Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies

Illuminating the oral microbiome and its host interactions: tools and approaches for molecular microbiology studies

Advancements in DNA sequencing technologies within the last decade have stimulated an unprecedented interest in the human microbiome, largely due the broad diversity of human diseases found to correlate with microbiome dysbiosis. As a direct consequence of these studies, a vast number of understudied and uncharacterized microbes have been identified as potential drivers of mucosal health and disease. The looming challenge in the field is to transition these observations into defined molecular mechanistic studies of symbiosis and dysbiosis. In order to meet this challenge, many of these newly identified microbes will need to be adapted for use in experimental models. Consequently, this review presents a comprehensive overview of the molecular microbiology tools and techniques that have played crucial roles in genetic studies of the bacteria found within the human oral microbiota. Here, we will use specific examples from the oral microbiome literature to illustrate the biology supporting these techniques, why they are needed in the field, and how such technologies have been implemented. It is hoped that this information can serve as a useful reference guide to help catalyze molecular microbiology studies of the many new understudied and uncharacterized species identified at different mucosal sites in the body.

Protein expression/secretion boost by a novel unique 21-mer cis-regulatory motif (Exin21) via mRNA stabilization

Boosting protein production is invaluable in both industrial and academic applications. We discovered a novel expression-increasing 21-mer cis-regulatory motif (Exin21) that inserts between SARS-CoV-2 envelope (E) protein-encoding sequence and luciferase reporter gene. This unique Exin21 (CAACCGCGGTTCGCGGCCGCT), encoding a heptapeptide (QPRFAAA, designated as Qα), significantly (34-fold on average) boosted E production. Both synonymous and nonsynonymous mutations within Exin21 diminished its boosting capability, indicating the exclusive composition and order of 21 nucleotides. Further investigations demonstrated that Exin21/Qα addition could boost the production of multiple SARS-CoV-2 structural proteins (S, M, and N) and accessory proteins (NSP2, NSP16, and ORF3), and host cellular gene products such as IL-2, IFN-γ, ACE2, and NIBP. Exin21/Qα enhanced the packaging yield of S-containing pseudoviruses and standard lentivirus. Exin21/Qα addition on the heavy and light chains of human anti-SARS-CoV monoclonal antibody robustly increased antibody production. The extent of such boosting varied with protein types, cellular density/function, transfection efficiency, reporter dosage, secretion signaling, and 2A-mediated auto-cleaving efficiency. Mechanistically, Exin21/Qα increased mRNA synthesis/stability, and facilitated protein expression and secretion. These findings indicate that Exin21/Qα has the potential to be used as a universal booster for protein production, which is of importance for biomedicine research and development of bioproducts, drugs, and vaccines.

Getting more out of FLAG-Tag co-immunoprecipitation mass spectrometry experiments using FAIMS

Co-immunoprecipitation of proteins coupled to mass spectrometry is critical for the understanding of protein interaction networks. In instances where a suitable antibody is not available, it is common to graft synthetic tags onto a target protein sequence thereby allowing the use of commercially available antibodies for affinity purification. A common approach is through FLAG-Tag co-immunoprecipitation. To allow the selective elution of protein complexes, competitive displacement using a large molar excess of the tag peptides is often carried out. Yet, this creates downstream challenges for the mass spectrometry analysis due to the presence of large quantities of these peptides. Here, we demonstrate that Field Asymmetric Ion Mobility Spectrometry (FAIMS), a gas phase ion separation device prior to mass spectrometry analysis can be applied to FLAG-Tag co-immunoprecipitation experiments to increase the depth of protein coverage. By excluding these abundant tag peptides, we were able to observe deeper coverage of interacting proteins and as a result, deeper biological insights, without the need for additional sample handling or altering sample preparation protocols. SIGNIFICANCE: We have shown that application of FAIMS separation in the gas phase can increase the proteome coverage of Flag-Tagged co-immunoprecipitation mass spectrometry experiments versus one without FAIMS. We were able to observe deeper coverage of interacting proteins and as a result, deeper biological insights, without additional sample handling, fractionation, machine run time or modifying the sample preparation protocol.

