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology (ZTI), University of Marburg, Marburg, Germany
| | - Wibke E Diederich
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology (ZTI), University of Marburg, Marburg, Germany
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Khaled A Selim
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Peter Sass
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Heike Brötz-Oesterhelt
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.,German Center for Infection Research, Partner Site Tuebingen, Tuebingen, Germany
| | - Chambers C Hughes
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.,German Center for Infection Research, Partner Site Tuebingen, Tuebingen, Germany
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA.
| | - Daniel Petras
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA. .,Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany. .,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.
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6
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Freckelton ML, Nedved BT, Cai YS, Cao S, Turano H, Alegado RA, Hadfield MG. Bacterial lipopolysaccharide induces settlement and metamorphosis in a marine larva. Proc Natl Acad Sci U S A 2022; 119:e2200795119. [PMID: 35467986 PMCID: PMC9651628 DOI: 10.1073/pnas.2200795119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/16/2022] [Indexed: 08/09/2023] Open
Abstract
How larvae of the many phyla of marine invertebrates find places appropriate for settlement, metamorphosis, growth, and reproduction is an enduring question in marine science. Biofilm-induced metamorphosis has been observed in marine invertebrate larvae from nearly every major marine phylum. Despite the widespread nature of this phenomenon, the mechanism of induction remains poorly understood. The serpulid polychaete Hydroides elegans is a well established model for investigating bacteria-induced larval development. A broad range of biofilm bacterial species elicit larval metamorphosis in H. elegans via at least two mechanisms, including outer membrane vesicles (OMVs) and complexes of phage-tail bacteriocins. We investigated the interaction between larvae of H. elegans and the inductive bacterium Cellulophaga lytica, which produces an abundance of OMVs but not phage-tail bacteriocins. We asked whether the OMVs of C. lytica induce larval settlement due to cell membrane components or through delivery of specific cargo. Employing a biochemical structure–function approach with a strong ecological focus, the cells and OMVs produced by C. lytica were interrogated to determine the class of the inductive compounds. Here, we report that larvae of H. elegans are induced to metamorphose by lipopolysaccharide produced by C. lytica. The widespread prevalence of lipopolysaccharide and its associated taxonomic and structural variability suggest it may be a broadly employed cue for bacterially induced larval settlement of marine invertebrates.
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Affiliation(s)
| | - Brian T. Nedved
- Kewalo Marine Laboratory, University of Hawaiʻi, Honolulu, HI 96813
| | - You-Sheng Cai
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawaiʻi at Hilo, Hilo, HI 96720
- Department of Nephrology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People’s Republic of China
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawaiʻi at Hilo, Hilo, HI 96720
| | - Helen Turano
- Department of Oceanography, University of Hawaiʻi Mānoa, Honolulu, HI 96813
| | - Rosanna A. Alegado
- Department of Oceanography, University of Hawaiʻi Mānoa, Honolulu, HI 96813
- Sea Grant College Program, University of Hawaiʻi Mānoa, Honolulu, HI 96813
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7
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Belaouni HA, Compant S, Antonielli L, Nikolic B, Zitouni A, Sessitsch A. In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region. Appl Microbiol Biotechnol 2022; 106:3113-3137. [PMID: 35435457 DOI: 10.1007/s00253-022-11907-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/16/2022] [Accepted: 03/26/2022] [Indexed: 11/02/2022]
Abstract
Endophytic strains belonging to the Bacillus cereus group were isolated from the halophytes Atriplex halimus L. (Amaranthaceae) and Tamarix aphylla L. (Tamaricaceae) from costal and continental regions in Algeria. Based on their salt tolerance (up to 5%), the strains were tested for their ability to alleviate salt stress in tomato and wheat. Bacillus sp. strain BH32 showed the highest potential to reduce salinity stress (up to + 50% and + 58% of dry weight improvement, in tomato and wheat, respectively, compared to the control). To determine putative mechanisms involved in salt tolerance and plant growth promotion, the whole genome of Bacillus sp. BH32 was sequenced, annotated, and used for comparative genomics against the genomes of closely related strains. The pangenome of Bacillus sp. BH32 and its closest relative was further analyzed. The phylogenomic analyses confirmed its taxonomic position, a member of the Bacillus cereus group, with intergenomic distances (GBDP analysis) pinpointing to a new taxon (digital DNA-DNA hybridization, dDDH < 70%). Genome mining unveiled several genes involved in stress tolerance, production of anti-oxidants and genes involved in plant growth promotion as well as in the production of secondary metabolites. KEY POINTS : • Bacillus sp. BH32 and other bacterial endophytes were isolated from halophytes, to be tested on tomato and wheat and to limit salt stress adverse effects. • The strain with the highest potential was then studied at the genomic level to highlight numerous genes linked to plant growth promotion and stress tolerance. • Pangenome approaches suggest that the strain belongs to a new taxon within the Bacillus cereus group.
