Ekyune Kim

Structural modifications of outer membrane vesicles to refine them as vaccine delivery vehicles.

In an effort to devise a safer and more effective vaccine delivery system, outer membrane vesicles (OMVs) were engineered to have properties of intrinsically low endotoxicity sufficient for the delivery of foreign antigens. Our strategy involved mutational inactivation of the MsbB (LpxM) lipid A acyltransferase to generate OMVs of reduced endotoxicity from Escherichia coli (E. coli) O157:H7. The chromosomal tagging of a foreign FLAG epitope within an OmpA-fused protein was exploited to localize the FLAG epitope in the OMVs produced by the E. coli mutant having the defined msbB and the ompA::FLAG mutations. It was confirmed that the desired fusion protein (OmpA::FLAG) was expressed and destined to the outer membrane (OM) of the E. coli mutant from which the OMVs carrying OmpA::FLAG are released during growth. A luminal localization of the FLAG epitope within the OMVs was inferred from its differential immunoprecipitation and resistance to proteolytic degradation. Thus, by using genetic engineering-based approaches, the native OMVs were modified to have both intrinsically low endotoxicity and a foreign epitope tag to establish a platform technology for development of multifunctional vaccine delivery vehicles.

Implication of mouse Vps26b-Vps29-Vps35 retromer complex in sortilin trafficking.

The retromer complex, which mediates retrograde transport from endosomes to the trans-Golgi network, is a heteropentameric complex that contains a multifunctional cargo recognition heterotrimer consisted of the vacuolar protein sorting (Vps) subunits Vps26, Vps29, and Vps35. In mammals, there are two different isoforms of Vps26, Vps26a and Vps26b, that localize to the endosome, and to the plasma membrane, respectively. To elucidate the biological significance of the Vps26b isoform, we generated Vps26b knockout mice and studied their molecular, histological, and behavioral phenotypes. We found that the loss of Vps26b results in no significant defects in the behavior, body size, and health of the mice. Vps26b-deficient mice showed a severe reduction of Vps35 protein at cellular level and lacked the Vps26b-Vps29-Vps35 retromer complex, despite the normal presence of the Vps26a-Vps29-Vps35 retromer complex. Relatively, the amount of sortilin was increased approximately 20% in the Vps26b-deficient mice, whereas the sorLA was normal. These results suggest that mouse Vps26b-Vps29-Vps35 retromer complex is implicated in the transport of sortilin from endosomes to the trans-Golgi network (TGN).

Identification of novel retromer complexes in the mouse testis

A family of vacuolar protein sorting (Vps) proteins, which are components of mammalian retromer complex, has been studied in the mouse. Vps26a is known as a retromer component that plays an important role in embryonic development: however, its cell-type expression and precise role remain to be elucidated. In this study, we identified a new isoform of Vps26a, called Vps26aT, which was expressed specifically in the mouse testis. Diverse expression patterns of Vps26 variants in mouse tissues were determined by Western blot and RT-PCR analyses, and the direct interaction of Vps26aT with Vps35 was also demonstrated by immunoprecipitation and pull-down assay using antibodies raised against each Vps component. Our results revealed that the retromer complex could be formed from different Vps26 isoforms in a tissue-specific manner, resulting in more than two types of the retromer complex, including the Vps26a-Vps29-Vps35, Vps26aT-Vps29-Vps35, and Vps26b-Vps29-Vps35 complexes in mouse tissues.

Genome-wide and molecular evolution analyses of the KT/HAK/KUP family in tomato (Solanum lycopersicum L.)

