Protein Multigene Family Research Articles

Anti-Claudin Treatments in Gastroesophageal Adenocarcinoma: Mainstream and Upcoming Strategies.

Claudins (CLDNs) are a multigene family of proteins and the principal components of tight junctions (TJs), which normally mediate cell-cell adhesion and selectively allow the paracellular flux of ions and small molecules between cells. Downregulation of claudin proteins increases the paracellular permeability of nutrients and growth stimuli to malignant cells, which aids the epithelial transition. Claudin 18.2 (CLDN18.2) was identified as a promising target for the treatment of advanced gastroesophageal adenocarcinoma (GEAC), with high levels found in almost 30% of metastatic cases. CLDN18.2 aberrations, enriched in the genomically stable subgroup of GEAC and the diffuse histological subtype, are ideal candidates for monoclonal antibodies and CAR-T cells. Zolbetuximab, a highly specific anti-CLDN18.2 monoclonal antibody, demonstrated efficacy in phase II studies and, more recently, in the phase III SPOTLIGHT trial, with improvements in both PFS and OS with respect to standard chemotherapy. Anti-CLDN18.2 chimeric antigen receptor (CAR)-T cells showed a safety profile with a prevalence of hematologic toxicity in early phase clinical trials. The aim of this review is to present new findings in the treatment of CLDN18.2-positive GEAC, with a particular focus on the monoclonal antibody zolbetuximab and on the use of engineered anti-CLDN18.2 CAR-T cells.

The role and mechanism of claudins in cancer.

Claudins are a tetraspan membrane protein multigene family that plays a structural and functional role in constructing tight junctions. Claudins perform crucial roles in maintaining cell polarity in epithelial and endothelial cell sheets and controlling paracellular permeability. In the last two decades, increasing evidence indicates that claudin proteins play a major role in controlling paracellular permeability and signaling inside cells. Several types of claudins are dysregulated in various cancers. Depending on where the tumor originated, claudin overexpression or underexpression has been shown to regulate cell proliferation, cell growth, metabolism, metastasis and cell stemness. Epithelial-to-mesenchymal transition is one of the most important functions of claudin proteins in disease progression. However, the exact molecular mechanisms and signaling pathways that explain why claudin proteins are so important to tumorigenesis and progression have not been determined. In addition, claudins are currently being investigated as possible diagnostic and treatment targets. Here, we discuss how claudin-related signaling pathways affect tumorigenesis, tumor progression, and treatment sensitivity.

Narrow‐leafed lupin (Lupinus angustifolius L.) β‐conglutin: A multifunctional family of proteins with roles in plant defence, human health benefits, and potential uses as functional food

AbstractLupinus angustifolius or narrow‐leafed lupin (NLL) is an important Pulse world‐wide and an outstanding alternative source of high quality proteins. NLL β‐conglutin (vicilin or 7S acid globulin), a multigene family of proteins, is the main representative protein in NLL seeds exhibiting multifunctional properties and benefits recently discovered. These functions may result from specific structural features of NLL β‐conglutins in comparison with most legume vicilin proteins. From the agricultural side, NLL β‐conglutin proteins (1a) exert antifungal properties promoting enhanced plant resistance to necrotrophic oomycete pathogens and (1b) displaying functional interplay between storage protein mobilization and seed oxidative metabolism as a functional regulatory and signalling crossroad for the control of physiological underlying processes of the seed dormancy breakage and release, during germination, and seedling growth. NLL β‐conglutins benefits go beyond nutritional properties because displayed nutraceutical functions make them an outstanding source of innovative ingredients for functional food. They have antioxidant activity and anti‐inflammatory properties, which are able to improve inflammatory‐related diseases such as type 2 diabetes through (a) regulation of insulin signalling pathway, (b) improving insulin sensitivity, (c) facilitating glucose uptake by cells, (d) together with their capacity for balancing the oxidative homeostasis, metabolic, and signalling pathways (e) while reducing reactive oxygen specie production and increase cellular oxidative defence capacity. Interestingly, NLL β‐conglutins also display anti‐nutritional properties as proteins capable to elicit allergic responses in sensitized individuals. This review outlines newly discovered knowledge of the narrow‐leafed lupin β‐conglutin proteins drawing on information gained from structure‐functional properties, agriculture benefits, as well as nutraceutics and molecular allergy point of views.