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Affiliation(s)
- Hadj Ahmed Belaouni
- Laboratoire de Biologie Des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria.
| | - Livio Antonielli
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria
| | - Branislav Nikolic
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria
| | - Abdelghani Zitouni
- Laboratoire de Biologie Des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, 3430, Tulln, Austria
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8
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Jameson JF, Pacheco MO, Butler JE, Stoppel WL. Estimating Kinetic Rate Parameters for Enzymatic Degradation of Lyophilized Silk Fibroin Sponges. Front Bioeng Biotechnol 2021; 9:664306. [PMID: 34295878 PMCID: PMC8290342 DOI: 10.3389/fbioe.2021.664306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/31/2021] [Indexed: 11/25/2022] Open
Abstract
Sponge-like biomaterials formed from silk fibroin are promising as degradable materials in clinical applications due to their controllable breakdown into simple amino acids or small peptides in vivo. Silk fibroin, isolated from Bombyx mori silkworm cocoons, can be used to form sponge-like materials with a variety of tunable parameters including the elastic modulus, porosity and pore size, and level of nanocrystalline domains. These parameters can be independently tuned during formulation resulting in a wide parameter space and set of final materials. Determining the mechanism and rate constants for biomaterial degradation of these tunable silk materials would allow scientists to evaluate and predict the biomaterial performance for the large array of tissue engineering applications and patient ailments a priori. We first measured in vitro degradation rates of silk sponges using common protein-degrading enzymes such as Proteinase K and Protease XIV. The concentration of the enzyme in solution was varied (1, 0.1, 0.01 U/mL) along with one silk sponge formulation parameter: the level of crystallinity within the sponge. Additionally, two experimental degradation methods were evaluated, termed continuous and discrete degradation methods. Silk concentration, polymer chain length and scaffold pore size were held constant during experimentation and kinetic parameter estimation. Experimentally, we observed that the enzyme itself, enzyme concentration within the bulk solution, and the sponge fabrication water annealing time were the major experimental parameters dictating silk sponge degradation in our experimental design. We fit the experimental data to two models, a Michaelis-Menten kinetic model and a modified first order kinetic model. Weighted, non-linear least squares analysis was used to determine the parameters from the data sets and Monte-Carlo simulations were utilized to obtain estimates of the error. We found that modified first order reaction kinetics fit the time-dependent degradation of lyophilized silk sponges and we obtained first order-like rate constants. These results represent the first investigations into determining kinetic parameters to predict lyophilized silk sponge degradation rates and can be a tool for future mathematical representations of silk biomaterial degradation.
