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Journal articles on the topic 'SfGFP, superfolder green fluorescent protein'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 February 2022

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1

Pedelacq, Jean-Denis, and Stéphanie Cabantous. "Development and Applications of Superfolder and Split Fluorescent Protein Detection Systems in Biology." International Journal of Molecular Sciences 20, no. 14 (2019): 3479. http://dx.doi.org/10.3390/ijms20143479.

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Molecular engineering of the green fluorescent protein (GFP) into a robust and stable variant named Superfolder GFP (sfGFP) has revolutionized the field of biosensor development and the use of fluorescent markers in diverse area of biology. sfGFP-based self-associating bipartite split-FP systems have been widely exploited to monitor soluble expression in vitro, localization, and trafficking of proteins in cellulo. A more recent class of split-FP variants, named « tripartite » split-FP, that rely on the self-assembly of three GFP fragments, is particularly well suited for the detection of prote

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2

Olenginski, Gregory M., Juliana Piacentini, Darcy R. Harris, et al. "Structural and spectrophotometric investigation of two unnatural amino-acid altered chromophores in the superfolder green fluorescent protein." Acta Crystallographica Section D Structural Biology 77, no. 8 (2021): 1010–18. http://dx.doi.org/10.1107/s2059798321006525.

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The spectrophotometric properties of the green fluorescent protein (GFP) result from the post-translationally cyclized chromophore composed of three amino acids including a tyrosine at the center of the β-barrel protein. Altering the amino acids in the chromophore or the nearby region has resulted in numerous GFP variants with differing photophysical properties. To further examine the effect of small atomic changes in the chromophore on the structure and photophysical properties of GFP, the hydroxyl group of the chromophore tyrosine was replaced with a nitro or a cyano group. The structures an

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Maurici, Nicole, Nicole Savidge, Byung Uk Lee, Scott H. Brewer, and Christine M. Phillips-Piro. "Crystal structures of green fluorescent protein with the unnatural amino acid 4-nitro-L-phenylalanine." Acta Crystallographica Section F Structural Biology Communications 74, no. 10 (2018): 650–55. http://dx.doi.org/10.1107/s2053230x1801169x.

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The X-ray crystal structures of two superfolder green fluorescent protein (sfGFP) constructs containing a genetically incorporated spectroscopic reporter unnatural amino acid, 4-nitro-L-phenylalanine (pNO2F), at two unique sites in the protein have been determined. Amber codon-suppression methodology was used to site-specifically incorporate pNO2F at a solvent-accessible (Asp133) and a partially buried (Asn149) site in sfGFP. The Asp133pNO2F sfGFP construct crystallized with two molecules per asymmetric unit in space group P3221 and the crystal structure was refined to 2.05 Å resolution. Cryst

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Lajoie, Patrick, Robyn D. Moir, Ian M. Willis, and Erik L. Snapp. "Kar2p availability defines distinct forms of endoplasmic reticulum stress in living cells." Molecular Biology of the Cell 23, no. 5 (2012): 955–64. http://dx.doi.org/10.1091/mbc.e11-12-0995.

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Accumulation of misfolded secretory proteins in the endoplasmic reticulum (ER) activates the unfolded protein response (UPR) stress pathway. To enhance secretory protein folding and promote adaptation to stress, the UPR upregulates ER chaperone levels, including BiP. Here we describe chromosomal tagging of KAR2, the yeast homologue of BiP, with superfolder green fluorescent protein (sfGFP) to create a multifunctional endogenous reporter of the ER folding environment. Changes in Kar2p-sfGFP fluorescence levels directly correlate with UPR activity and represent a robust reporter for high-through

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Jahangir, ZMG Sarwar, and Arleta Helena Marnik. "A study protocol to prepare an RBD protein for vaccine against COVID-19." F1000Research 10 (September 20, 2021): 943. http://dx.doi.org/10.12688/f1000research.54738.1.

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Background: The SARS-CoV-2 pandemic is a global threat to humans and the world’s economy. Effective and safe vaccines against this virus are essential to control and eradicate the pandemic. The currently applied vaccines carry SARS-CoV-2 spike-protein mRNA/cDNA. These vaccines go through several cellular processes in the recipients for producing antigens. On the contrary, the SARS-CoV-2 RBD (receptor binding domain)-protein is an antigen. It will directly stimulate antibody production against SARS-CoV-2. Hence, we propose to produce SARS-CoV-2 RBD-protein as a fast acting, effective and safe v

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Ramadani-Muja, Jeta, Benjamin Gottschalk, Katharina Pfeil, et al. "Visualization of Sirtuin 4 Distribution between Mitochondria and the Nucleus, Based on Bimolecular Fluorescence Self-Complementation." Cells 8, no. 12 (2019): 1583. http://dx.doi.org/10.3390/cells8121583.

