Novel surface display system for heterogonous proteins on Lactobacillus plantarum

Aims: To establish a novel cell surface display system that would enable the display of target proteins on Lactobacillus plantarum. Methods and Results: Blast P analysis of the amino acids sequence data revealed that the N‐terminus of the putative muropeptidase MurO from L. plantarum contained two putative lysin motif (LysM) repeat regions, implying that the MurO was involved in bacterial cell wall binding. To investigate the potential of MurO for surface display, green fluorescent protein (GFP) was fused to MurO at its C‐terminus and the resulting fusion protein was expressed in Escherichia coli. After being mixed with L. plantarum cells in vitro, GFP was successfully displayed on the surfaces of L. plantarum cells. Increases in the fluorescence intensities of chemically pretreated L. plantarum cells compared to those of nonpretreated cells suggested that the peptidoglycan was the binding ligand for MurO. SDS sensitivity assay showed that the GFP fluorescence intensity was reduced after being treated with SDS. To demonstrate the applicability of the MurO‐mediated surface display system, β‐galactosidase from Bifidobacterium bifidium, in place of GFP, was functionally displayed on the surface of L. plantarum cells via MurO. Conclusions: The MurO was a novel anchor protein for constructing a surface display system for L. plantarum. Significance and Impact of Study: The success in surface display of GFP and β‐galactosidase opened up the feasibility of employing the cell wall anchor of MurO for surface display in L. plantarum.     

NMR reveals structural rearrangements associated to substrate insertion in nucleotide‐adding enzymes

The protein NP_344798.1 from Streptococcus pneumoniae TIGR4 exhibits a head and base‐interacting neck domain architecture, as observed in class II nucleotide‐adding enzymes. Although it has less than 20% overall sequence identity with any member of this enzyme family, the residues involved in substrate‐recognition and catalysis are highly conserved in NP_344798.1. NMR studies showed binding affinity of NP_344798.1 for nucleotides and revealed μs to ms time scale rate processes involving residues constituting the active site. The results thus obtained indicate that large‐amplitude rearrangements of regular secondary structures facilitate the penetration of the substrate into the occluded nucleotide‐binding site of NP_344798.1 and, by inference based on sequence and structural homology, probably a wide range of other nucleotide‐adding enzymes.     

Kinetic improvement of an algal diacylglycerol acyltransferase 1 via fusion with an acyl‐CoA binding protein

Microalgal oils in the form of triacylglycerols (TAGs) are broadly used as nutritional supplements and biofuels. Diacylglycerol acyltransferase (DGAT) catalyzes the final step of acyl‐CoA‐dependent biosynthesis of TAG, and is considered a key target for manipulating oil production. Although a growing number of DGAT1s have been identified and over‐expressed in some algal species, the detailed structure?function relationship, as well as the improvement of DGAT1 performance via protein engineering, remain largely untapped. Here, we explored the structure?function features of the hydrophilic N‐terminal domain of DGAT1 from the green microalga Chromochloris zofingiensis (CzDGAT1). The results indicated that the N‐terminal domain of CzDGAT1 was less disordered than those of the higher eukaryotic enzymes and its partial truncation or complete removal could substantially decrease enzyme activity, suggesting its possible role in maintaining enzyme performance. Although the N‐terminal domains of animal and plant DGAT1s were previously found to bind acyl‐CoAs, replacement of CzDGAT1 N‐terminus by an acyl‐CoA binding protein (ACBP) could not restore enzyme activity. Interestingly, the fusion of ACBP to the N‐terminus of the full‐length CzDGAT1 could enhance the enzyme affinity for acyl‐CoAs and augment protein accumulation levels, which ultimately drove oil accumulation in yeast cells and tobacco leaves to higher levels than the full‐length CzDGAT1. Overall, our findings unravel the distinct features of the N‐terminus of algal DGAT1 and provide a strategy to engineer enhanced performance in DGAT1 via protein fusion, which may open a vista in generating improved membrane‐bound acyl‐CoA‐dependent enzymes and boosting oil biosynthesis in plants and oleaginous microorganisms.     

