Protein G genes: structure and distribution of IgG-binding and albumin-binding domains

Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.

A gold nanoparticle-protein G electrochemical affinity biosensor for the detection of SARS-CoV-2 antibodies: a surface modification approach

As COVID-19 waves continue to spread worldwide, demand for a portable, inexpensive and convenient biosensor to determine community immune/infection status is increasing. Here we describe an impedance-based affinity biosensor using Interdigitated Electrode (IDE) arrays to detect antibodies to SARS-CoV-2 in serum. We created the biosensor by functionalizing the IDEs' surface with abaculaovirus-expressed and purified Spike (S) protein to bind anti-SARS CoV-2antibodies. Gold nanoparticles (GNP) fused to protein G were used to probe for bound antibodies. An ELISA assay using horseradish peroxidase-protein G to probe for bound IgG confirmed that the purified S protein bound a commercial source of anti-SARS-CoV-2 antibodies specifically and bound anti-SARS-CoV-2 antibodies in COVID-19 positive serum. Then we demonstrated that our biosensor could detect anti-SARS-CoV-2 antibodies with 72% sensitivity in 2 h. Using GNP-protein G, the affinity biosensor had increased impedance changes with COVID-19positive serum and minimal or decreased impedance changes with negative serum. This demonstrated that our biosensor could discriminate between COVID-19 positive and negative sera, which were further improved using poly(vinyl alcohol)as a blocking agent.

Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery

Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.

Quantitative assessment of serum heat shock protein 27 for the diagnosis of epithelial ovarian cancer using targeted proteomics coupled with immunoaffinity enrichment

BACKGROUND

Heat shock protein 27 (HSP27) may take part in the epithelial ovarian cancer (EOC) malignant process because it is elevated in the serum of EOC patients, suggesting that HSP27 may serve as an EOC biomarker to complement the standard serum carbohydrate antigen 125 (CA125) test. Thus, accurate quantification of serum HSP27 would assist the diagnosis of EOC.

METHODS

Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics coupled with an immunoaffinity enrichment assay was developed and validated to monitor HSP27 concentrations in serum.

RESULTS

Tryptic peptide 80QLSSGVSEIR89 was selected as a surrogate analyte for quantification, and an immuno-depleted serum extract was used as a surrogate matrix. Immunoaffinity enrichment was effective for protein enrichment and sensitivity enhancement, and the resulting LOQ was 500 pg/ml (>10-fold increase). Then, serum HSP27 concentrations in EOC patients, benign ovarian tumors patients and healthy volunteers were accurately determined to be 4.95 ± 0.37 ng/ml, 2.98 ± 0.16 ng/ml and 2.82 ± 0.15 ng/ml, respectively, suggesting that the EOC samples had significantly higher concentrations of HSP27 than a sample from benign ovarian tumor patients. The experimental values for the samples were compared with those obtained from enzyme-linked immune sorbent assays (ELISAs). The ROC curve analysis showed that the combined area under the curve (AUC) for CA125 and HSP27 was 0.88, which is significantly superior to that of CA125 alone.

CONCLUSIONS

Targeted proteomics coupled with immunoaffinity enrichment may provide more accurate quantification of low-abundant proteins.

Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models

The importance of charge-charge interactions in the thermal stability of proteins is widely known. pH and ionic strength play a crucial role in these electrostatic interactions, as well as in the arrangement of ionizable residues in each protein-folding stage. In this study, two coarse-grained models were used to evaluate the effect of pH and salt concentration on the thermal stability of a protein G variant (1PGB-QDD), which was chosen due to the quantity of experimental data exploring these effects on its stability. One of these coarse-grained models, the TKSA, calculates the electrostatic free energy of the protein in the native state via the Tanford-Kirkwood approach for each residue. The other one, CpHMD-SBM, uses a Coulomb screening potential in addition to the structure-based model Cα. Both models simulate the system in constant pH. The comparison between the experimental stability analysis and the computational results obtained by these simple models showed a good agreement. Through the TKSA method, the role of each charged residue in the protein's thermal stability was inferred. Using CpHMD-SBM, it was possible to evaluate salt and pH effects throughout the folding process. Finally, the computational pKa values were calculated by both methods and presented a good level of agreement with the experiments. This study provides, to our knowledge, new information and a comprehensive description of the electrostatic contribution to protein G stability.