Transcriptomic Response of Saccharomyces cerevisiae during Fermentation under Oleic Acid and Ergosterol Depletion

Under anaerobic/hypoxic conditions, Saccharomyces cerevisiae relies on external lipid supplements to modulate membrane lipid fraction in response to different stresses. Here, transcriptomic responses of two S. cerevisiae wine strains were evaluated during hypoxic fermentation of a synthetic must with/without ergosterol and oleic acid supplementation. In the absence of lipids, the two strains, namely EC1118 and M25, showed different behaviour, with M25 significantly decreasing its fermentation rate from the 72 h after inoculum. At this time point, the whole genome transcriptomic analysis revealed common and strain-specific responses to the lack of lipid supplementation. Common responses included the upregulation of the genes involved in ergosterol biosynthesis, as well as the seripauperin and the heat shock protein multigene families. In addition, the upregulation of the aerobic isoforms of genes involved in mitochondrial electron transport is compatible with the previously observed accumulation of reactive oxygen species in the two strains during growth in absence of lipids. Considering the strain-specific responses, M25 downregulated the transcription of genes involved in glucose transport, methionine biosynthesis and of those encoding mannoproteins required for adaptation to low temperatures and hypoxia. The identification of these pathways, which are presumably involved in yeast resistance to stresses, will assist industrial strain selection.

Compression of Large Sets of Sequence Data Reveals Fine Diversification of Functional Profiles in Multigene Families of Proteins: A Study for Peptidyl-Prolyl cis/trans Isomerases (PPIase).

In this technical note, we describe analyses of more than 15,000 sequences of FK506-binding proteins (FKBP) and cyclophilins, also known as peptidyl-prolyl cis/trans isomerases (PPIases). We have developed a novel way of displaying relative changes of amino acid (AA)-residues at a given sequence position by using heat-maps. This type of representation allows simultaneous estimation of conservation level in a given sequence position in the entire group of functionally-related paralogues (multigene family of proteins). We have also proposed that at least two FKBPs, namely FKBP36, encoded by the Fkbp6 gene and FKBP51, encoded by the Fkbp5 gene, can form dimers bound via a disulfide bridge in the nucleus. This type of dimer may have some crucial function in the regulation of some nuclear complexes at different stages of the cell cycle.

Molecular dissection of the membrane aggregation mechanisms induced by monomeric annexin A2

Annexins are a multigene family of proteins involved in aggregation and fusion processes of biological membranes. One of its best-known members is annexin A2 (or p36), capable of binding to acidic phospholipids in a calcium-dependent manner, as occurs with other members of the same family. In its heterotetrameric form, especially with protein S100A10 (p11), annexin A2 has been involved as a determinant factor in innumerable biological processes like tumor development or anticoagulation. However, the subcellular coexistence of different pools of the protein, in which the monomeric form of annexin A2 is growing in functional relevance, is to date poorly described. In this work we present an exhaustive structural and functional characterization of monomeric human annexin A2 by using different recombinant mutants. The important role of the amphipathic N-terminal α-helix in membrane binding and aggregation has been analyzed. We have also studied the potential implication of lateral “antiparallel” protein dimers in membrane aggregation. In contrast to what was previously suggested, formation of these dimers negatively regulate aggregation. We have also confirmed the essential role of three lysine residues located in the convex surface of the molecule in calcium-free and calcium-dependent membrane binding and aggregation. Finally, we propose models for annexin A2-mediated vesicle aggregation mechanisms.