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Affiliation(s)
- Julie F Jameson
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, United States
| | - Marisa O Pacheco
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, United States
| | - Jason E Butler
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, United States
| | - Whitney L Stoppel
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, United States
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9
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Peng J, Lu Y, Song J, Vallance BA, Jacobson K, Yu HB, Sun Z. Direct Clinical Evidence Recommending the Use of Proteinase K or Dithiothreitol to Pretreat Sputum for Detection of SARS-CoV-2. Front Med (Lausanne) 2020; 7:549860. [PMID: 33043036 PMCID: PMC7530184 DOI: 10.3389/fmed.2020.549860] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/27/2020] [Indexed: 01/08/2023] Open
Abstract
One of the primary tools for diagnosing COVID-19 is the nucleic acid-based real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test performed on respiratory specimens. The detection rate of SARS-CoV-2 in lower respiratory specimens (such as sputum) is higher than that for upper respiratory specimens (such as nasal and pharyngeal swabs). However, sputum specimens are usually quite viscous, requiring a homogenization process prior to nucleic acid (NA) extraction for RT-PCR. Sputum specimens from COVID-19 and non-COVID-19 patients were treated with four commonly used reagents—saline, N-acetyl-L-cysteine (NALC), proteinase K (PK), and dithiothreitol (DTT), prior to NA extraction. These reagents were then compared for their performance in diagnosing COVID-19 in real clinical practice. The detection rate of SARS-CoV-2 in PK- or DTT-treated sputum was comparable, and higher than that in sputum treated with NALC or saline. While there was a 4.8% (1/21) false negative rate for the PK- and DTT-treated sputum, neither treatment showed any false positive cases among patients with non-COVID diseases. Moreover, sputum pretreated with saline, NALC, PK or DTT showed higher detection rates of SARS-CoV-2 as compared to pharyngeal swabs. Taken together, we provide direct evidence recommending the use of PK or DTT to pretreat sputum samples to facilitate SARS-CoV-2 detection by clinical laboratories. Moreover, our methods should help to standardize the procedure of processing sputum specimens and improve the ability to detect SARS-CoV-2 in these samples.
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Affiliation(s)
- Jing Peng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Song
- Department of Gastroenterology & Endocrinology, Wuhan No. 9 Hospital, Wuhan, China
| | - Bruce A Vallance
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kevan Jacobson
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Hong Bing Yu
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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10
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Huhmann S, Koksch B. Fine-Tuning the Proteolytic Stability of Peptides with Fluorinated Amino Acids. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800803] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Susanne Huhmann
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustr. 3 14169 Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustr. 3 14169 Berlin Germany
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11
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Diaz G, Bridges C, Lucas M, Cheng Y, Schorey JS, Dobos KM, Kruh-Garcia NA. Protein Digestion, Ultrafiltration, and Size Exclusion Chromatography to Optimize the Isolation of Exosomes from Human Blood Plasma and Serum. J Vis Exp 2018. [PMID: 29708539 DOI: 10.3791/57467] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Exosomes, a type of nanovesicle released from all cell types, can be isolated from any bodily fluid. The contents of exosomes, including proteins and RNAs, are unique to the cells from which they are derived and can be used as indicators of disease. Several common enrichment protocols, including ultracentrifugation, yield exosomes laden with soluble protein contaminants. Specifically, we have found that the most abundant proteins within blood often co-purify with exosomes and can confound downstream proteomic studies, thwarting the identification of low abundance biomarker candidates. Of additional concern is irreproducibility of exosome protein quantification due to inconsistent representation of non-exosomal protein levels. The protocol detailed here was developed to remove non-exosomal proteins that co-purify along with exosomes, adding rigor to the exosome purification process. Five methods were compared using paired blood plasma and serum from five donors. Analysis using nanoparticle tracking analysis and micro bicinchoninic acid protein assay revealed that a combined protocol utilizing ultrafiltration and size exclusion chromatography yielded the optimal vesicle enrichment and soluble protein removal. Western blotting was used to verify that the expected abundant blood proteins, including albumin and apolipoproteins, were depleted.