IgG-binding proteins of bacteria

Proteins capable of non-immune binding of immunoglobulins G (IgG) of various mammalian species, i.e. without the involvement of the antigen-binding sites of the immunoglobulins, are widespread in bacteria. These proteins are located on the surface of bacterial cells and help them to evade the host's immune response due to protection against the action of complement and to decrease in phagocytosis. This review summarizes data on the structure of immunoglobulin-binding proteins (IBP) and their complexes with IgG. Common and distinctive structural features of IBPs of gram-positive bacteria (staphylococci, streptococci, peptostreptococci) are discussed. Conditions for IBP expression by bacteria and their functional heterogeneity are considered. Data on IBPs of gram-negative bacteria are presented.

Practical applications of high-affinity, albumin-binding proteins from a group G streptococcal isolate

Binding proteins that have high affinities for mammalian plasma proteins that are expressed on the surface of bacteria have proven valuable for the purification and detection of several biologically important molecules from human and animal plasma or serum. In this study, we have isolated a high affinity albumin-binding molecule from a group G streptococcal isolate of bovine origin and have demonstrated that the isolated protein can be biotinylated without loss of binding activity and can be used as a tracer for quantification of human serum albumin (HSA). The binding protein can be immobilized and used as a selective capture reagent in a competitive ELISA format using a biotinylated HSA tracer. In this assay format, the sensitivity of detection for 50% inhibition of binding of HSA was less than 1 microg/ml. When attached to the bacterial surface, this binding protein can be used to deplete albumin from human plasma, as analyzed by surface-enhanced laser desorption ionization time of flight mass spectrometry.

Directional gene movement from human-pathogenic to commensal-like streptococci

Group A streptococci (GAS) are highly pathogenic for humans, and their closest genetic relatives, group C and G streptococci (GCS and GGS, respectively), are generally regarded as commensals, although they can be found in association with human disease. As part of an effort to better understand the evolution of virulence, the phylogenetic relationships between GAS, GCS, and GGS were examined. The nucleotide sequence was determined for an internal portion of seven housekeeping (neutral) loci among >200 isolates of GAS and 34 isolates of GCS or GGS obtained from human subjects. Genotypic analysis failed to show support for the separation of GCS and GGS into two distinct populations. Unlike GAS, there was poor concordance between emm type and genetic relatedness among GCS and GGS. All housekeeping genes within GAS displayed relatively low levels of sequence diversity. In contrast, individual GCS and GGS strains had mosaic genomes, containing alleles at some loci that were similar or identical to GAS alleles, whereas the alleles at other loci were about 10 to 30% diverged. The data provide evidence for a history of recent interspecies transfer of neutral genes that exhibits a strong net directionality from GAS donors to GCS and GGS recipients. A model for the evolution of GAS and of GCS and GGS is described.

Characterization of clinical isolates of group C and G streptococci on the basis of protein G gene

Treatment of human group C and G streptococci with cyanogen bromide results in solubilization of surface protein G molecules. Strain-to-strain variation in the quantity, molar mass and functional activity of protein G extracted from representative group C and G isolates led to the identification of three structurally and functionally distinct forms of the protein. Using different molecular biological approaches it was possible to determine the group of streptococci (C or G), or the quantity of IgG and HSA domains.

Protein G expressed by human group C and G streptococci: cloning of gene and binding properties

PCR generated fragments of the protein G gene from three GCS and GGS strains belonging to different G types had been cloned. The resulting PCR products were cloned into E. coli using expression vector pQE31. The clones, producing IgG-binding peptides were selected. Recombinant plasmids carried different inserts and encoded proteins of different size and with different binding properties.

Pulsed-field gel electrophoresis and distribution of the genes zag and fnz in isolates of Streptococcus equi

Streptococcus equi subsp. equi and subsp. zooepidemicus are important pathogens of the equine respiratory tract. Isolates of both subspecies were examined by pulsed-field gel electrophoresis (PFGE). With the exception of eight isolates, a unique band pattern was displayed for each of the 48 subsp. zooepidemicus isolates tested. A method to distinguish isolates of the genetically very homogeneous subsp. equi has hitherto not been available, although several methods have been tested. By the use of PFGE, 50 isolates of subsp. equi could be divided into eleven groups, each with a unique pulsotype. In addition, the recently characterised genes encoding the cell-wall proteins ZAG and FNZ of S. equi subsp. zooepidemicus strain ZV were shown by Southern blots to be present in all 98 tested isolates, including the type strains of the two subspecies. Binding assays showed that the expression of the two genes clearly differentiate between the two subspecies.