A wheat gene TaSAP17-D encoding an AN1/AN1 zinc finger protein improves salt stress tolerance in transgenic Arabidopsis

The stress-associated protein (SAP) multigene family is conserved in both animals and plants. Its function in some animals and plants are known, but it is yet to be deciphered in wheat (Triticum aestivum L.). We identified the wheat gene TaSAP17-D, a member of the SAP gene family with an AN1/AN1 conserved domain. Subcellular localization indicated that TaSAP17-D localized to the nucleus, cytoplasm, and cell membrane. Expression pattern analyses revealed that TaSAP17-D was highly expressed in seedlings and was involved in NaCl response, polyethylene glycol (PEG), cold, and exogenous abscisic acid (ABA). Constitutive expression of TaSAP17-D in transgenic Arabidopsis resulted in enhanced tolerance to salt stress, confirmed by improved multiple physiological indices and significantly upregulated marker genes related to salt stress response. Our results suggest that TaSAP17-D is a candidate gene that can be used to protect crop plants from salt stress.

Constitutive expression of Brassica juncea annexin, AnnBj2 confers salt tolerance and glucose and ABA insensitivity in mustard transgenic plants

Annexins belong to a plasma membrane binding (in a calcium dependent manner), multi-gene family of proteins, which play ameliorating roles in biotic and abiotic stresses. The expression of annexin AnnBj2 of Indian mustard is tissue specific with higher expression in roots and under treatments with sodium chloride and abscisic acid (ABA) at seedling stage. The effect of constitutive expression of AnnBj2 in mustard was analyzed in detail. AnnBj2 OE (over expression) plants exhibited insensitivity to ABA, glucose and sodium chloride. The insensitivity/tolerance of the transgenic plants was associated with enhanced total chlorophylls, relative water content, proline, calcium and potassium with reduced thiobarbituric acid reactive substances and sodium ion accumulation. The altered ABA insensitivity of AnnBj2 OE lines is linked to downregulation of ABI4 and ABI5 transcription factors and upregulation of ABA catabolic gene CYP707A2. Furthermore, we found that overexpression of AnnBj2 upregulated the expression of ABA-dependent RAB18 and ABA-independent DREB2B stress marker genes suggesting that the tolerance phenotype exhibited by AnnBj2 OE lines is probably controlled by both ABA-dependent and −independent mechanisms.

Unravelling the Role of Metallothionein on Development, Reproduction and Detoxification in the Wall Lizard Podarcis sicula.

Metallothioneins (MTs) are an evolutionary conserved multigene family of proteins whose role was initially identified in binding essential metals. The physiological role of MT, however, has been revealed to be more complex than expected, since not only are MTs able to bind to toxic heavy metals, but many isoforms have shown specialized and alternative functions. Within this uncertainty, the information available on MTs in non-mammalian vertebrates, particularly in neglected tetrapods such as the reptiles, is even more scant. In this review, we provide a summary of the current understanding on metallothionein presence and function in the oviparous lizard Podarcis sicula, highlighting the results obtained by studying MT gene expression in most representative adult and embryonic tissues. The results demonstrate that in adults, cadmium induces MT transcription in a dose- and tissue-specific manner. Thus, the MT mRNAs appear, at least in some cases, to be an unsuitable tool for detecting environmental ion contamination. In early embryos, maternal RNAs sustain developmental needs for MT protein until organogenesis is well on its way. At this time, transcription starts, but again in a tissue- and organ-specific manner, suggesting an involvement in alternative roles. In conclusion, the spatiotemporal distribution of transcripts in adults and embryos definitively confirms that MT has deserved the title of elusive protein.

Identification and expression profiling of novel plant cell wall degrading enzymes from a destructive pest of palm trees, Rhynchophorus ferrugineus.

Plant cell wall degrading enzymes (PCWDEs) from insects were recently identified as a multigene family of proteins that consist primarily of glycoside hydrolases (GHs) and carbohydrate esterases (CEs) and play essential roles in the degradation of the cellulose/hemicellulose/pectin network in the invaded host plant. Here we applied transcriptomic and degenerate PCR approaches to identify the PCWDEs from a destructive pest of palm trees, Rhynchophorus ferrugineus, followed by a gut-specific and stage-specific differential expression analysis. We identified a total of 27 transcripts encoding GH family members and three transcripts of the CE family with cellulase, hemicellulase and pectinase activities. We also identified two GH9 candidates, which have not previously been reported from Curculionidae. The gut-specific quantitative expression analysis identified key cellulases, hemicellulases and pectinases from R.ferrugineus. The expression analysis revealed a pectin methylesterase, RferCE8u02, and a cellulase, GH45c34485, which showed the highest gut enriched expression. Comparison of PCWDE expression patterns revealed that cellulases and pectinases are significantly upregulated in the adult stages, and we observed specific high expression of the hemicellulase RferGH16c4170. Overall, our study revealed the potential of PCWDEs from R.ferrugineus, which may be useful in biotechnological applications and may represent new tools in R.ferrugineus pest management strategies.