Adhesion of Lactobacillus fermentum 104-S to Porcine Stomach Mucus

The adhesion to whole and fractionated porcine gastric mucus of both Lactobacillus fermentum 104-S cells and a saccharide extracted from this strain was investigated. It has been shown previously that this saccharide had affinity for nonsecreting gastric epithelium. The mucus component(s) with affinity the bacterial cells was partly characterized by gel filtration and treatment with protease or metaperiodate. L. fermentum 104-S extracts containing the saccharide were radioactively labeled, fractionated by gel filtration, and tested for affinity for the gastric mucus component showing receptor activity for the whole cells of strain 104-S. The mucus material with affinity for the bacterial cells had a relative molecular weight of 30–70 K. From the results of treatment with protease or metaperiodate, it is proposed that the mucus components(s) that adhered to the whole bacterial cells contained glycoprotein groups. The radioactively labeled saccharide extracted from L. fermentum 104-S cells did not bind to the mucus fraction that had affinity for the whole cells. Conclusively, we suggest that the mechanism by which cells of L. fermentum 104-S adhere to the gastric mucus is different from the mechanism mediating the adhesion of this strain to the nonsecreting gastric epithelium. Cells of L. fermentum 104-S adhere to a glycoproteinaceous mucus component with a relative molecular weight of 30–70 K. Received: 29 August 1995 / Accepted: 26 December 1995     

Extract of Lactobacillus plantarum strain 06CC2 induces JNK/p38 MAPK pathway-mediated apoptosis through endoplasmic reticulum stress in Caco2 colorectal cancer cells

Colorectal cancer is a multi-factorial disease involving genetic, environmental and lifestyle risk factors. In recent years, many changes in the bacterial composition of the intestinal microflora have been reported in colorectal cancer, suggesting the involvement of the intestinal microflora in the development and progression of colorectal cancer. Along with these reports, research on lactic acid bacteria that have a beneficial effect on the human body for the purpose of improving the intestinal environment and treating intestinal diseases has advanced. Among these studies, biogenics (defined as a component derived from lactic acid bacteria that acts directly on diseases regardless of the state of intestinal microflora) is a recent concept derived from the work on probiotics. Based on this concept, it is important to evaluate the effectiveness of various components derived from lactic acid bacteria in the treatment to diseases from and apply them in prevention and treatment. In this study, we investigated the antitumor effect of an extract obtained from Lactobacillus plantarum strain 06CC2 on colorectal cancer cells. In in vitro experiments, the extract derived from Lactobacillus plantarum 06CC2 significantly suppressed the proliferation of Caco2 colorectal cancer cells in comparison to control and non-cancer cells. Furthermore, we found that endoplasmic reticulum stress and the JNK/p38 MAPK signaling system are involved in the induction of apoptosis. These findings indicate the direct antitumor effect of the Lactobacillus plantarum 06CC2 extract on Caco2 colorectal cancer cells, and that this extract may have potential application as a biogenics.     

MotifAnalyzer‐PDZ: A computational program to investigate the evolution of PDZ‐binding target specificity

Recognition of short linear motifs (SLiMs) or peptides by proteins is an important component of many cellular processes. However, due to limited and degenerate binding motifs, prediction of cellular targets is challenging. In addition, many of these interactions are transient and of relatively low affinity. Here, we focus on one of the largest families of SLiM‐binding domains in the human proteome, the PDZ domain. These domains bind the extreme C‐terminus of target proteins, and are involved in many signaling and trafficking pathways. To predict endogenous targets of PDZ domains, we developed MotifAnalyzer‐PDZ, a program that filters and compares all motif‐satisfying sequences in any publicly available proteome. This approach enables us to determine possible PDZ binding targets in humans and other organisms. Using this program, we predicted and biochemically tested novel human PDZ targets by looking for strong sequence conservation in evolution. We also identified three C‐terminal sequences in choanoflagellates that bind a choanoflagellate PDZ domain, the Monsiga brevicollis SHANK1 PDZ domain (mbSHANK1), with endogenously‐relevant affinities, despite a lack of conservation with the targets of a homologous human PDZ domain, SHANK1. All three are predicted to be signaling proteins, with strong sequence homology to cytosolic and receptor tyrosine kinases. Finally, we analyzed and compared the positional amino acid enrichments in PDZ motif‐satisfying sequences from over a dozen organisms. Overall, MotifAnalyzer‐PDZ is a versatile program to investigate potential PDZ interactions. This proof‐of‐concept work is poised to enable similar types of analyses for other SLiM‐binding domains (e.g., MotifAnalyzer‐Kinase). MotifAnalyzer‐PDZ is available at http://motifAnalyzerPDZ.cs.wwu.edu .     