Potassium transporters belonging to the KT/HAK/KUP family play an important role in plant growth, development, mineral nutrition, and stress adaptation. In this study, we identified 19 KT/HAK/KUP family genes in tomato, distributed on 10 chromosomes, by using bioinformatics methods. A complete overview of the KT/HAK/KUP (SlHAK) genes in tomato is presented, including chromosome location, phylogeny, gene structure, and evolution pattern. Phylogenetic analysis of 19 SlHAK proteins suggested that group IV of the KT/HAK/KUP family is absent in the tomato genome. In addition, five pairs of segmental duplicated paralogs and two pairs of tandem duplicated paralogs were identified in the tomato KT/HAK/KUP family. This suggests that segmental duplication is predominant for the expansion of the SlHAK genes. Calculation of the approximate dates of duplication events using the synonymous substitution rate indicated that the segmental duplication of the KT/HAK/KUP genes in tomato originated 35.89–62.77 million years ago. Adaptive evolution analysis showed that purifying selection contributed to the evolution of segmental duplicated pairs. Furthermore, Tajima’s relative rate test indicated that all segmental duplicated pairs evolved at similar rates. As a first step toward a genome-wide analysis of the KT/HAK/KUP gene family in tomato, our results provide valuable information for understanding the function and evolution of the KT/HAK/KUP gene family in tomato and other species.

Molecular cloning, characterization of porcine IZUMO1, an IgSF family member.

IZUMO1, belonging to the family of mammalian immunoglobulin proteins, has been well characterized in the mouse. Here, we describe the molecular cloning and expression analysis of porcine IZUMO1 (pIZUMO1). Partial sequence information published in the National Center for Biotechnology Information (NCBI) database was used to generate the full-length sequence for IZUMO1 using rapid amplification of cDNA ends (RACE). A search of the porcine genomic sequence in the NCBI database identified a bacterial artificial chromosome (BAC) encoding the pIZUMO1 gene. This BAC is derived from porcine chromosome 6 and is syntenic with the corresponding regions of mouse, bovine, and human genomes encoding the IZUMO gene family. This BAC was found to encode an IZUMO1 protein with a predicted amino acid sequence having high similarity with mouse and human IZUMO1. Western blot analysis of proteins from porcine tissues indicated that pIZUMO1 was specifically expressed in the sperm. Furthermore, to confirm whether pIZUMO1 forms complexes, we overexpressed pIZUMO1 in HEK293 cells. The recombinant pIZUMO1 from cell extracts was found to form complexes. Our finding suggests that pIZUMO1 forms homodimeric complex on the sperm membrane. Furthermore, an IVF inhibition assay with an antibody for the porcine IZUMO1 Ig-like domain showed that Ig-like domain effectively prevented pig sperm-egg interactions.

Alu-derived old world monkeys exonization event and experimental validation of the LEPR gene

The leptin receptor (LEPR) is a crucial regulatory protein that interacts with Leptin. In our analysis of LEPR, novel AluJb-derived alternative transcripts were identified in the genome of the rhesus monkey. In order to investigate the occurrence of AluJb-derived alternative transcripts and the mechanism underlying exonization events, we conducted analyses using a number of primate genomic DNAs and adipose RNAs of tissue and primary cells derived from the crab-eating monkey. Our results demonstrate that the AluJb element has been integrated into our common ancestor genome prior to the divergence of simians and prosimians. The lineage-specific exonization event of the LEPR gene in chimpanzees, orangutans, and Old World monkeys appear to have been accomplished via transition mutations of the 5′ splicing site (second position of C to T). However, in New World monkeys and prosimians, the AluJb-related LEPR transcript should be silenced by the additional transversion mutation (fourth position of T to G). The AluJb-related transcript of human LEPR should also be silenced by a mutation of the 5′ splicing site (first position of G to A) and the insertion of one nucleotide sequence (minus fourth position of A). Our data suggests that lineage-specific exonization events should be determined by the combination event of the formation of splicing sites and protection against site-specific mutation pressures. These evolutionary mechanisms could be major sources for primate diversification.

Processing and subcellular localization of ADAM2 in the Macaca fascicularis testis and sperm

Fertilin, a heterodimeric protein complex composed of ADAM1 and ADAM2 located on the sperm surface, is involved in sperm-egg interaction. In our study, we examined the physiological processing and subcellular localization of M. fascicularis ADAM2 during spermatogenesis in the testis and epididymal tract. M. fascicularis ADAM2 was initially synthesized as a 100 kDa precursor in testicular germ cells. After passing into 50 kDa intermediate form in the epididymal tracts, the precursor form was finally processed into a 47 kDa protein in sperm. We found that M. fascicularis ADAM2 is localized on the sperm surface and contributes to the formation of a candidate fertilin complex. In particular, Far-Western blot analysis revealed that M. fascicularis ADAM2 cystein-rich domain may be related to protein-protein interaction. Therefore, the cystein-rich domain of ADAM2 could provide a mechanism to form a fertilin complex.