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Mitochondrial sirtuins (Sirts) control important cellular processes related to stress. Despite their regulatory importance, however, the dynamics and subcellular distributions of Sirts remain debatable. Here, we investigate the subcellular localization of sirtuin 4 (Sirt4), a sirtuin variant with a mitochondrial targeting sequence (MTS), by expressing Sirt4 fused to the superfolder green fluorescent protein (Sirt4-sfGFP) in HeLa and pancreatic β-cells. Super resolution fluorescence microscopy revealed the trapping of Sirt4-sfGFP to the outer mitochondrial membrane (OMM), possibly due to slow m

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7

Gao, Wei, Ning Bu, and Yuan Lu. "Efficient Incorporation of Unnatural Amino Acids into Proteins with a Robust Cell-Free System." Methods and Protocols 2, no. 1 (2019): 16. http://dx.doi.org/10.3390/mps2010016.

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Unnatural proteins are crucial biomacromolecules and have been widely applied in fundamental science, novel biopolymer materials, enzymes, and therapeutics. Cell-free protein synthesis (CFPS) system can serve as a robust platform to synthesize unnatural proteins by highly effective site-specific incorporation of unnatural amino acids (UNAAs), without the limitations of cell membrane permeability and the toxicity of unnatural components. Here, we describe a quick and simple method to synthesize unnatural proteins in CFPS system based on Escherichia coli crude extract, with unnatural orthogonal

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8

Subach, Oksana M., and Fedor V. Subach. "GAF-CaMP3–sfGFP, An Enhanced Version of the Near-Infrared Genetically Encoded Positive Phytochrome-Based Calcium Indicator for the Visualization of Neuronal Activity." International Journal of Molecular Sciences 21, no. 18 (2020): 6883. http://dx.doi.org/10.3390/ijms21186883.

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The first generation of near-infrared, genetically encoded calcium indicators (NIR-GECIs) was developed from bacterial phytochrome-based fluorescent proteins that utilize biliverdin (BV) as the chromophore moiety. However, NIR-GECIs have some main drawbacks such as either an inverted response to calcium ions (in the case of NIR-GECO1) or a limited dynamic range and a lack of data about their application in neurons (in the case of GAF-CaMP2–superfolder green fluorescent protein (sfGFP)). Here, we developed an enhanced version of the GAF-CaMP2–sfGFP indicator, named GAF-CaMP3–sfGFP. The GAF-CaMP

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Dippel, Andrew B., Gregory M. Olenginski, Nicole Maurici, Melanie T. Liskov, Scott H. Brewer, and Christine M. Phillips-Piro. "Probing the effectiveness of spectroscopic reporter unnatural amino acids: a structural study." Acta Crystallographica Section D Structural Biology 72, no. 1 (2016): 121–30. http://dx.doi.org/10.1107/s2059798315022858.

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The X-ray crystal structures of superfolder green fluorescent protein (sfGFP) containing the spectroscopic reporter unnatural amino acids (UAAs) 4-cyano-L-phenylalanine (pCNF) or 4-ethynyl-L-phenylalanine (pCCF) at two unique sites in the protein have been determined. These UAAs were genetically incorporated into sfGFP in a solvent-exposed loop region and/or a partially buried site on the β-barrel of the protein. The crystal structures containing the UAAs at these two sites permit the structural implications of UAA incorporation for the native protein structure to be assessed with high resolut

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10

Khmelinskii, Anton, Matthias Meurer, Chi-Ting Ho, et al. "Incomplete proteasomal degradation of green fluorescent proteins in the context of tandem fluorescent protein timers." Molecular Biology of the Cell 27, no. 2 (2016): 360–70. http://dx.doi.org/10.1091/mbc.e15-07-0525.

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Tandem fluorescent protein timers (tFTs) report on protein age through time-dependent change in color, which can be exploited to study protein turnover and trafficking. Each tFT, composed of two fluorescent proteins (FPs) that differ in maturation kinetics, is suited to follow protein dynamics within a specific time range determined by the maturation rates of both FPs. So far, tFTs have been constructed by combining slower-maturing red fluorescent proteins (redFPs) with the faster-maturing superfolder green fluorescent protein (sfGFP). Toward a comprehensive characterization of tFTs, we compar

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11

Shen, Jing, Wenlu Zhang, Chunyang Gan, et al. "Strategies to improve the fluorescent signal of the tripartite sfGFP system." Acta Biochimica et Biophysica Sinica 52, no. 9 (2020): 998–1006. http://dx.doi.org/10.1093/abbs/gmaa073.