A proteomic approach based on peptide affinity chromatography, 2-dimensional electrophoresis and mass spectrometry to identify multiprotein complexes interacting with membrane-bound receptors

There is accumulating evidence that membrane-bound receptors interact with many intracellular proteins. Multiprotein complexes associated with ionotropic receptors have been extensively characterized, but the identification of proteins interacting with G protein-coupled receptors (GPCRs) has so far only been achieved in a piecemeal fashion, focusing on one or two protein species. We describe a method based on peptide affinity chromatography, two-dimensional electrophoresis, mass spectrometry and immunoblotting to identify the components of multiprotein complexes interacting directly or indirectly with intracellular domains of GPCRs or, more generally, any other membrane-bound receptor. Using this global approach, we have characterized multiprotein complexes that bind to the carboxy-terminal tail of the 5-hydroxytryptamine type 2C receptor and are important for its subcellular localization in CNS cells (Bécamel et al., EMBO J., 21(10): 2332, 2002). Published: December 9, 2002     

Butanol production from corncob residue using Clostridium beijerinckii NCIMB 8052

Aims: Not all lactic acid bacteria possess the ability to confer health benefits for the host. Thus, it becomes necessary to screen and characterize numerous strains to obtain ideal probiotics. Here, two Lactobacillus plantarum strains (CECT 7315 and CECT 7316) were isolated and characterized. Methods and Results: In vitro and in vivo tests were carried out for demonstrating the abilities as probiotics of CECT 7315/CECT 7316 Lact. plantarum strains. Both strains showed high ability to survive at gastro‐intestinal tract conditions and to adhere to intestinal epithelial cells, as well as great inhibitory activity against a wide range of enteropathogens and ability to induce the production of anti‐inflammatory cytokine IL‐10. Conclusions: Lactobacillus plantarum CECT 7315/CECT 7316 because of their potential probiotic properties could be excellent candidates for being tested in clinical trials aimed to demonstrate beneficial effects on human health. Significance and Impact of the Study: Probiotics are live micro‐organisms that confer a health benefit for the host. However, not all the lactic acid bacteria possess the ability to confer health benefits for the host. In this study, two Lact. plantarum strains (CECT 7315 and CECT 7316) were isolated and characterized to demonstrate their excellent qualities as potential probiotic strains.     

The proteins (12 and 15 kDa) isolated from heat‐killed Lactobacillus plantarum L67 induces apoptosis in HT‐29 cells

A number of scientific studies have revealed that Lactobacillus strains have beneficial bioactivities in the gastrointestinal tract. In this study, the production of intracellular reactive oxygen species (ROS) and the amounts of intracellular calcium, protein kinase C activity, cytochrome c, Bid, Bcl‐2, Bax and the apoptosis‐mediated proteins [caspase‐8, caspase‐3 and poly ADP ribose polymerase (PARP)] were evaluated to understand the induction of programmed cell death in HT‐29 cells by Lactobacillus plantarum L67. The results obtained from this study indicated that the relative intensities of the apoptotic‐related factors (intracellular ROS and intracellular calcium) and of apoptotic signals (Bax and t‐Bid) increased with increasing concentrations of the membrane proteins isolated from heat‐killed L. plantarum L67, whereas the relative intensities of cytochrome c, Bcl‐2, caspase‐8, caspase‐3 and PARP decreased. This study determines whether proteins (12 and 15 kDa) isolated from heat‐killed L. plantarum L67 induce programmed cell death in HT‐29 cells. Proteins isolated from L. plantarum L67 can stimulate the apoptotic signals and then consequently induce programmed cell death in HT‐29 cells. The results in this study suggest that the proteins isolated from L. plantarum L67 could be used as an antitumoural agent in probiotics and as a component of supplements or health foods. Copyright © 2015 John Wiley & Sons, Ltd.     