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Affiliation(s)
- Gustavo Diaz
- Department of Microbiology, Immunology and Pathology, Colorado State University
| | - Chandler Bridges
- Department of Microbiology, Immunology and Pathology, Colorado State University
| | - Megan Lucas
- Department of Microbiology, Immunology and Pathology, Colorado State University
| | - Yong Cheng
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame
| | - Jeff S Schorey
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame
| | - Karen M Dobos
- Department of Microbiology, Immunology and Pathology, Colorado State University
| | - Nicole A Kruh-Garcia
- Department of Microbiology, Immunology and Pathology, Colorado State University;
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12
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Yu F, Qiu T, Zeng Y, Wang Y, Zheng S, Chen X, Chen Y. Comparative Evaluation of Three Preprocessing Methods for Extraction and Detection of Influenza A Virus Nucleic Acids from Sputum. Front Med (Lausanne) 2018; 5:56. [PMID: 29552562 PMCID: PMC5840144 DOI: 10.3389/fmed.2018.00056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/16/2018] [Indexed: 11/13/2022] Open
Abstract
Viscous sputum specimens usually cannot undergo automated extraction, and thus, a pre-homogenization process is desirable before isolating nucleic acids for real-time reverse transcription PCR. In this study, we compared three preprocessing methods [preprocessing with normal saline (NS), dithiothreitol (DTT), and proteinase K (PK)] of sputum specimens on the extraction and detection of influenza A virus (IAV) nucleic acids. Based on the experimental results of 217 specimens, we found that DTT and PK could be used to improve the homogenization effects of sputum and increase the positive rates by 5.53-6.91% higher than that of the NS group. Comparison of 49 positive specimens in all of the three groups demonstrated that the threshold cycle values of the DTT group and PK group were significantly lower and their nucleic acid concentration and A260/A280 ratio within 1.8-2.0 were higher than those of the NS group. Thus, sputum homogenization before nucleic acid extraction is essential for the accurate diagnosis of IAV infection.
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Affiliation(s)
- Fei Yu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ting Qiu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Ying Zeng
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Yiyin Wang
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shufa Zheng
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Chen
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yu Chen
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
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13
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Huhmann S, Stegemann AK, Folmert K, Klemczak D, Moschner J, Kube M, Koksch B. Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion. Beilstein J Org Chem 2017; 13:2869-2882. [PMID: 29564015 PMCID: PMC5753150 DOI: 10.3762/bjoc.13.279] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/13/2017] [Indexed: 12/22/2022] Open
Abstract
Rapid digestion by proteases limits the application of peptides as therapeutics. One strategy to increase the proteolytic stability of peptides is the modification with fluorinated amino acids. This study presents a systematic investigation of the effects of fluorinated leucine and isoleucine derivatives on the proteolytic stability of a peptide that was designed to comprise substrate specificities of different proteases. Therefore, leucine, isoleucine, and their side-chain fluorinated variants were site-specifically incorporated at different positions of this peptide resulting in a library of 13 distinct peptides. The stability of these peptides towards proteolysis by α-chymotrypsin, pepsin, proteinase K, and elastase was studied, and this process was followed by an FL-RP-HPLC assay in combination with mass spectrometry. In a few cases, we observed an exceptional increase in proteolytic stability upon introduction of the fluorine substituents. The opposite phenomenon was observed in other cases, and this may be explained by specific interactions of fluorinated residues with the respective enzyme binding sites. Noteworthy is that 5,5,5-trifluoroisoleucine is able to significantly protect peptides from proteolysis by all enzymes included in this study when positioned N-terminal to the cleavage site. These results provide valuable information for the application of fluorinated amino acids in the design of proteolytically stable peptide-based pharmaceuticals.
