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Han SI, Sarkes DA, Hurley MM, Renberg R, Huang C, Li Y, Jahnke JP, Sumner JJ, Stratis-Cullum DN, Han A. Identification of Microorganisms that Bind Specifically to Target Materials of Interest Using a Magnetophoretic Microfluidic Platform. ACS APPLIED MATERIALS & INTERFACES 2023; 15:11391-11402. [PMID: 36847552 PMCID: PMC10848205 DOI: 10.1021/acsami.2c15192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Discovery of microorganisms and their relevant surface peptides that specifically bind to target materials of interest can be achieved through iterative biopanning-based screening of cellular libraries having high diversity. Recently, microfluidics-based biopanning methods have been developed and exploited to overcome the limitations of conventional methods where controlling the shear stress applied to remove cells that do not bind or only weakly bind to target surfaces is difficult and the overall experimental procedure is labor-intensive. Despite the advantages of such microfluidic methods and successful demonstration of their utility, these methods still require several rounds of iterative biopanning. In this work, a magnetophoretic microfluidic biopanning platform was developed to isolate microorganisms that bind to target materials of interest, which is gold in this case. To achieve this, gold-coated magnetic nanobeads, which only attached to microorganisms that exhibit high affinity to gold, were used. The platform was first utilized to screen a bacterial peptide display library, where only the cells with surface peptides that specifically bind to gold could be isolated by the high-gradient magnetic field generated within the microchannel, resulting in enrichment and isolation of many isolates with high affinity and high specificity toward gold even after only a single round of separation. The amino acid profile of the resulting isolates was analyzed to provide a better understanding of the distinctive attributes of peptides that contribute to their specific material-binding capabilities. Next, the microfluidic system was utilized to screen soil microbes, a rich source of extremely diverse microorganisms, successfully isolating many naturally occurring microorganisms that show strong and specific binding to gold. The results show that the developed microfluidic platform is a powerful screening tool for identifying microorganisms that specifically bind to a target material surface of interest, which can greatly accelerate the development of new peptide-driven biological materials and hybrid organic-inorganic materials.
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Affiliation(s)
- Song-I Han
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Deborah A. Sarkes
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Margaret M. Hurley
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Rebecca Renberg
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Can Huang
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Yuwen Li
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Justin P. Jahnke
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - James J. Sumner
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Dimitra N. Stratis-Cullum
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Arum Han
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, USA
- Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
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Stellwagen SD, Sarkes DA, Adams BL, Hunt MA, Renberg RL, Hurley MM, Stratis-Cullum DN. The next generation of biopanning: next gen sequencing improves analysis of bacterial display libraries. BMC Biotechnol 2019; 19:100. [PMID: 31864334 PMCID: PMC6925417 DOI: 10.1186/s12896-019-0577-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/12/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Bacterial surface display libraries are a popular tool for novel ligand discovery due to their ease of manipulation and rapid growth rates. These libraries typically express a scaffold protein embedded within the outer membrane with a short, surface-exposed peptide that is either terminal or is incorporated into an outer loop, and can therefore interact with and bind to substrates of interest. RESULTS In this study, we employed a novel bacterial peptide display library which incorporates short 15-mer peptides on the surface of E. coli, co-expressed with the inducible red fluorescent protein DsRed in the cytosol, to investigate population diversity over two rounds of biopanning. The naive library was used in panning trials to select for binding affinity against 3D printing plastic coupons made from polylactic acid (PLA). Resulting libraries were then deep-sequenced using next generation sequencing (NGS) to investigate selection and diversity. CONCLUSIONS We demonstrated enrichment for PLA binding versus a sapphire control surface, analyzed population composition, and compared sorting rounds using a binding assay and fluorescence microscopy. The capability to produce and describe display libraries through NGS across rounds of selection allows a deeper understanding of population dynamics that can be better directed towards peptide discovery.
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Affiliation(s)
- Sarah D. Stellwagen
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, 21250 MD USA
| | - Deborah A. Sarkes
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
| | - Bryn L. Adams
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
| | - Mia A. Hunt
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
- General Technical Services, Suite 301, 1451 Route 34 South, Wall Township, 07727 NJ USA
| | - Rebecca L. Renberg
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
- General Technical Services, Suite 301, 1451 Route 34 South, Wall Township, 07727 NJ USA
| | - Margaret M. Hurley
- Biotechnology Branch, CCDC US Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, 20783 MD USA
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Dong H, Sarkes DA, Rice JJ, Hurley MM, Fu AJ, Stratis-Cullum DN. Living Bacteria-Nanoparticle Hybrids Mediated through Surface-Displayed Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5837-5848. [PMID: 29692178 DOI: 10.1021/acs.langmuir.8b00114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, we investigated the preparation of living bacteria-nanoparticle hybrids mediated by surface-displayed peptides. The assembly of metallic nanoparticles on living bacteria has been achieved under mild conditions utilizing metal-peptide interactions, whereas the viability of the bacterial cells was greatly preserved. Escherichia coli was engineered with inducible gene circuits to control the display of peptides with desired sequences. Several designed peptide sequences as well as known gold-binding peptides were expressed on the cell surface using enhanced circularly permuted outer membrane protein X (eCPX) scaffolds. Driven by metal-peptide affinity, "biofriendly" citrate-stabilized gold nanoparticles were self-assembled onto the surface of bacteria with displayed peptides, which required overcoming the repulsive force between negatively charged nanoparticles and negatively charged cells. The bacteria/Au nanoparticle hybrids were highly viable and maintained the ability to grow and divide, which is a crucial step toward the creation of living material systems. Further activity and preservation of the bacterial hybrid assembly was demonstrated. The method described herein enables the conjugation of bacterial surfaces with diverse metal-rich nanoparticles in an inducible, and therefore easily controlled, manner. The expressed peptide sequences can be easily modified to alter the binding affinity and specificity for a wide variety of materials to form on-demand, high-density living biohybrids.