Identification of DC-SIGN as the receptor during the interaction of <Emphasis Type="Italic">Lactobacillus plantarum</Emphasis> CGMCC 1258 and dendritic cells

Lactobacillus plantarum can exert additional probiotic effects via regulation of human immune system. However, the direct interaction between probiotics and the receptors of immune cells still needs to be further studied. To identify the receptor of dendritic cells during the interaction with L. plantarum. Dendritic cells were pretreated with L. plantarum and the antibody to dendritic cells specific intercellular adhesion molecule-grabbing nonintegrin (DC-SIGN), toll like receptor (TLR)-2 and TLR-4. The maturation of immature dendritic cells, cytokine production, and modulation of T cells were studied by flow cytometry. Adherence between L. plantarum and dendritic cells were studied by ELISA, flow cytometry, and Western blot. L. plantarum could mature dendritic cells by up-regulating MHC-II and CD80 and CD86. Anti-inflammatory interlectin (IL)-10 and IL-6 was up-regulated and pro-inflammatory IL-12p70 was retro-regulated by L. plantarum. L. plantarum may interact with DC-SIGN and modulate of T to differentiate into IL-4 producing T cells. The interaction of L. plantarum and DC-SIGN and the biological effects could be blocked by EDTA and antibody to DC-SIGN. Effects of L. plantarum were concentration-dependent. L. plantarum could bind to DC-SIGN to improve DC maturation at different ratios, regulate the secretion of anti-inflammatory and pro-inflammatory cytokines, and induce the polarization of interlectin-4-producing T cells.     

Structural and molecular insights into novel surface‐exposed mucus adhesins from Lactobacillus reuteri human strains

The mucus layer covering the gastrointestinal tract is the first point of contact of the intestinal microbiota with the host. Cell surface macromolecules are critical for adherence of commensal bacteria to mucus but structural information is scarce. Here we report the first molecular and structural characterization of a novel cell‐surface protein, Lar_0958 from Lactobacillus reuteri JCM 1112^T, mediating adhesion of L. reuteri human strains to mucus. Lar_0958 is a modular protein of 133 kDa containing six repeat domains, an N‐terminal signal sequence and a C‐terminal anchoring motif (LPXTG). Lar_0958 homologues are expressed on the cell‐surface of L. reuteri human strains, as shown by flow‐cytometry and immunogold microscopy. Adhesion of human L. reuteri strains to mucus in vitro was significantly reduced in the presence of an anti‐Lar_0958 antibody and Lar_0958 contribution to adhesion was further confirmed using a L. reuteri ATCC PTA 6475 lar_0958 KO mutant (6475‐KO). The X‐ray crystal structure of a single Lar_0958 repeat, determined at 1.5 Å resolution, revealed a divergent immunoglobulin (Ig)‐like β‐sandwich fold, sharing structural homology with the Ig‐like inter‐repeat domain of internalins of the food borne pathogen Listeria monocytogenes. These findings provide unique structural insights into cell‐surface protein repeats involved in adhesion of Gram‐positive bacteria to the intestine.     

Revisiting the structure of the Vps10 domain of human sortilin and its interaction with neurotensin

Sortilin is a multifunctional receptor involved in sorting and apoptosis. We have previously reported a 2.0‐Å structure of the Vps10 ectodomain in complex with one of its ligands, the tridecapeptide neurotensin. Here we set out to further characterize the structural properties of sortilin and its interaction with neurotensin. To this end, we have determined a new 2.7 Å structure using a crystal grown with a 10‐fold increased concentration of neurotensin. Here a second peptide fragment was observed within the Vps10 β‐propeller, which may in principle either represent a second molecule of neurotensin or the N‐terminal part of the molecule bound at the previously identified binding site. However, in vitro binding experiments strongly favor the latter hypothesis. Neurotensin thus appears to bind with a 1:1 stoichiometry, and whereas the N‐terminus does not bind on its own, it enhances the affinity in context of full‐length neurotensin. We conclude that the N‐terminus of neurotensin probably functions as an affinity enhancer for binding to sortilin by engaging the second binding site. Crystal packing differs partly from the previous structure, which may be due to variations in the degree and pattern of glycosylations. Consequently, a notable hydrophobic loop, not modeled previously, could now be traced. A computational analysis suggests that this and a neighboring loop may insert into the membrane and thus restrain movement of the Vps10 domain. We have, furthermore, mapped all N‐linked glycosylations of CHO‐expressed human sortilin by mass spectrometry and find that their locations are compatible with membrane insertion of the hydrophobic loops.     