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Affiliation(s)
- Susanne Huhmann
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Anne-Katrin Stegemann
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Kristin Folmert
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Damian Klemczak
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Johann Moschner
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Michelle Kube
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Beate Koksch
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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14
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Comprehensive Spatial Analysis of the Borrelia burgdorferi Lipoproteome Reveals a Compartmentalization Bias toward the Bacterial Surface. J Bacteriol 2017; 199:JB.00658-16. [PMID: 28069820 DOI: 10.1128/jb.00658-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/03/2017] [Indexed: 12/13/2022] Open
Abstract
The Lyme disease spirochete Borrelia burgdorferi is unique among bacteria in its large number of lipoproteins that are encoded by a small, exceptionally fragmented, and predominantly linear genome. Peripherally anchored in either the inner or outer membrane and facing either the periplasm or the external environment, these lipoproteins assume varied roles. A prominent subset of lipoproteins functioning as the apparent linchpins of the enzootic tick-vertebrate infection cycle have been explored as vaccine targets. Yet, most of the B. burgdorferi lipoproteome has remained uncharacterized. Here, we comprehensively and conclusively localize the B. burgdorferi lipoproteome by applying established protein localization assays to a newly generated epitope-tagged lipoprotein expression library and by validating the obtained individual protein localization results using a sensitive global mass spectrometry approach. The derived consensus localization data indicate that 86 of the 125 analyzed lipoproteins encoded by B. burgdorferi are secreted to the bacterial surface. Thirty-one of the remaining 39 periplasmic lipoproteins are retained in the inner membrane, with only 8 lipoproteins being anchored in the periplasmic leaflet of the outer membrane. The localization of 10 lipoproteins was further defined or revised, and 52 surface and 23 periplasmic lipoproteins were newly localized. Cross-referencing prior studies revealed that the borrelial surface lipoproteome contributing to the host-pathogen interface is encoded predominantly by plasmids. Conversely, periplasmic lipoproteins are encoded mainly by chromosomal loci. These studies close a gap in our understanding of the functional lipoproteome of an important human pathogen and set the stage for more in-depth studies of thus-far-neglected spirochetal lipoproteins.IMPORTANCE The small and exceptionally fragmented genome of the Lyme disease spirochete Borrelia burgdorferi encodes over 120 lipoproteins. Studies in the field have predominantly focused on a relatively small number of surface lipoproteins that play important roles in the transmission and pathogenesis of this global human pathogen. Yet, a comprehensive spatial assessment of the entire borrelial lipoproteome has been missing. The current study newly identifies 52 surface and 23 periplasmic lipoproteins. Overall, two-thirds of the B. burgdorferi lipoproteins localize to the surface, while outer membrane lipoproteins facing the periplasm are rare. This analysis underscores the dominant contribution of lipoproteins to the spirochete's rather complex and adaptable host-pathogen interface, and it encourages further functional exploration of its lipoproteome.
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15
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Sung H, Yong D, Ki CS, Kim JS, Seong MW, Lee H, Kim MN. Comparative Evaluation of Three Homogenization Methods for Isolating Middle East Respiratory Syndrome Coronavirus Nucleic Acids From Sputum Samples for Real-Time Reverse Transcription PCR. Ann Lab Med 2017; 36:457-62. [PMID: 27374711 PMCID: PMC4940489 DOI: 10.3343/alm.2016.36.5.457] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/22/2016] [Accepted: 05/17/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Real-time reverse transcription PCR (rRT-PCR) of sputum samples is commonly used to diagnose Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Owing to the difficulty of extracting RNA from sputum containing mucus, sputum homogenization is desirable prior to nucleic acid isolation. We determined optimal homogenization methods for isolating viral nucleic acids from sputum. METHODS We evaluated the following three sputum-homogenization methods: proteinase K and DNase I (PK-DNase) treatment, phosphate-buffered saline (PBS) treatment, and N-acetyl-L-cysteine and sodium citrate (NALC) treatment. Sputum samples were spiked with inactivated MERS-CoV culture isolates. RNA was extracted from pretreated, spiked samples using the easyMAG system (bioMérieux, France). Extracted RNAs were then subjected to rRT-PCR for MERS-CoV diagnosis (DiaPlex Q MERS-coronavirus, SolGent, Korea). RESULTS While analyzing 15 spiked sputum samples prepared in technical duplicate, false-negative results were obtained with five (16.7%) and four samples (13.3%), respectively, by using the PBS and NALC methods. The range of threshold cycle (Ct) values observed when detecting upE in sputum samples was 31.1-35.4 with the PK-DNase method, 34.7-39.0 with the PBS method, and 33.9-38.6 with the NALC method. Compared with the control, which were prepared by adding a one-tenth volume of 1:1,000 diluted viral culture to PBS solution, the ranges of Ct values obtained by the PBS and NALC methods differed significantly from the mean control Ct of 33.2 (both P<0.0001). CONCLUSIONS The PK-DNase method is suitable for homogenizing sputum samples prior to RNA extraction.