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Abstract Bimolecular fluorescence complementation (BiFC) is a popular method used to detect protein–protein interactions. For a BiFC assay, a fluorescent protein is usually split into two parts, and the fluorescence is recovered upon the interaction between the fused proteins of interest. As an elegant extension of BiFC, a tripartite superfold green fluorescent protein (sfGFP) system that has the advantages of low background fluorescence and small fusion tag size has been developed. However, the tripartite system exhibits a low fluorescence signal in some cases. To address this problem, we pro

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12

Wu, Xudong, Di Wu, Zhisheng Lu, Wentao Chen, Xiaojian Hu, and Yu Ding. "A Novel Method for High-Level Production of TEV Protease by Superfolder GFP Tag." Journal of Biomedicine and Biotechnology 2009 (2009): 1–8. http://dx.doi.org/10.1155/2009/591923.

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Because of its stringent sequence specificity, tobacco etch virus (TEV) protease is widely used to remove fusion tags from recombinant proteins. Due to the poor solubility of TEV protease, many strategies have been employed to increase the expression level of this enzyme. In our work, we introduced a novel method to produce TEV protease by using visible superfolder green fluorescent protein (sfGFP) as the fusion tag. The soluble production and catalytic activity of six variants ofsfGFP-TEV was examined, and then the best variant was selected for large-scale production. After purified by Ni-NTA

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13

Bai, Chaoxian, Yang Zhang, Xuejin Zhao, et al. "Exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products in Streptomyces." Proceedings of the National Academy of Sciences 112, no. 39 (2015): 12181–86. http://dx.doi.org/10.1073/pnas.1511027112.

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There is a great demand for precisely quantitating the expression of genes of interest in synthetic and systems biotechnology as new and fascinating insights into the genetics of streptomycetes have come to light. Here, we developed, for the first time to our knowledge, a quantitative method based on flow cytometry and a superfolder green fluorescent protein (sfGFP) at single-cell resolution in Streptomyces. Single cells of filamentous bacteria were obtained by releasing the protoplasts from the mycelium, and the dead cells could be distinguished from the viable ones by propidium iodide (PI) s

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14

Liauw, Pasqual, Daniela Kannchen, Raphael Gasper, Nina Dyczmons-Nowaczyk, Marc M. Nowaczyk, and Eckhard Hofmann. "Cloning, expression, crystallization and preliminary X-ray studies of a superfolder GFP fusion of cyanobacterial Psb32." Acta Crystallographica Section F Structural Biology Communications 71, no. 4 (2015): 409–13. http://dx.doi.org/10.1107/s2053230x15003970.

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A fusion of Psb32 from the thermophilic cyanobacteriumThermosynechococcus elongatusBP-1 (TePsb32) with superfolder GFP was created for enhanced solubility and improved detection and purification. The fusion protein readily formed large hexagonal crystals belonging to space groupP6122. A full data set extending to 2.3 Å resolution was collected at the Swiss Light Source. The phase problem could be solved by using only the sfGFP fusion partner or by using GFP andAtTLP18.3 fromArabidopsis thalianaas search models. Based on this expression construct, a versatile library of 24 vectors combining fou

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15

Valbuena, Fernando M., Ivy Fitzgerald, Rita L. Strack, Neal Andruska, Luke Smith, and Benjamin S. Glick. "A photostable monomeric superfolder green fluorescent protein." Traffic 21, no. 8 (2020): 534–44. http://dx.doi.org/10.1111/tra.12737.

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16

Dinh, T., and T. G. Bernhardt. "Using Superfolder Green Fluorescent Protein for Periplasmic Protein Localization Studies." Journal of Bacteriology 193, no. 18 (2011): 4984–87. http://dx.doi.org/10.1128/jb.00315-11.

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17

Pédelacq, Jean-Denis, Stéphanie Cabantous, Timothy Tran, Thomas C. Terwilliger, and Geoffrey S. Waldo. "Engineering and characterization of a superfolder green fluorescent protein." Nature Biotechnology 24, no. 1 (2005): 79–88. http://dx.doi.org/10.1038/nbt1172.

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18

Pe´delacq, Jean-Denis, Stéphanie Cabantous, Timothy Tran, Thomas C. Terwilliger, and Geoffrey S. Waldo. "Correction: Corrigendum: Engineering and characterization of a superfolder green fluorescent protein." Nature Biotechnology 24, no. 9 (2006): 1170. http://dx.doi.org/10.1038/nbt0906-1170d.