Paired receptor specificity explained by structures of signal regulatory proteins alone and complexed with CD47

CD47 is a widely distributed cell-surface protein that acts a marker of self through interactions of myeloid and neural cells. We describe the high-resolution X-ray crystallographic structures of the immunoglobulin superfamily domain of CD47 alone and in complex with the N-terminal ligand-binding domain of signal regulatory protein alpha (SIRPalpha). The unusual and convoluted interacting face of CD47, comprising the N terminus and loops at the end of the domain, intercalates with the corresponding regions in SIRPalpha. We have also determined structures of the N-terminal domains of SIRPbeta, SIRPbeta(2), and SIRPgamma; proteins that are closely related to SIRPalpha but bind CD47 with negligible or reduced affinity. These results explain the specificity of CD47 for the SIRP family of paired receptors in atomic detail. Analysis of SIRPalpha polymorphisms suggests that these, as well as the activating SIRPs, may have evolved to counteract pathogen binding to the inhibitory SIRPalpha receptor.     

Hyaluronate binding properties of versican.

We have previously cloned a large chondroitin sulfate proteoglycan (versican) from human fibroblasts. The primary sequence shows that the N terminus contains sequence homology with known hyaluronate-binding molecule, suggesting that versican can bind hyaluronate. To test this hypothesis we have reconstructed a full-length versican cDNA and a versican cDNA fragment encoding the N terminus and have transfected Chinese hamster ovary cells and mouse 3T3 fibroblasts, respectively, with these constructs. The transfected Chinese hamster ovary cells make a proteoglycan shown to be versican by enzymatic and immunologic analysis. No corresponding proteoglycan was seen in the control cells. Using hyaluronate affinity chromatography, we show that recombinant versican specifically binds hyaluronate and does not bind to heparin or chondroitin sulfate. The transfected fibroblasts make a 78-kDa truncated form of versican that also binds hyaluronate and does not bind the related polysaccharides, showing that the hyaluronate binding activity resides at the N terminus of versican. The binding of versican to hyaluronate is substrate-concentration dependent and time dependent and can be competed with unlabeled versican. The dissociation constant for versican binding to hyaluronate was determined to be 4 x 10(-9) M.     

A biophysical characterization of the folded domains of KCTD12: insights into interaction with the GABAB2 receptor

Recent investigations have shown that members of the KCTD family play important roles in fundamental biological processes. Despite their roles, very limited information is available on their structures and molecular organization. By combining different experimental and theoretical techniques, we have here characterized the two folded domains of KCTD12, an integral component and modulator of the GABA_B2 receptor. Secondary prediction methods and CD spectroscopy have shown that the N‐terminal domain KCTD12_BTB assumes an α/β structure, whereas the C‐terminal domain KCTD12_H1 is predominantly characterized by a β‐structure. Binding assays indicate that the two domains independently expressed show a good affinity for each other. This suggests that the overall protein is likely endowed with a rather compact structure with two interacting structured domains joint by a long disordered region. Notably, both KCTD12_BTB and KCTD12_H1 are tetrameric when individually expressed. This finding could modify the traditional view that ascribes only to POZ/BTB domain a specific oligomerization role. The first quantification of the affinity of KCTD12_POZ/BTB for the C‐terminal region of GABA_B2 shows that it falls in the low micromolar range. Interestingly, we also demonstrate that a GABA_B2‐related peptide is able to bind KCTD12_BTB with a very high affinity. This peptide may represent a useful tool for modulating KCTD12/GABA_B2 interaction in vitro and may also constitute the starting point for the development of peptidomimetic compounds with a potential for therapeutic applications. Copyright © 2013 John Wiley & Sons, Ltd.     