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Affiliation(s)
- Heungsup Sung
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea.
| | - Dongeun Yong
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Chang Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hallym University Kangdong Sacred Heart Hospital, Seoul, Korea
| | - Moon Woo Seong
- Department of Laboratory Medicine, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine, International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon, Korea
| | - Mi Na Kim
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea.
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16
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Ma Y, Sato R, Li Z, Numata K. Chemoenzymatic Synthesis of Oligo(L-cysteine) for Use as a Thermostable Bio-Based Material. Macromol Biosci 2015; 16:151-9. [PMID: 26388290 DOI: 10.1002/mabi.201500255] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/13/2015] [Indexed: 11/06/2022]
Abstract
Oligomerization of thiol-unprotected L-cysteine ethyl ester (Cys-OEt) catalyzed by proteinase K in aqueous solution has been used to synthesize oligo(L-cysteine) (OligoCys) with a well-defined chemical structure and relatively large degree of polymerization (DP) up to 16-17 (average 8.8). By using a high concentration of Cys-OEt, 78.0% free thiol content was achieved. The thermal properties of OligoCys are stable, with no glass transition until 200 °C, and the decomposition temperature could be increased by oxidation. Chemoenzymatically synthesized OligoCys has great potential for use as a thermostable bio-based material with resistance to oxidation.
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Affiliation(s)
- Yinan Ma
- Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ryota Sato
- Enzyme Research Team, Biomass Engineering Program Cooperation Division, Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Zhibo Li
- Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. .,School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Keiji Numata
- Enzyme Research Team, Biomass Engineering Program Cooperation Division, Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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17
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Ulasi GN, Creese AJ, Hui SX, Penn CW, Cooper HJ. Comprehensive mapping of O-glycosylation in flagellin from Campylobacter jejuni 11168: A multienzyme differential ion mobility mass spectrometry approach. Proteomics 2015; 15:2733-45. [PMID: 25884275 PMCID: PMC4975691 DOI: 10.1002/pmic.201400533] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/09/2015] [Accepted: 04/14/2015] [Indexed: 11/19/2022]
Abstract
Glycosylation of flagellin is essential for the virulence of Campylobacter jejuni, a leading cause of bacterial gastroenteritis. Here, we demonstrate comprehensive mapping of the O‐glycosylation of flagellin from Campylobacter jejuni 11168 by use of a bottom‐up proteomics approach that incorporates differential ion mobility spectrometry (also known as high field asymmetric waveform ion mobility spectrometry or FAIMS) together with proteolysis with proteinase K. Proteinase K provides complementary sequence coverage to that achieved following trypsin proteolysis. The use of FAIMS increased the number of glycopeptides identified. Novel glycans for this strain were identified (pseudaminic acid and either acetamidino pseudaminic acid or legionaminic acid), as were novel glycosylation sites: Thr208, Ser343, Ser348, Ser349, Ser395, Ser398, Ser423, Ser433, Ser436, Ser445, Ser448, Ser451, Ser452, Ser454, Ser457 and Thr465. Multiply glycosylated peptides were observed, as well as variation at individual residues in the nature of the glycan and its presence or absence. Such extreme heterogeneity in the pattern of glycosylation has not been reported previously, and suggests a novel dimension in molecular variation within a bacterial population that may be significant in persistence of the organism in its natural environment. These results demonstrate the usefulness of differential ion mobility in proteomics investigations of PTMs.