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19

Nguyen, Nam Hoai, Trang Thi Phuong Phan, Thuoc Linh Tran, and Hoang Duc Nguyen. "Cloning and investigating GFP (green fluorescent protein) allowing higher expression in Bacillus subtilis." Science and Technology Development Journal 18, no. 2 (2015): 46–55. http://dx.doi.org/10.32508/stdj.v18i2.1142.

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Gfp gene coding for protein GFP (green fluorescent protein) from the jellyfish Aequorea victoria is the most popular indicator protein, due to (i) easy to recognize the expression through the fluorescent ability, (ii) without substrate or cofactor, (iii) less impact on the fusion protein target form. A lot of modifications of GFP have been studied and improved, in which GFP superfolder containing beneficial properties such as rapid folding, structural stability and strong fluorescence showed great applicability. However, GFP superfolder has just been developed in Escherichia coli. It is diffic

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20

Zhou, Jun, Jian Lin, Cuihong Zhou, Xiaoyan Deng, and Bin Xia. "An improved bimolecular fluorescence complementation tool based on superfolder green fluorescent protein." Acta Biochimica et Biophysica Sinica 43, no. 3 (2011): 239–44. http://dx.doi.org/10.1093/abbs/gmq128.

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21

Slocum, Joshua D., and Lauren J. Webb. "A Double Decarboxylation in Superfolder Green Fluorescent Protein Leads to High Contrast Photoactivation." Journal of Physical Chemistry Letters 8, no. 13 (2017): 2862–68. http://dx.doi.org/10.1021/acs.jpclett.7b01101.

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22

Al-Homsi, Lamis, Souad Al-Okla, and Abdul Q. Abbady. "Preparation of Specific Polyclonal Antibody Against the Recombinant Mutacin Produced by sfGFP Fusion Protein Technology." Open Microbiology Journal 9, no. 1 (2015): 70–80. http://dx.doi.org/10.2174/1874285801509010070.

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Mutacin I, a bacteriocin produced bystreptococcus mutans, displays an antimicrobial activity against many gram positive and some gram negative bacteria. Because of its medical importance, production of this short peptide in large scale for future applications is a significant challenge. This work described the improvement of a novel system to produce the recombinant mutacin using fusion protein technology.The short peptide was expressed directly as a fusion protein with a superfolder form of the green florescent protein (sfGFP), resulting in a high yield expression of solublesfGFP-mutacin fusi

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23

Tansila, Natta, Kristian Becker, Chartchalerm Isarankura Na-Ayudhya, Virapong Prachayasittikul, and Leif Bülow. "Metal ion accessibility of histidine-modified superfolder green fluorescent protein expressed in Escherichia coli." Biotechnology Letters 30, no. 8 (2008): 1391–96. http://dx.doi.org/10.1007/s10529-008-9692-7.

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Bose, Jeffrey L., Paul D. Fey, and Kenneth W. Bayles. "Genetic Tools To Enhance the Study of Gene Function and Regulation in Staphylococcus aureus." Applied and Environmental Microbiology 79, no. 7 (2013): 2218–24. http://dx.doi.org/10.1128/aem.00136-13.

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ABSTRACTThebursa aurealistransposon has been used to create transposon insertion libraries ofBacillus anthracisandStaphylococcus aureus. To provide a set of genetic tools to enhance the utility of these libraries, we generated an allelic-exchange system that allows for the replacement of the transposon with useful genetic markers and fluorescent reporter genes. These tools were tested in the Nebraska Transposon Mutant Library (NTML), containing defined transposon insertions in 1,952 nonessentialS. aureusgenes. First, we generated a plasmid that allows researchers to replace the genes encoding

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Sakhabeev, R. G., D. S. Polyakov, A. D. Goshina, et al. "Enhancing the specific T cell immune response against micro- and nanoparticle immobilized antigen." Russian Journal of Infection and Immunity 11, no. 4 (2021): 777–83. http://dx.doi.org/10.15789/2220-7619-ets-1374.

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The current study was a part of the project on generating viral particle traps occurring due to covalent immobilization on the interface of recombinant virus-specific polymer-based nano- and microparticles. It is assumed that protein-particle conjugates could be able to bind virions followed by engulfment by immune cells. The study was aimed to examine the effect of polylactic acid (PLA) and PLA block-copolymer with polyethylene glycol (PLA-PEG)-based micro- and nanoparticles on the cellular immune response against polymeric particle-bound antigen. Materials and methods. A recombinant chimeric

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Overkamp, Wout, Katrin Beilharz, Ruud Detert Oude Weme, et al. "Benchmarking Various Green Fluorescent Protein Variants in Bacillus subtilis, Streptococcus pneumoniae, and Lactococcus lactis for Live Cell Imaging." Applied and Environmental Microbiology 79, no. 20 (2013): 6481–90. http://dx.doi.org/10.1128/aem.02033-13.