Surface proteins of gram-positive bacteria and mechanisms of their targeting to the cell wall envelope

The cell wall envelope of gram-positive bacteria is a macromolecular, exoskeletal organelle that is assembled and turned over at designated sites. The cell wall also functions as a surface organelle that allows gram-positive pathogens to interact with their environment, in particular the tissues of the infected host. All of these functions require that surface proteins and enzymes be properly targeted to the cell wall envelope. Two basic mechanisms, cell wall sorting and targeting, have been identified. Cell well sorting is the covalent attachment of surface proteins to the peptidoglycan via a C-terminal sorting signal that contains a consensus LPXTG sequence. More than 100 proteins that possess cell wall-sorting signals, including the M proteins of Streptococcus pyogenes, protein A of Staphylococcus aureus, and several internalins of Listeria monocytogenes, have been identified. Cell wall targeting involves the noncovalent attachment of proteins to the cell surface via specialized binding domains. Several of these wall-binding domains appear to interact with secondary wall polymers that are associated with the peptidoglycan, for example teichoic acids and polysaccharides. Proteins that are targeted to the cell surface include muralytic enzymes such as autolysins, lysostaphin, and phage lytic enzymes. Other examples for targeted proteins are the surface S-layer proteins of bacilli and clostridia, as well as virulence factors required for the pathogenesis of L. monocytogenes (internalin B) and Streptococcus pneumoniae (PspA) infections. In this review we describe the mechanisms for both sorting and targeting of proteins to the envelope of gram-positive bacteria and review the functions of known surface proteins.

Characterization of a gene coding for a type IIo bacterial IgG-binding protein

Two antigenic classes of non-immune IgG-binding proteins can be expressed by group A streptococci. One antigenic group of proteins is recognized by an antibody prepared against the product of a cloned fcrA gene (anti-FcRA). In this study, the immunogen used to prepare the antibody that defines the second antigenic class was shown to be the product of the emm-like (emmL) gene of M serotype 55 group A isolate, A928. The emmL55 gene expressed in E. coli produced an M(r) approximately 58,000 molecule which bound human IgG1, IgG2, IgG3 and IgG4, as well as horse, rabbit and pig IgG in a non-immune fashion. These properties are characteristic of the previously described type IIo IgG-binding protein isolated from this strain. In addition, the recombinant protein was reactive with human serum albumin and fibrinogen. The emmL 55 gene sequence was analysed and found to have the organization and sequence characteristics of a typical class I emm-like gene.

M1 protein and protein H: IgGFc- and albumin-binding streptococcal surface proteins encoded by adjacent genes

M1 protein and Protein H are surface proteins simultaneously present at the surface of certain strains of Streptococcus pyogenes, important pathogenic bacteria in humans. The present study concerns the structure, protein-binding properties and relationship between these two molecules. The gene encoding M1 protein (emm1) was found immediately upstream of the Protein H gene (sph). Both genes were preceded by a promoter region. Comparison of the sequences revealed a high degree of similarity in the signal peptides, the C repeats located in the central parts of the molecules and in the C-terminal cell-wall-attached regions, whereas the N-terminal sequences showed no significant similarity. Protein H has affinity for the Fc region of IgG antibodies. Also M1 protein, isolated from streptococcal culture supernatants or from Escherichia coli expressing emm1, was found to bind human IgGFc. When tested against polyclonal IgG from eight other mammalian species, M1 protein and Protein H both showed affinity for baboon, rabbit and pig IgG. M1 protein also reacted with guinea-pig IgG, whereas both streptococcal proteins were negative in binding experiments with rat, mouse, bovine and horse IgG. The two proteins were also tested against other members of the immunoglobulin super family: human IgM, IgA, IgD, IgE, beta 2-microglobulin, and major histocompatibility complex (MHC) class-I and class-II antigens. M1 protein showed no affinity for any of these molecules whereas Protein H reacted with MHC class-II antigens. M1 protein is known to bind albumin and fibrinogen also. The binding sites for these two plasma proteins and for IgGFc were mapped to different sites on M1 protein. Thus albumin bound to the C repeats and IgGFc to a region (S) immediately N-terminal of the C repeats. Finally, fibrinogen bound further towards the N-terminus but close to the IgGFc-binding site. On the fibrinogen molecule, fragment D was found to mediate binding to M1 protein. The IgGFc-binding region of M1 protein showed no similarity to that of Protein H. Still, competitive binding experiments demonstrated that the two streptococcal proteins bound to overlapping sites on IgGFc.