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Affiliation(s)
- Gloria N Ulasi
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Andrew J Creese
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Sam Xin Hui
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Charles W Penn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
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18
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Hua S, Hu CY, Kim BJ, Totten SM, Oh MJ, Yun N, Nwosu CC, Yoo JS, Lebrilla CB, An HJ. Glyco-Analytical Multispecific Proteolysis (Glyco-AMP): A Simple Method for Detailed and Quantitative Glycoproteomic Characterization. J Proteome Res 2013; 12:4414-23. [DOI: 10.1021/pr400442y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Serenus Hua
- Asia Glycomics Reference Site, Daejeon 305-764, South Korea
- Cancer
Research Institute, Chungnam National University, Daejeon 305-764, South Korea
| | - Chloe Y. Hu
- Department
of Chemistry, University of California—Davis, Davis, California 95616, United States
| | - Bum Jin Kim
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, South Korea
| | - Sarah M. Totten
- Department
of Chemistry, University of California—Davis, Davis, California 95616, United States
| | - Myung Jin Oh
- Asia Glycomics Reference Site, Daejeon 305-764, South Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, South Korea
| | - Nayoung Yun
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, South Korea
| | - Charles C. Nwosu
- Department
of Chemistry, University of California—Davis, Davis, California 95616, United States
| | - Jong Shin Yoo
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, South Korea
- Division
of Mass Spectrometry Research, Korea Basic Science Institute, Ochang 363-883, South Korea
| | - Carlito B. Lebrilla
- Department
of Chemistry, University of California—Davis, Davis, California 95616, United States
| | - Hyun Joo An
- Asia Glycomics Reference Site, Daejeon 305-764, South Korea
- Cancer
Research Institute, Chungnam National University, Daejeon 305-764, South Korea
- Graduate
School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, South Korea
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19
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Narita J, Katagiri M, Tsuji H. Highly enhanced accelerating effect of melt-recrystallized stereocomplex crystallites on poly(L-lactic acid) crystallization: effects of molecular weight of poly(D-lactic acid). POLYM INT 2012. [DOI: 10.1002/pi.4381] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Junichi Narita
- Mitsui Chemicals Tohcello Co. Ltd; Kanda Mitoshiro-cho; Chiyoda-ku, Tokyo; 101-8485; Japan
| | - Mikio Katagiri
- Mitsui Chemicals Tohcello Co. Ltd; Kanda Mitoshiro-cho; Chiyoda-ku, Tokyo; 101-8485; Japan
| | - Hideto Tsuji
- Department of Environmental and Life Sciences; Graduate School of Engineering, Toyohashi University of Technology; Tempaku-cho; Toyohashi, Aichi; 441-8580; Japan
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20
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Chatake T, Ishikawa T, Yanagisawa Y, Yamada T, Tanaka I, Fujiwara S, Morimoro Y. High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1334-8. [PMID: 22102227 PMCID: PMC3212446 DOI: 10.1107/s1744309111031903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 08/06/2011] [Indexed: 11/11/2022]
Abstract
Deuteration of macromolecules is an important technique in neutron protein crystallography. Solvent deuteration of protein crystals is carried out by replacing water (H(2)O) with heavy water (D(2)O) prior to neutron diffraction experiments in order to diminish background noise. The effects of solvent deuteration on the crystallization of proteinase K (PK) with polyethylene glycol as a precipitant were investigated using high-resolution X-ray crystallography. In previous studies, eight NO(3)(-) anions were included in the PK crystal unit cell grown in NaNO(3) solution. In this study, however, the PK crystal structure did not contain NO(3)(-) anions; consequently, distortions of amino acids arising from the presence of NO(3)(-) anions were avoided in the present crystal structures. High-resolution (1.1 Å) X-ray diffraction studies showed that the degradation of PK crystals induced by solvent deuteration was so small that this degradation would be negligible for the purpose of neutron protein crystallography experiments at medium resolution. Comparison of the nonhydrogen structures of nondeuterated and deuterated crystal structures demonstrated very small structural differences. Moreover, a positive correlation between the root-mean-squared differences and B factors indicated that no systematic difference existed.