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ABSTRACTGreen fluorescent protein (GFP) offers efficient ways of visualizing promoter activity and protein localizationin vivo, and many different variants are currently available to study bacterial cell biology. Which of these variants is best suited for a certain bacterial strain, goal, or experimental condition is not clear. Here, we have designed and constructed two “superfolder” GFPs with codon adaptation specifically forBacillus subtilisandStreptococcus pneumoniaeand have benchmarked them against five other previously available variants of GFP inB. subtilis,S. pneumoniae, andLactococcus

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Wang, Rongzhi, Shuangshuang Xiang, Yonghui Zhang, Qiuyu Chen, Yanfang Zhong, and Shihua Wang. "Development of a Functional Antibody by Using a Green Fluorescent Protein Frame as the Template." Applied and Environmental Microbiology 80, no. 14 (2014): 4126–37. http://dx.doi.org/10.1128/aem.00936-14.

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ABSTRACTSingle-chain variable fragment (scFv) antibodies are widely used as diagnostic and therapeutic agents or biosensors for a majority of human disease. However, the limitations of the present scFv antibody in terms of stability, solubility, and affinity are challenging to produce by traditional antibody screening and expression formats. We describe here a feasible strategy for creating the green fluorescent protein (GFP)-based antibody. Complementarity-determining region 3 (CDR3), which retains the antigen binding activity, was introduced into the structural loops of superfolder GFP, and

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Benítez-Mateos, Mehravar, Velasco-Lozano, RadmilaTomovska, Salassa, and López-Gallego. "Selective Immobilization of Fluorescent Proteins for the Fabrication of Photoactive Materials." Molecules 24, no. 15 (2019): 2775. http://dx.doi.org/10.3390/molecules24152775.

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The immobilization of fluorescent proteins is a key technology enabling to fabricate a new generation of photoactive materials with potential technological applications. Herein we have exploited superfolder green (sGFP) and red (RFP) fluorescent proteins expressed with different polypeptide tags. We fused these fluorescent proteins to His-tags to immobilize them on graphene 3D hydrogels, and Cys-tags to immobilize them on porous microparticles activated with either epoxy or disulfide groups and with Lys-tags to immobilize them on upconverting nanoparticles functionalized with carboxylic groups

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Bishop, Alexa, Maki Kamoshita, Josiah B. Passmore, et al. "Fluorescent Tools to Analyze Peroxisome–Endoplasmic Reticulum Interactions in Mammalian Cells." Contact 2 (January 2019): 251525641984864. http://dx.doi.org/10.1177/2515256419848641.

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Peroxisomes (POs) and the endoplasmic reticulum (ER) cooperate extensively in lipid-related metabolic pathways, and the ER also provides phospholipids to enable the peroxisomal membrane to expand prior to division. Recently, we identified peroxisomal proteins, ACBD5 and ACBD4, and the ER protein vesicle-associated membrane protein-associated protein-B (VAPB) as tethering components, which physically interact to foster PO–ER associations at membrane contact sites. Overexpression or loss of these tether proteins alters the extent of PO–ER interactions, impacting on lipid exchange between these t

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Liu, Min, Bin Wang, Fei Wang, et al. "Soluble expression of single-chain variable fragment (scFv) in Escherichia coli using superfolder green fluorescent protein as fusion partner." Applied Microbiology and Biotechnology 103, no. 15 (2019): 6071–79. http://dx.doi.org/10.1007/s00253-019-09925-6.

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Cava, Felipe, Miguel Angel de Pedro, Emilio Blas-Galindo, Geoffrey S. Waldo, Lars F. Westblade, and José Berenguer. "Expression and use of superfolder green fluorescent protein at high temperatures in vivo: a tool to study extreme thermophile biology." Environmental Microbiology 10, no. 3 (2008): 605–13. http://dx.doi.org/10.1111/j.1462-2920.2007.01482.x.

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Beilharz, Katrin, Renske van Raaphorst, Morten Kjos, and Jan-Willem Veening. "Red Fluorescent Proteins for Gene Expression and Protein Localization Studies in Streptococcus pneumoniae and Efficient Transformation with DNA Assembled via the Gibson Assembly Method." Applied and Environmental Microbiology 81, no. 20 (2015): 7244–52. http://dx.doi.org/10.1128/aem.02033-15.

