1
|
Dhamane S, Patil U, Smith M, Adhikari M, Nazem A, Conrad JC, Kourentzi K, Willson RC. Isocratic reporter-exclusion immunoassay using restricted-access adsorbents. Analyst 2021; 146:4835-4840. [PMID: 34198311 PMCID: PMC9798887 DOI: 10.1039/d1an00396h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We introduce analyte-dependent exclusion of reporter reagents from restricted-access adsorbents as the basis of an isocratic reporter-exclusion immunoassay for viruses, proteins, and other analytes. Capto™ Core 700 and related resins possess a noninteracting size-selective outer layer surrounding a high-capacity nonspecific mixed-mode capture adsorbent core. In the absence of analyte, antibody-enzyme reporter conjugates can enter the adsorbent and be captured, and their signal is lost. In the presence of large or artificially-expanded analytes, reporter reagents bind to analyte species to form complexes large enough to be excluded from the adsorbent core, allowing their signal to be observed. This assay principle is demonstrated using M13 bacteriophage virus and human chorionic gonadotropin as model analytes. The simple isocratic detection approach described here allows a rapid implementation of immunoassay for detection of a wide range of analytes and uses inexpensive, generally-applicable, and stable column materials instead of costly analyte-specific immunoaffinity adsorbents.
Collapse
Affiliation(s)
- Sagar Dhamane
- Department of Biology and Biochemistry, University of Houston, Houston, TX USA
| | - Ujwal Patil
- Department of Biology and Biochemistry, University of Houston, Houston, TX USA
| | - Maxwell Smith
- Department of Chemical and Biomolecular Engineering, University of Houston, TX USA
| | - Meena Adhikari
- Department of Biology and Biochemistry, University of Houston, Houston, TX USA
| | - Ahmad Nazem
- Department of Biomedical Engineering, University of Houston, Houston, TX USA
| | - Jacinta C. Conrad
- Department of Chemical and Biomolecular Engineering, University of Houston, TX USA
| | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, TX USA
| | - Richard C. Willson
- Department of Biology and Biochemistry, University of Houston, Houston, TX USA,Department of Biomedical Engineering, University of Houston, Houston, TX USA,Department of Chemical and Biomolecular Engineering, University of Houston, TX USA,Escuela de Medicina y Ciencias de las Salud ITESM, Monterrey, Mexico,Corresponding author. (Richard C. Willson)
| |
Collapse
|
2
|
Bacterial non-specific nucleases of the phospholipase D superfamily and their biotechnological potential. Appl Microbiol Biotechnol 2020; 104:3293-3304. [PMID: 32086594 DOI: 10.1007/s00253-020-10459-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 12/19/2022]
Abstract
Bacterial non-specific nucleases are ubiquitously distributed and involved in numerous intra- and extracellular processes. Although all nucleases share the basic chemistry for the hydrolysis of phosphodiester bonds in nucleic acid molecules, the catalysis comprises diverse modes of action, which offers great potential for versatile biotechnological applications. A major criterium for their differentiation is substrate specificity. Specific endonucleases are widely used as restriction enzymes in molecular biology approaches, whereas the main applications of non-specific nucleases (NSNs) are the removal of nucleic acids from crude extracts in industrial downstream processing and the prevention of cell clumping in microfabricated channels. In nature, the predominant role of NSNs is the acquisition of nutrient sources such as nucleotides and phosphates. The number of extensively characterized NSNs and available structures is limited. Moreover, their applicability is mostly challenged by the presence of metal chelators that impede the hydrolysis of nucleic acids in a metal ion-dependent manner. However, a few metal ion-independent NSNs that tolerate the presence of metal chelators have been characterized in recent years with none being commercially available to date. The classification and biotechnological potential of bacterial NSNs with a special focus on metal ion-independent nucleases are presented and discussed.Key Points • Bacterial phospholipases (PLD-family) exhibit nucleolytic activity. • Bacterial nucleases of the PLD-family are metal ion-independent. • NSNs can be used in downstream processing approaches.
Collapse
|
3
|
Litvinov J, Hagström AEV, Lopez Y, Adhikari M, Kourentzi K, Strych U, Monzon FA, Foster W, Cagle PT, Willson RC. Ultrasensitive immuno-detection using viral nanoparticles with modular assembly using genetically-directed biotinylation. Biotechnol Lett 2014; 36:1863-8. [PMID: 24930095 DOI: 10.1007/s10529-014-1555-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 05/09/2014] [Indexed: 01/19/2023]
Abstract
We report a novel, modular approach to immuno-detection based on antibody recognition and PCR read-out that employs antibody-conjugated bacteriophage and easily-manipulated non-pathogenic viruses as affinity agents. Our platform employs phage genetically tagged for in vivo biotinylation during phage maturation that can easily be linked, through avidin, to any biotinylated affinity agent, including full-length antibodies, peptides, lectins or aptamers. The presence of analyte is reported with high sensitivity through real-time PCR. This approach avoids the need to clone antibody-encoding DNA fragments, allows the use of full-length, high affinity antibodies and, by having DNA reporters naturally encapsulated inside the bacteriophage, greatly reduces nonspecific binding of DNA. We validate the efficacy of this new approach through the detection of Vascular Endothelial Growth Factor, a known angiogenic cancer biomarker protein, at attomolar concentrations in bronchoalveolar lavage fluid.