Nucleotide sequence of the gene for peptostreptococcal protein L

A gene bank of Peptostreptococcus magnus DNA was established using an E. coli host-vector system. Western blot analysis identified a clone expressing protein L which bound to the light chain of human immunoglobulins. DNA sequence determination and analysis revealed an open reading frame of 992 amino acids, giving a theoretical secreted protein of 106 kD with a pl of 4.67.

Proton nuclear magnetic resonance sequential assignments and secondary structure of an immunoglobulin light chain-binding domain of protein L

The 1H NMR assignments have been made for the immunoglobulin (Ig) light chain-binding B1 domain of protein L from Peptostreptococcus magnus. The secondary structure elements and the global folding pattern were determined from nuclear Overhauser effects, backbone coupling constants, and slowly exchanging amide protons. The B1 domain was found to be folded into a globular unit of 61 amino acid residues, preceded by a 15 amino acid long disordered N-terminus. The folded portion of the molecule contains a four-stranded beta-sheet spanned by a central alpha-helix. The fold is similar to the IgG-binding domains of streptococcal protein G, despite the fact that the binding sites on immunoglobulins for the two proteins are different; protein G binds IgG through the constant (Fc) part of the heavy chain, whereas protein L has affinity for the variable domain of Ig light chains.

Isolation and molecular characterization of a novel albumin-binding protein from group G streptococci

Many streptococcal strains are known to bind the two most abundant plasma proteins, namely, immunoglobulin G and albumin. Protein G isolated from group C and G streptococci has been demonstrated to have separate binding regions for each of these proteins. However, some group G streptococcal strains bind only serum albumin. This report describes the isolation of a 48-kDa albumin-binding protein from such a strain (DG12). The affinity constant of this protein for human serum albumin was determined to be 5 x 10(9) M-1, and the protein interacted strongly also with serum albumin from several other mammalian species. The gene encoding the albumin-binding protein was cloned and expressed in Escherichia coli. DNA sequence analysis of this gene revealed a unique NH2-terminal sequence and three types of repeats in the encoded protein. One of these repeated sequences has significant homology with the albumin-binding domains of protein G, and it was demonstrated that the albumin binding of the DG12 protein was localized within these domains. Another type of repeat is localized in the putative wall-spanning region of the molecule. This repeat sequence, which has the length of only 4 amino acids (LysProGluVal), is repeated 14 times. The relationship of the albumin-binding protein to other cell-wall-associated proteins of pathogenic streptococci is discussed.

Isolation and partial characterization of a type IV bacterial immunoglobulin binding protein

A series of bovine G streptococcal isolates were screened for expression of type IV Fc binding proteins. An isolate expressing high levels of type IV binding proteins was selected and expanded by use of a colony selection technique. A variety of different extraction procedures were compared and the optimal solubilization procedure was found to be hot acid extraction of the bacteria. The extracted protein could be affinity purified on a column of immobilized rabbit IgG. The type IV Fc binding protein was found to be antigenically unrelated to the type I, II or III bacterial Fc binding proteins and displayed the lowest affinity and most limited range of species and subclass reactivity of any bacterial Fc binding protein thus far characterized.

Potential for vaccination against infections caused by Staphylococcus aureus

Surface polysaccharides and proteins from S. aureus which could serve as components of a future subunit vaccine against staphylococcal disease in man and animals have recently been characterized. The majority of bovine mastitis and human clinical isolates of S. aureus produce a thin polysaccharide capsule which probably impairs phagocytosis. Protective immunity to S. aureus infections in laboratory animals has been induced by immunization with polysaccharide, and immune serum promotes phagocytosis of bacteria in vitro. S. aureus expresses several surface-exposed proteins that bind host plasma proteins to the bacterial cell or promote adherence of bacteria to host cells or to tissues. These activities may help bacteria avoid host defences and stimulate adherence and colonization to form foci of infection. In this article the properties of S. aureus surface polysaccharides and proteins are reviewed. Their contribution to virulence and the possibility that they could be used as components of new vaccine to combat mastitis in ruminants and nosocomial infections is discussed.