Shiga toxin A subunit mutant of Escherichia coli O157:H7 releases outer membrane vesicles containing the B-pentameric complex.

Shiga toxins (STx) are secreted extracellularly through the outer membrane vesicles (OMVs) of Escherichia coli O157:H7. In an attempt to produce STxA-deficient OMVs from E. coli O157:H7, site-specific deletions of the stx1A and stx2A subunit genes were carried out. The STxA-deficient phenotype of the stx1A/stx2A mutant was confirmed by Vero cell cytotoxicity and VTEC-RPLA assay. Western blot analyses showed that the B (STxB) subunits were present without coupling to STxA in the OMVs of the STxA-deficient mutant. Furthermore, STxB was located in its homo-pentameric complexes, as revealed by immunoprecipitation and immunoblotting with anti-STxB antibodies. These results suggest that STxB alone can be oligomerized into the B pentamer in the periplasm, and subsequently entrapped into the OMVs. Determination of the median lethal dose concentration for the OMV preparations suggests that the STxA-deficient OMVs containing STxB complex could be safely used as vaccine delivery vehicles.

Characterization of pig sperm hyaluronidase and improvement of the digestibility of cumulus cell mass by recombinant pSPAM1 hyaluronidase in an in vitro fertilization assay

Although sperm hyaluronidase is thought to play an important role in mammalian fertilization, the molecular function underlying these steps remains largely unknown. In mouse models, sperm-specific SPAM1 and HYAL5 hyaluronidase are believed to function in both sperm penetration of the cumulus matrix and sperm-ZP binding. However, gene-targeting studies for SPAM1 or HYAL5 show that hyaluronidases are not essential for fertilization, despite the fact that exogenous hyaluronidase can disrupt the cumulus matrix. Therefore, to evaluate whether sperm hyaluronidase is essential for mammalian fertilization, it is necessary to generate HYAL5/SPAM1 double-knockout mice. However, generating double-knockout mice is very difficult because these two genes exist on the same chromosome. Recently, investigators have begun to employ the pig model system to study human disease due to its similarities to human anatomy and physiology. In this study, we confirmed that pig SPAM1 exists as a single copy gene on chromosome 18 and is specifically expressed in the testis. In addition, we expressed recombinant pig SPAM1 in human embryonic kidney 293 cells and showed that these enzymes possess hyaluronidase activity. We also demonstrated that a polyclonal antibody against pig sperm hyaluronidase inhibits sperm-egg interactions in an in vitro fertilization (IVF) assay. Our results suggest that pig SPAM1 may play a critical role in pig fertilization and that recombinant SPAM1 can disperse the oocyte-cumulus complex in an IVF assay.

Instability of toxin A subunit of AB5 toxins in the bacterial periplasm caused by deficiency of their cognate B subunits

Shiga toxin (STx) belongs to the AB(5) toxin family and is transiently localized in the periplasm before secretion into the extracellular milieu. While producing outer membrane vesicles (OMVs) containing only A subunit of the toxin (STxA), we created specific STx1B- and STx2B-deficient mutants of E. coli O157:H7. Surprisingly, STxA subunit was absent in the OMVs and periplasm of the STxB-deficient mutants. In parallel, the A subunit of heat-labile toxin (LT) of enterotoxigenic E. coli (ETEC) was absent in the periplasm of the LT-B-deficient mutant, suggesting that instability of toxin A subunit in the absence of the B subunit is a common phenomenon in the AB(5) bacterial toxins. Moreover, STx2A was barely detectable in the periplasm of E. coli JM109 when stx2A was overexpressed alone, while it was stably present when stxB was co-expressed. Compared with STx2 holotoxin, purified STx2A was degraded rapidly by periplasmic proteases when assessed for in vitro proteolytic susceptibility, suggesting that the B subunit contributes to stability of the toxin A subunit in the periplasm. We propose a novel role for toxin B subunits of AB(5) toxins in protection of the A subunit from proteolysis during holotoxin assembly in the periplasm.