Purification of Prospective Vaccine Antigens from Gram-Positive Pathogens by Immunoprecipitation

Immunoprecipitation is an affinity purification technique that exploits the highly specific interactions formed between antibodies and their cognate antigens to purify molecules of interest from complex biological solutions. The generation of an effective humoral response provides protection against a wide range of gram-positive pathogens, and thus immunoprecipitation using antibodies purified from immune humans or animals provides a simple but effective means of isolating prospective vaccine antigens from fractionated bacterial cells for downstream identification. The commercial availability of antibody preparations from donated human plasma, containing antibodies against many common gram-positive pathogens, allows the protocol to be performed in the absence of bespoke vaccination experiments. Thus, immunoprecipitation has the potential to reduce the number of animals used in vaccine studies by allowing an initial screen for promising antigens to be conducted in vitro.

Evaluation of [Cys(ATTO 488)8]Dermorphin-NH2 as a novel tool for the study of μ-opioid peptide receptors

The μ-opioid peptide (MOP) receptor is a member of the opioid receptor family and an important clinical target for analgesia. Measuring MOP receptor location and tracking its turnover traditionally used radiolabels or antibodies with attendant problems of utility of radiolabels in whole cells and poor antibody selectivity. To address these issues we have synthesized and characterised a novel ATTO488 based fluorescent Dermorphin analogue; [Cys(ATTO 488)⁸]Dermorphin-NH₂ (Derm_ATTO488). We initially assessed the binding profile of Derm_ATTO488 in HEK cells expressing human MOP and CHO cells expressing human MOP, δ-opioid peptide (DOP), κ-opioid peptide (KOP) and Nociceptin/Orphanin FQ peptide (NOP) receptors using radioligand binding. Functional activity of the conjugated peptide was assessed by measuring (i) the ability of the ligand to engage G-protein by measuring the ability to stimulate GTPγ[³⁵S] binding and (ii) the ability to stimulate phosphorylation of ERK1/2. Receptor location was visualised using confocal scanning laser microscopy. Dermorphin and Derm_ATTO488 bound to HEK_MOP (pK_i: 8.29 and 7.00; p<0.05), CHO_MOP (pK_i: 9.26 and 8.12; p<0.05) and CHO_DOP (pK_i: 7.03 and 7.16; p>0.05). Both ligands were inactive at KOP and NOP. Dermorphin and Derm_ATTO488 stimulated the binding of GTPγ[³⁵S] with similar pEC₅₀ (7.84 and 7.62; p>0.05) and E_max (1.52 and 1.34fold p>0.05) values. Moreover, Dermorphin and Derm_ATTO488 produced a monophasic stimulation of ERK1/2 phosphorylation peaking at 5mins (6.98 and 7.64-fold; p>0.05). Finally, in confocal microscopy Derm_ATTO488 bound to recombinant MOP receptors on CHO and HEK cells in a concentration dependent manner that could be blocked by pre-incubation with unlabelled Dermorphin or Naloxone. Collectively, addition to ATTO488 to Dermorphin produced a ligand not dissimilar to Dermorphin; with ~10fold selectivity over DOP. This new ligand Derm_ATTO488 retained functional activity and could be used to visualise MOP receptor location.

Immunoprecipitation

Immunoprecipitation, commonly referred to as IP, involves the binding of proteinaceous antigen in solution by an antigen-specific antibody followed by purification of the antigen-antibody complex via attachment to a solid-phase matrix such as Protein A or G agarose. This rather simplistic and rapid technique yields highly purified immune complexes from multifactorial solutions, including cell lysates or homogenized tissues, and is most commonly used to identify and determine the relative abundance of interacting proteins, referred to as coimmunoprecipitation or co-IP. Although methods encompassing immunoblotting or western blotting of cell lysate preparations can also be applied to determine the presence and quantity of a specific antigen, its relative molecular weight, rate of synthesis or degradation, and state of target-specific posttranslational modification, immunoprecipitation can significantly increase the sensitivity for these methodologies.