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ABSTRACTDuring the last decades, a wide range of fluorescent proteins (FPs) have been developed and improved. This has had a great impact on the possibilities in biological imaging and the investigation of cellular processes at the single-cell level. Recently, we have benchmarked a set of green fluorescent proteins (GFPs) and generated a codon-optimized superfolder GFP for efficient use in the important human pathogenStreptococcus pneumoniaeand other low-GC Gram-positive bacteria. In the present work, we constructed and compared four red fluorescent proteins (RFPs) inS. pneumoniae. Two orange-

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Fernandez, Juliette, Cédric Hassen-Khodja, Virginie Georget, et al. "Measuring the subcellular compartmentalization of viral infections by protein complementation assay." Proceedings of the National Academy of Sciences 118, no. 2 (2021): e2010524118. http://dx.doi.org/10.1073/pnas.2010524118.

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The recent emergence and reemergence of viruses in the human population has highlighted the need to develop broader panels of therapeutic molecules. High-throughput screening assays opening access to untargeted steps of the viral replication cycle will provide powerful leverage to identify innovative antiviral molecules. We report here the development of an innovative protein complementation assay, termed αCentauri, to measure viral translocation between subcellular compartments. As a proof of concept, the Centauri fragment was either tethered to the nuclear pore complex or sequestered in the

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Fleurot, Isabelle, Marina Aigle, Renaud Fleurot, et al. "Following Pathogen Development and Gene Expression in a Food Ecosystem: the Case of a Staphylococcus aureus Isolate in Cheese." Applied and Environmental Microbiology 80, no. 16 (2014): 5106–15. http://dx.doi.org/10.1128/aem.01042-14.

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ABSTRACTHuman intoxication or infection due to bacterial food contamination constitutes an economic challenge and a public health problem. Information on thein situdistribution and expression of pathogens responsible for this risk is to date lacking, largely because of technical bottlenecks in detecting signals from minority bacterial populations within a complex microbial and physicochemical ecosystem. We simulated the contamination of a real high-risk cheese with a natural food isolate ofStaphylococcus aureus, an enterotoxin-producing pathogen responsible for food poisoning. To overcome the

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Kim, Hyeran, Seul Gee Hwang, Kyeonghye Guk, et al. "Development of antibody against drug-resistant respiratory syncytial virus: Rapid detection of mutant virus using split superfolder green fluorescent protein-antibody system." Biosensors and Bioelectronics 194 (December 2021): 113593. http://dx.doi.org/10.1016/j.bios.2021.113593.

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Kjos, Morten, Rieza Aprianto, Vitor E. Fernandes, et al. "Bright Fluorescent Streptococcus pneumoniae for Live-Cell Imaging of Host-Pathogen Interactions." Journal of Bacteriology 197, no. 5 (2014): 807–18. http://dx.doi.org/10.1128/jb.02221-14.

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Streptococcus pneumoniaeis a common nasopharyngeal resident in healthy people but, at the same time, one of the major causes of infectious diseases such as pneumonia, meningitis, and sepsis. The shift from commensal to pathogen and its interaction with host cells are poorly understood. One of the major limitations for research on pneumococcal-host interactions is the lack of suitable tools for live-cell imaging. To address this issue, we developed a generally applicable strategy to create genetically stable, highly fluorescent bacteria. Our strategy relies on fusing superfolder green fluoresce

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Shields, R. C., J. R. Kaspar, K. Lee, S. A. M. Underhill, and R. A. Burne. "Fluorescence Tools Adapted for Real-Time Monitoring of the Behaviors ofStreptococcusSpecies." Applied and Environmental Microbiology 85, no. 15 (2019). http://dx.doi.org/10.1128/aem.00620-19.

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ABSTRACTTagging of bacteria with fluorescent proteins has become an essential component of modern microbiology. Fluorescent proteins can be used to monitor gene expression and biofilm growth and to visualize host-pathogen interactions. Here, we developed a collection of fluorescent protein reporter plasmids forStreptococcus mutansUA159 and other oral streptococci. Using superfolder green fluorescent protein (sfGFP) as a reporter for transcriptional activity, we were able to characterize four strong constitutive promoters inS. mutans. These promoter-sfgfpfusions worked both for single-copy chro

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Miki, Takayuki, Taichi Nakai, Masahiro Hashimoto, Keigo Kajiwara, Hiroshi Tsutsumi, and Hisakazu Mihara. "Intracellular artificial supramolecules based on de novo designed Y15 peptides." Nature Communications 12, no. 1 (2021). http://dx.doi.org/10.1038/s41467-021-23794-6.