Collapse
Affiliation(s)
- Julia Litvinov
- Department of Biomedical Engineering, University of Houston, 4800 Calhoun Rd., Houston, TX, 77204, USA,
| | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Affiliation(s)
- Robert O J Weinzierl
- Department of Life Sciences, Division of Biomolecular Sciences, Imperial College London , Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
| |
Collapse
|
5
|
Midon M, Schäfer P, Pingoud A, Ghosh M, Moon AF, Cuneo MJ, London RE, Meiss G. Mutational and biochemical analysis of the DNA-entry nuclease EndA from Streptococcus pneumoniae. Nucleic Acids Res 2010; 39:623-34. [PMID: 20846957 PMCID: PMC3025545 DOI: 10.1093/nar/gkq802] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
EndA is a membrane-attached surface-exposed DNA-entry nuclease previously known to be required for genetic transformation of Streptococcus pneumoniae. More recent studies have shown that the enzyme also plays an important role during the establishment of invasive infections by degrading extracellular chromatin in the form of neutrophil extracellular traps (NETs), enabling streptococci to overcome the innate immune system in mammals. As a virulence factor, EndA has become an interesting target for future drug design. Here we present the first mutational and biochemical analysis of recombinant forms of EndA produced either in a cell-free expression system or in Escherichia coli. We identify His160 and Asn191 to be essential for catalysis and Asn182 to be required for stability of EndA. The role of His160 as the putative general base in the catalytic mechanism is supported by chemical rescue of the H160A variant of EndA with imidazole added in excess. Our study paves the way for the identification and development of protein or low-molecular-weight inhibitors for EndA in future high-throughput screening assays.
Collapse
Affiliation(s)
- Marika Midon
- Institute of Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Basile LJ, Willson RC, Sewell BT, Benedik MJ. Genome mining of cyanide-degrading nitrilases from filamentous fungi. Appl Microbiol Biotechnol 2008; 80:427-35. [DOI: 10.1007/s00253-008-1559-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 05/28/2008] [Accepted: 05/30/2008] [Indexed: 10/21/2022]
|
7
|
Lunin VY, Levdikov VM, Shlyapnikov SV, Blagova EV, Lunin VV, Wilson KS, Mikhailov AM. Three-dimensional structure of Serratia marcescens nuclease at 1.7 A resolution and mechanism of its action. FEBS Lett 1997; 412:217-22. [PMID: 9257723 DOI: 10.1016/s0014-5793(97)00512-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The three-dimensional crystal structure of Serratia marcescens (Sm) nuclease has been refined at 1.7 A resolution to the R-factor of 17.3% and R-free of 22.2%. The final model consists of 3678 non-hydrogen atoms and 443 water molecules. The analysis of the secondary and the tertiary structures of the Sm nuclease suggests a topology which reveals essential inner symmetry in all the three layers forming the monomer. We propose the plausible mechanism of its action based on a concerted participation of the catalytically important amino acid residues of the enzyme active site.
Collapse
Affiliation(s)
- V Y Lunin
- Institute of Mathematical Problems in Biology, Russian Academy of Sciences, Pushino, Moscow region
| | | | | | | | | | | | | |
Collapse
|
8
|
Miller MD, Krause KL. Identification of the Serratia endonuclease dimer: structural basis and implications for catalysis. Protein Sci 1996; 5:24-33. [PMID: 8771193 PMCID: PMC2143236 DOI: 10.1002/pro.5560050104] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The Serratia endonuclease is an extracellularly secreted enzyme capable of cleaving both single- and double-stranded forms of DNA and RNA. It is the first member of a large class of related and usually dimeric endonucleases for which a structure is known. Using X-ray crystallography, the structure of monomer of this enzyme was reported by us previously (Miller MD et al., 1994, Nature Struct Biol 1:461-468). We now confirm the dimeric nature of this enzyme through light-scattering experiments and identify the physiologic dimer interface through crystal packing analysis. This dimerization occurs through an isologous twofold interaction localized to the carboxy-terminal subdomain of the enzyme. The dimer is a prolate ellipsoid with dimensions 30 A x 35 A x 90 A. The dimer interface is flat and contains four salt links, several hydrogen bonds, and nonpolar interactions. Buried water is prominent in this interface and it includes an unusual "cubic" water cluster. The position of the two active sites in the dimer suggests that they can act independently in their cleavage of DNA, but have a geometrical advantage in attacking substrate relative to the monomer.