Secreted expression of an active human interferon‐beta (HuIFNβ) in Kluyveromyces lactis

Interferon‐beta (IFNβ) is a cytokine involved in the antiviral, anti‐proliferative and immunomodulatory responses of cells, and a potent drug for multiple sclerosis. Human interferon beta (HuIFNβ) gene fused with the glucoamylase signal sequence in the N‐terminus and 6 His Tag in the C‐terminus was cloned into pKlac1 vector and introduced in Kluyveromyces lactis to allow secreted expression and one‐step purification of the protein. Recombinant yeast transformant with the highest level of HuIFNβ production was identified, and this secreted up to 1 mg/L of the cytokine after 72 h of incubation. Glycosylated and non‐glycosylated forms of the cytokine were elaborated by the yeast, the latter in higher quantities. His tag of the protein allowed easy one‐step purification by nickel‐nitriloacetic acid affinity chromatography, yielding close to 100% purity. SDS‐PAGE, western blot and MALDI‐TOF‐TOF confirmed the identity of the protein. The biological activity of the recombinant HuIFNβ was confirmed by its anti cell proliferative activity on HeLa cells. Expression of HuIFNβ in K. lactis is advantageous since it is a very safe organism to produce proteins for therapeutic applications, allows glycosylation and offers a cost effective method for large scale production as it can be grown in cheap carbon sources.     

Expression of an immunogenic Ebola immune complex in Nicotiana benthamiana

Filoviruses (Ebola and Marburg viruses) cause severe and often fatal haemorrhagic fever in humans and non‐human primates. The US Centers for Disease Control identifies Ebola and Marburg viruses as ‘category A’ pathogens (defined as posing a risk to national security as bioterrorism agents), which has lead to a search for vaccines that could prevent the disease. Because the use of such vaccines would be in the service of public health, the cost of production is an important component of their development. The use of plant biotechnology is one possible way to cost‐effectively produce subunit vaccines. In this work, a geminiviral replicon system was used to produce an Ebola immune complex (EIC) in Nicotiana benthamiana. Ebola glycoprotein (GP1) was fused at the C‐terminus of the heavy chain of humanized 6D8 IgG monoclonal antibody, which specifically binds to a linear epitope on GP1. Co‐expression of the GP1‐heavy chain fusion and the 6D8 light chain using a geminiviral vector in leaves of N. benthamiana produced assembled immunoglobulin, which was purified by ammonium sulphate precipitation and protein G affinity chromatography. Immune complex formation was confirmed by assays to show that the recombinant protein bound the complement factor C1q. Size measurements of purified recombinant protein by dynamic light scattering and size‐exclusion chromatography also indicated complex formation. Subcutaneous immunization of BALB/C mice with purified EIC resulted in anti‐Ebola virus antibody production at levels comparable to those obtained with a GP1 virus‐like particle. These results show excellent potential for a plant‐expressed EIC as a human vaccine.     

Elg1, an alternative subunit of the RFC clamp loader,preferentially interacts with SUMOylated PCNA

Replication‐factor C (RFC) is a protein complex that loads the processivity clamp PCNA onto DNA. Elg1 is a conserved protein with homology to the largest subunit of RFC, but its function remained enigmatic. Here, we show that yeast Elg1 interacts physically and genetically with PCNA, in a manner that depends on PCNA modification, and exhibits preferential affinity for SUMOylated PCNA. This interaction is mediated by three small ubiquitin‐like modifier (SUMO)‐interacting motifs and a PCNA‐interacting protein box close to the N‐terminus of Elg1. These motifs are important for the ability of Elg1 to maintain genomic stability. SUMOylated PCNA is known to recruit the helicase Srs2, and in the absence of Elg1, Srs2 and SUMOylated PCNA accumulate on chromatin. Strains carrying mutations in both ELG1 and SRS2 exhibit a synthetic fitness defect that depends on PCNA modification. Our results underscore the importance of Elg1, Srs2 and SUMOylated PCNA in the maintenance of genomic stability.