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AbstractDe novo designed self-assembling peptides (SAPs) are promising building blocks of supramolecular biomaterials, which can fulfill a wide range of applications, such as scaffolds for tissue culture, three-dimensional cell culture, and vaccine adjuvants. Nevertheless, the use of SAPs in intracellular spaces has mostly been unexplored. Here, we report a self-assembling peptide, Y15 (YEYKYEYKYEYKYEY), which readily forms β-sheet structures to facilitate bottom-up synthesis of functional protein assemblies in living cells. Superfolder green fluorescent protein (sfGFP) fused to Y15 assembles

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Kulkarni, Surashree S., Joseph J. Johnston, Yongtao Zhu, Zachary T. Hying, and Mark J. McBride. "The Carboxy-Terminal Region ofFlavobacterium johnsoniaeSprB Facilitates Its Secretion by the Type IX Secretion System and Propulsion by the Gliding Motility Machinery." Journal of Bacteriology 201, no. 19 (2019). http://dx.doi.org/10.1128/jb.00218-19.

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ABSTRACTFlavobacterium johnsoniaeSprB moves rapidly along the cell surface, resulting in gliding motility. SprB secretion requires the type IX secretion system (T9SS). Proteins secreted by the T9SS typically have conserved C-terminal domains (CTDs) belonging to the type A CTD or type B CTD family. Attachment of 70- to 100-amino-acid type A CTDs to a foreign protein allows its secretion. Type B CTDs are common but have received little attention. Secretion of the foreign protein superfolder green fluorescent protein (sfGFP) fused to regions spanning the SprB type B CTD (sfGFP-CTDSprB) was analyz

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Kulkarni, Surashree S., Yongtao Zhu, Colton J. Brendel, and Mark J. McBride. "Diverse C-Terminal Sequences Involved in Flavobacterium johnsoniae Protein Secretion." Journal of Bacteriology 199, no. 12 (2017). http://dx.doi.org/10.1128/jb.00884-16.

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ABSTRACT Flavobacterium johnsoniae and many related bacteria secrete proteins across the outer membrane using the type IX secretion system (T9SS). Proteins secreted by T9SSs have amino-terminal signal peptides for export across the cytoplasmic membrane by the Sec system and carboxy-terminal domains (CTDs) targeting them for secretion across the outer membrane by the T9SS. Most but not all T9SS CTDs belong to the family TIGR04183 (type A CTDs). We functionally characterized diverse CTDs for secretion by the F. johnsoniae T9SS. Attachment of the CTDs from F. johnsoniae RemA, AmyB, and ChiA to th

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Inaba, Yuta, Indrani Banerjee, Timothy Kernan, and Scott Banta. "Transposase-Mediated Chromosomal Integration of Exogenous Genes inAcidithiobacillus ferrooxidans." Applied and Environmental Microbiology 84, no. 21 (2018). http://dx.doi.org/10.1128/aem.01381-18.

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ABSTRACTThe development ofAcidithiobacillus ferrooxidansas a non-model host organism for synthetic biology is hampered by a lack of genetic tools and techniques. New plating and liquid-based selection methods were developed to improve the identification of transformed cell lines. Enabled by these methods, a hyperactive transposase was used to generate mutants with integrated genes for the expression of the superfolder green fluorescent protein (sfGFP) gene or a 2-keto decarboxylase (KDC) gene, which enabled the production and secretion of isobutyric acid (IBA). An inverse PCR method was used t

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Godeux, Anne-Sophie, Agnese Lupo, Marisa Haenni, et al. "Fluorescence-Based Detection of Natural Transformation in Drug-ResistantAcinetobacter baumannii." Journal of Bacteriology 200, no. 19 (2018). http://dx.doi.org/10.1128/jb.00181-18.

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ABSTRACTAcinetobacter baumanniiis a nosocomial agent with a high propensity for developing resistance to antibiotics. This ability relies on horizontal gene transfer mechanisms occurring in theAcinetobactergenus, including natural transformation. To study natural transformation in bacteria, the most prevalent method uses selection for the acquisition of an antibiotic resistance marker in a target chromosomal locus by the recipient cell. Most clinical isolates ofA. baumanniiare resistant to multiple antibiotics, limiting the use of such selection-based methods. Here, we report the development o

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Goudeau, Jérôme, Catherine S. Sharp, Jonathan Paw, et al. "Split-wrmScarlet and split-sfGFP: tools for faster, easier fluorescent labeling of endogenous proteins in Caenorhabditis elegans." Genetics 217, no. 4 (2021). http://dx.doi.org/10.1093/genetics/iyab014.