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Affiliation(s)
- Toshiyuki Chatake
- Research Reactor Institute, Kyoto University, Ashashironishi 2, Kumatori, Osaka, Japan.
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21
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Abstract
Recently, the concept of apoptotic cell elimination was expanded and programed cell death is no longer viewed as an individual cellular event. The complete description of the apoptotic process now includes two phases: the self-driven cell disassembly and the externally-controlled elimination of apoptotic cell corpses by phagocytizing cells. The second, phagocytic phase is essential, highly conserved, and is even more important than the internal phase of cell disassembly. This is because it ensures the complete degradation of the dying cell's DNA, preventing the release of pathological, viral and tumor DNA, and self-immunization. In different cells and species from mammals to flies, a single conserved enzyme--DNase II is responsible for the elimination of cellular DNA in the second "mopping up" phase of apoptosis. Here, we present an assay for the selective detection of the phagocytic phase of apoptosis. The technology capitalizes on the fact that phagocytic DNase II produces identifiable signature DNA breaks, which can be labeled by vaccinia topoisomerase. The assay permits labeling of the previously underestimated phase of apoptotic execution and is a useful tool in the apoptosis detection arsenal.
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Affiliation(s)
- Vladimir V Didenko
- Departments of Neurosurgery and Molecular & Cellular Biology, Baylor College of Medicine, and Michael E. DeBakey VA Medical Center, Houston, TX, USA.
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22
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Tsuji H. Poly(lactide) Stereocomplexes: Formation, Structure, Properties, Degradation, and Applications. Macromol Biosci 2005; 5:569-97. [PMID: 15997437 DOI: 10.1002/mabi.200500062] [Citation(s) in RCA: 882] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Poly(lactide)s [i.e. poly(lactic acid) (PLA)] and lactide copolymers are biodegradable, compostable, producible from renewable resources, and nontoxic to the human body and the environment. They have been used as biomedical materials for tissue regeneration, matrices for drug delivery systems, and alternatives for commercial polymeric materials to reduce the impact on the environment. Since stereocomplexation or stereocomplex formation between enantiomeric PLA, poly(L-lactide) [i.e. poly(L-lactic acid) (PLLA)] and poly(D-lactide) [i.e. poly(D-lactic acid) (PDLA)] was reported in 1987, numerous studies have been carried out with respect to the formation, structure, properties, degradation, and applications of the PLA stereocomplexes. Stereocomplexation enhances the mechanical properties, the thermal-resistance, and the hydrolysis-resistance of PLA-based materials. These improvements arise from a peculiarly strong interaction between L-lactyl unit sequences and D-lactyl unit sequences, and stereocomplexation opens a new way for the preparation of biomaterials such as hydrogels and particles for drug delivery systems. It was revealed that the crucial parameters affecting stereocomplexation are the mixing ratio and the molecular weight of L-lactyl and D-lactyl unit sequences. On the other hand, PDLA was found to form a stereocomplex with L-configured polypeptides in 2001. This kind of stereocomplexation is called "hetero-stereocomplexation" and differentiated from "homo-stereocomplexation" between L-lactyl and D-lactyl unit sequences. This paper reviews the methods for tracing PLA stereocomplexation, the methods for inducing PLA stereocompelxation, the parameters affecting PLA stereocomplexation, and the structure, properties, degradation, and applications of a variety of stereocomplexed PLA materials.
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Affiliation(s)
- Hideto Tsuji
- Department of Ecological Engineering, Faculty of Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan.
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