Collapse
Affiliation(s)
- M D Miller
- Department of Biochemical and Biophysical Sciences, University of Houston, Texas 77204-5934, USA
| | | |
Collapse
|
9
|
Suh Y, Alpaugh M, Krause KL, Benedik MJ. Differential secretion of isoforms of Serratia marcescens extracellular nuclease. Appl Environ Microbiol 1995; 61:4083-8. [PMID: 8526522 PMCID: PMC167715 DOI: 10.1128/aem.61.11.4083-4088.1995] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Extracellular secretion of the Serratia marcescens nuclease occurs in a two-step process: (i) rapidly to the periplasm via a signal sequence-dependent pathway and then (ii) slowly to the extracellular growth medium without cell lysis. There are two major isoforms of the nuclease in the culture supernatant of S. marcescens. We have isolated, purified, and determined the sequences of both isoforms. The first isoform, the mature nuclease (Sm2), is the result of signal sequence processing. The second isoform (Sm1) has three additional amino acids missing from the N terminus of the mature nuclease. Sm1 starts to appear extracellularly only during prolonged growth of a culture (16 to 48 h), probably because of cell lysis. However, pulse-chase experiments show that it is made early with Sm2 but is not secreted efficiently.
Collapse
Affiliation(s)
- Y Suh
- Department of Biochemical and Biophysical Sciences, University of Houston, Texas 77204-5934, USA
| | | | | | | |
Collapse
|
10
|
Friedhoff P, Gimadutdinow O, Pingoud A. Identification of catalytically relevant amino acids of the extracellular Serratia marcescens endonuclease by alignment-guided mutagenesis. Nucleic Acids Res 1994; 22:3280-7. [PMID: 8078761 PMCID: PMC523719 DOI: 10.1093/nar/22.16.3280] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
By sequence alignment of the extracellular Serratia marcescens nuclease with three related nucleases we have identified seven charged amino acid residues which are conserved in all four sequences. Six of these residues together with four other partially conserved His or Asp residues were changed to alanine by site-directed PCR-mediated mutagenesis using a variant of the nuclease gene in which the coding sequence of the signal peptide was replaced by the coding sequence for an N-terminal affinity tag [Met(His)6GlySer]. Four of the mutant proteins showed almost no reduction in nuclease activity but five displayed a 10- to 1000-fold reduction in activity and one (His110Ala) was inactive. Based upon these results it is suggested that the S.marcescens nuclease employs a mechanism in which His110 acts in concert with a Mg2+ ion and three carboxylates (Asp107, Glu148 and Glu232) as well as one or two basic amino acid residues (Arg108, Arg152).
Collapse
Affiliation(s)
- P Friedhoff
- Institut für Biochemie, Justus-Liebig-Universität, Giessen, Germany
| | | | | |
Collapse
|
11
|
Miller MD, Tanner J, Alpaugh M, Benedik MJ, Krause KL. 2.1 A structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA. NATURE STRUCTURAL BIOLOGY 1994; 1:461-8. [PMID: 7664065 DOI: 10.1038/nsb0794-461] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The crystal structure of Serratia endonuclease has been solved to 2.1 A by multiple isomorphous replacement. This magnesium-dependent enzyme is equally active against single- and double-stranded DNA, as well as RNA, without any apparent base preference. The Serratia endonuclease fold is distinct from that of other nucleases that have been solved by X-ray diffraction. The refined structure consists of a central layer containing six antiparallel beta-strands which is flanked on one side by a helical domain and on the opposite side by one dominant helix and a very long coiled loop. Electrostatic calculations reveal a strongly polarized molecular surface and suggest that a cleft between this long helix and loop, near His 89, may contain the active site of the enzyme.
Collapse
Affiliation(s)
- M D Miller
- Department of Biochemical and Biophysical Sciences, University of Houston, Texas 77204-5934, USA
| | | | | | | | | |
Collapse
|
12
|
Ahrenholtz I, Lorenz MG, Wackernagel W. The extracellular nuclease of Serratia marcescens: studies on the activity in vitro and effect on transforming DNA in a groundwater aquifer microcosm. Arch Microbiol 1994; 161:176-83. [PMID: 8141644 DOI: 10.1007/bf00276480] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A quantitative endonuclease assay, which relies on the introduction of single and double strand breaks into supercoiled plasmid DNA, was used to study the activity of the extracellular nuclease of Serratia marcescens SM6 in buffer and in groundwater. The parallel enzyme concentration-dependent production of relaxed and linear plasmid molecules suggests that the nuclease produces single and double strand breaks in duplex DNA. Bovine serum albumin stimulated the nuclease activity towards DNA and RNA and increased the stability of the enzyme against thermal inactivation. The DNase activity at 4 degrees C and 50 degrees C was almost half of that at the optimum temperature (37 degrees C). The nuclease was active in groundwater, although the specific activity was lower than in buffer. In a groundwater aquifer microcosm, mineral-adsorbed transforming DNA was substantially less accessible to the nuclease than was dissolved DNA. The data suggest that the extracellular nuclease of Serratia marcescens may contribute to DNA turnover in the environment and that adsorption of DNA to minerals provides protection against the nuclease.
Collapse
Affiliation(s)
- I Ahrenholtz
- Fachbereich Biologie, Universität Oldenburg, Germany
| | | | | |
Collapse
|