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Abstract We create and share a new red fluorophore, along with a set of strains, reagents and protocols, to make it faster and easier to label endogenous Caenorhabditis elegans proteins with fluorescent tags. CRISPR-mediated fluorescent labeling of C. elegans proteins is an invaluable tool, but it is much more difficult to insert fluorophore-size DNA segments than it is to make small gene edits. In principle, high-affinity asymmetrically split fluorescent proteins solve this problem in C. elegans: the small fragment can quickly and easily be fused to almost any protein of interest, and can be

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Ernst, Patrick, Andreas Plückthun, and Peer R. E. Mittl. "Structural analysis of biological targets by host:guest crystal lattice engineering." Scientific Reports 9, no. 1 (2019). http://dx.doi.org/10.1038/s41598-019-51017-y.

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Abstract To overcome the laborious identification of crystallisation conditions for protein X-ray crystallography, we developed a method where the examined protein is immobilised as a guest molecule in a universal host lattice. We applied crystal engineering to create a generic crystalline host lattice under reproducible, predefined conditions and analysed the structures of target guest molecules of different size, namely two 15-mer peptides and green fluorescent protein (sfGFP). A fusion protein with an N-terminal endo-α-N-acetylgalactosaminidase (EngBF) domain and a C-terminal designed ankyr

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Liang, Tianxin, Jun Sun, Shuyun Ju, Shenyi Su, Lirong Yang, and Jianping Wu. "Construction of T7-Like Expression System in Pseudomonas putida KT2440 to Enhance the Heterologous Expression Level." Frontiers in Chemistry 9 (July 16, 2021). http://dx.doi.org/10.3389/fchem.2021.664967.

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Pseudomonas putida KT2440 has become an attractive chassis for heterologous expression with the development of effective genetic manipulation tools. Improving the level of transcriptional regulation is particularly important for extending the potential of P. putida KT2440 in heterologous expression. Although many strategies have been applied to enhance the heterologous expression level in P. putida KT2440, it was still at a relatively low level. Herein we constructed a T7-like expression system in P. putida KT2440, mimicking the pET expression system in Escherichia coli, which consisted of T7-

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Attia, Mohamed A., and Harry Brumer. "Characterization of a galactosyl-binding protein module from a Cellvibrio japonicus endo-xyloglucanase defines a new family of Carbohydrate Binding Modules." Applied and Environmental Microbiology, December 18, 2020, AEM.02634–20. http://dx.doi.org/10.1128/aem.02634-20.

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Carbohydrate-binding modules (CBMs) are usually appended to carbohydrate-active enzymes (CAZymes) and serve to potentiate catalytic activity, e.g. by increasing substrate affinity. The Gram-negative soil saprophyte Cellvibrio japonicus is valuable source for CAZyme and CBM discovery and characterization, due to its innate ability to degrade a wide array of plant polysaccharides. Bioinformatic analysis of the CJA_2959 gene product from C. japonicus revealed a modular architecture consisting of a fibronectin type III (Fn3) module, a cryptic module of unknown function (“X181”), and a Glycoside Hy

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Söderberg, Jenny Johansson, Miriam Grgic, Erik Hjerde, and Peik Haugen. "Aliivibrio wodanis as a production host: development of genetic tools for expression of cold-active enzymes." Microbial Cell Factories 18, no. 1 (2019). http://dx.doi.org/10.1186/s12934-019-1247-1.

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Abstract Background Heterologous production of cold-adapted proteins currently represents one of the greatest bottlenecks in the ongoing bioprospecting efforts to find new enzymes from low-temperature environments, such as, the polar oceans that represent essentially untapped resources in this respect. In mesophilic expression hosts such as Escherichia coli, cold-adapted enzymes often form inactive aggregates. Therefore it is necessary to develop new low-temperature expression systems, including identification of new host organisms and complementary genetic tools. Psychrophilic bacteria, inclu

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Moradali, M. Fata, Shirin Ghods, and Bernd H. A. Rehm. "Activation Mechanism and Cellular Localization of Membrane-Anchored Alginate Polymerase in Pseudomonas aeruginosa." Applied and Environmental Microbiology 83, no. 9 (2017). http://dx.doi.org/10.1128/aem.03499-16.

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ABSTRACT The exopolysaccharide alginate, produced by the opportunistic human pathogen Pseudomonas aeruginosa, confers a survival advantage to the bacterium by contributing to the formation of characteristic biofilms during infection. Membrane-anchored proteins Alg8 (catalytic subunit) and Alg44 (copolymerase) constitute the alginate polymerase that is being activated by the second messenger molecule bis-(3′, 5′)-cyclic dimeric GMP (c-di-GMP), but the mechanism of activation remains elusive. To shed light on the c-di-GMP-mediated activation of alginate polymerization in vivo, an in silico struc

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