Comparison of albumin receptors expressed on bovine and human group G streptococci

The albumin receptor expressed by bovine group G streptococci was extracted and affinity purified. The protein was characterized for species reactivity, and monospecific antibodies were prepared to the purified receptor. The bovine group G albumin receptor was compared functionally, antigenically, and for DNA homology with the albumin-binding protein expressed by human group G streptococci. In agreement with previous reports, the albumin-binding activity of human strains was mediated by a unique domain of the type III immunoglobulin G-Fc-binding molecule, protein G. The albumin receptor expressed by bovine group G strains was found to lack any immunoglobulin G-binding potential but displayed a wider profile of species albumin reactivity than protein G. Both albumin receptors could inhibit the binding of the other to immobilized human serum albumin, and each displayed similar binding properties. Antigenic comparison of the two albumin receptors demonstrated a low level of cross-reactivity; however comparison at the DNA level, using an oligonucleotide probe specific for the albumin-binding region of protein G, demonstrated that the two albumin receptors expressed by human and bovine group G streptococcal strains do not display significant homology.

Protein L, a bacterial immunoglobulin-binding protein and possible virulence determinant

Protein L, an immunoglobulin kappa light chain-binding protein, is expressed on the surfaces of certain strains of Peptostreptococcus magnus. Thirty strains of P. magnus were isolated from clinical specimens, and four of them were found to express protein L. Among the 30 strains, 7 were isolated from the vaginas of patients with bacterial vaginosis, and the 4 immunoglobulin-binding strains all belonged to this group, results demonstrating that expression of protein L is correlated to peptostreptococcal virulence (P less than 0.001 in the chi-square test) and indicating that the molecule could be a virulence determinant. Similar amounts of protein L were expressed by the four strains, and when protein L was isolated from three of them and analyzed in Western blots, the same immunoglobulin-binding patterns were obtained. The N-terminal amino acid sequences of tryptic fragments of protein L were determined, and on the basis of these sequence data, oligonucleotides were synthesized and used to screen a genomic library of peptostreptococcal DNA in the lambda ZAP vector. The nucleotide sequence was determined for one of the clones detected in this way. In dot blots and Southern blots of peptostreptococcal DNA, another synthetic oligonucleotide probe based on this sequence showed no hybridization with DNA samples from the nonexpressing strains, whereas similar Southern blot patterns were seen when DNA samples from protein L-expressing strains were analyzed. These results suggest that the protein L gene is missing rather than being down regulated in protein L-negative strains of P. magnus. Finally, the probe did not hybridize with DNA purified from immunoglobulin-binding streptococcal and staphylococcal strains or with Escherichia coli DNA, suggesting that the protein L gene is unique to protein L-expressing strains of P. magnus.

Expression and purification of a truncated recombinant streptococcal protein G

The gene for Protein G from Streptococcus strain G148 was cloned and expressed in Escherichia coli. The regions on the gene corresponding to the albumin-binding domains and the Fab-binding region were then deleted by site-directed mutagenesis. The translation of regions corresponding to the cell-wall- and membrane-binding domains was prevented by introduction of stop codons upstream of these domains. This recombinant DNA sequence codes for a protein (G') that contains repetitive regions and that binds only the Fc portion of IgG, analogously to Protein A. Translation of the sequence produces a protein with an Mr of about 20,000. The nucleotide sequence differs from those published previously [Guss, Eliasson, Olsson, Uhlén, Frej, Jornvall, Flock & Lindberg (1986) EMBO J. 5, 1567-1575; Olsson, Eliasson, Guss, Nilsson, Hellman, Lindberg & Uhlén (1987) Eur. J. Biochem. 168, 319-324]. The protein can be substantially purified on a large scale by chromatography on IgG-Sepharose 4B. Homogeneous Protein G' can be prepared by anion-exchange f.p.l.c. on Mono Q HR. This Protein G' has a pI of 4.19 and SDS/PAGE gives an apparent anomalous Mr of 35,000.