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Affiliation(s)
- Hong Dong
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
- General Technical Services , 1451 Route 34 South , Wall Township , New Jersey 07727 , United States
| | - Deborah A Sarkes
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
| | - Jeffrey J Rice
- Department of Chemical Engineering , Auburn University , 212 Ross Hall , Auburn , Alabama 36849 , United States
- Oak Ridge Associated Universities , 4692 Millennium Drive, Suite 101 , Belcamp , Maryland 21017 , United States
| | - Margaret M Hurley
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
| | - Adele J Fu
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
- Oak Ridge Associated Universities , 4692 Millennium Drive, Suite 101 , Belcamp , Maryland 21017 , United States
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
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Sarkes DA, Jahnke JP, Stratis-Cullum DN. Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates. J Vis Exp 2017. [PMID: 29286465 PMCID: PMC5755526 DOI: 10.3791/56061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Biopanning bacterial display libraries is a proven technique for peptide affinity reagent discovery for recognition of both biotic and abiotic targets. Peptide affinity reagents can be used for similar applications to antibodies, including sensing and therapeutics, but are more robust and able to perform in more extreme environments. Specific enrichment of peptide capture agents to a protein target of interest is enhanced using semi-automated sorting methods which improve binding and wash steps and therefore decrease the occurrence of false positive binders. A semi-automated sorting method is described herein for use with a commercial automated magnetic-activated cell sorting device with an unconstrained bacterial display sorting library expressing random 15-mer peptides. With slight modifications, these methods are extendable to other automated devices, other sorting libraries, and other organisms. A primary goal of this work is to provide a comprehensive methodology and expound the thought process applied in analyzing and minimizing the resulting pool of candidates. These techniques include analysis of on-cell binding using fluorescence-activated cell sorting (FACS), to assess affinity and specificity during sorting and in comparing individual candidates, and the analysis of peptide sequences to identify trends and consensus sequences for understanding and potentially improving the affinity to and specificity for the target of interest.
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Affiliation(s)
- Deborah A Sarkes
- Sensors and Electron Devices Directorate, US Army Research Laboratory;
| | - Justin P Jahnke
- Sensors and Electron Devices Directorate, US Army Research Laboratory
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Sarkes DA, Hurley MM, Stratis-Cullum DN. Unraveling the Roots of Selectivity of Peptide Affinity Reagents for Structurally Similar Ribosomal Inactivating Protein Derivatives. Molecules 2016; 21:E1504. [PMID: 27834872 PMCID: PMC6272918 DOI: 10.3390/molecules21111504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 11/17/2022] Open
Abstract
Peptide capture agents have become increasingly useful tools for a variety of sensing applications due to their ease of discovery, stability, and robustness. Despite the ability to rapidly discover candidates through biopanning bacterial display libraries and easily mature them to Protein Catalyzed Capture (PCC) agents with even higher affinity and selectivity, an ongoing challenge and critical selection criteria is that the peptide candidates and final reagent be selective enough to replace antibodies, the gold-standard across immunoassay platforms. Here, we have discovered peptide affinity reagents against abrax, a derivative of abrin with reduced toxicity. Using on-cell Fluorescence Activated Cell Sorting (FACS) assays, we show that the peptides are highly selective for abrax over RiVax, a similar derivative of ricin originally designed as a vaccine, with significant structural homology to abrax. We rank the newly discovered peptides for strongest affinity and analyze three observed consensus sequences with varying affinity and specificity. The strongest (Tier 1) consensus was FWDTWF, which is highly aromatic and hydrophobic. To better understand the observed selectivity, we use the XPairIt peptide-protein docking protocol to analyze binding location predictions of the individual Tier 1 peptides and consensus on abrax and RiVax. The binding location profiles on the two proteins are quite distinct, which we determine is due to differences in pocket size, pocket environment (including hydrophobicity and electronegativity), and steric hindrance. This study provides a model system to show that peptide capture candidates can be quite selective for a structurally similar protein system, even without further maturation, and offers an in silico method of analysis for understanding binding and down-selecting candidates.
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Affiliation(s)
- Deborah A Sarkes
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Margaret M Hurley
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
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