Genetic clustering and polymorphism of the merozoite surface protein-3 of Plasmodium knowlesi clinical isolates from Peninsular Malaysia

BackgroundThe simian malaria parasite Plasmodium knowlesi has been reported to cause significant numbers of human infection in South East Asia. Its merozoite surface protein-3 (MSP3) is a protein that belongs to a multi-gene family of proteins first found in Plasmodium falciparum. Several studies have evaluated the potential of P. falciparum MSP3 as a potential vaccine candidate. However, to date no detailed studies have been carried out on P. knowlesi MSP3 gene (pkmsp3). The present study investigates the genetic diversity, and haplotypes groups of pkmsp3 in P. knowlesi clinical samples from Peninsular Malaysia.MethodsBlood samples were collected from P. knowlesi malaria patients within a period of 4 years (2008–2012). The pkmsp3 gene of the isolates was amplified via PCR, and subsequently cloned and sequenced. The full length pkmsp3 sequence was divided into Domain A and Domain B. Natural selection, genetic diversity, and haplotypes of pkmsp3 were analysed using MEGA6 and DnaSP ver. 5.10.00 programmes.ResultsFrom 23 samples, 48 pkmsp3 sequences were successfully obtained. At the nucleotide level, 101 synonymous and 238 non-synonymous mutations were observed. Tests of neutrality were not significant for the full length, Domain A or Domain B sequences. However, the dN/dS ratio of Domain B indicates purifying selection for this domain. Analysis of the deduced amino acid sequences revealed 42 different haplotypes. Neighbour Joining phylogenetic tree and haplotype network analyses revealed that the haplotypes clustered into two distinct groups.ConclusionsA moderate level of genetic diversity was observed in the pkmsp3 and only the C-terminal region (Domain B) appeared to be under purifying selection. The separation of the pkmsp3 into two haplotype groups provides further evidence of the existence of two distinct P. knowlesi types or lineages. Future studies should investigate the diversity of pkmsp3 among P. knowlesi isolates in North Borneo, where large numbers of human knowlesi malaria infection still occur.

Transcriptional regulation by VirR and VirS of members of the Rhodococcus equi virulence-associated protein multigene family.

A virulence plasmid of Rhodococcus equi harbors the vap mutigene family. Here it is shown that transcription of vap gene family members other than vapA (vapD, vapE and vapG) is regulated by temperature and pH and abolished when either virS or virR is deleted. Expression of VirS in the absence of functional VirR was found to increase the transcription of vap genes to the amount expressed in the presence of VirR. These findings suggest that transcription of vap genes is regulated by VirS and that VirR is involved in the mechanism of transcriptional responses to temperature and pH.

Overexpression of a cotton annexin gene, GhAnn1, enhances drought and salt stress tolerance in transgenic cotton.

Plant annexins are members of a diverse, multigene protein family that has been associated with a variety of cellular processes and responses to abiotic stresses. GhAnn1, which encodes a putative annexin protein, was isolated from a cotton (Gossypium hirsutum L. acc 7235) cDNA library. Tissue-specific expression showed that GhAnn1 is expressed at differential levels in all tissues examined and strongly induced by various phytohormones and abiotic stress. In vivo and in vitro subcellular localization suggested that GhAnn1 is located in the plasma membrane. In response to drought and salt stress, transgenic cotton plants overexpressing GhAnn1 showed significantly higher germination rates, longer roots, and more vigorous growth than wild-type plants. In addition, plants overexpressing GhAnn1 had higher total chlorophyll content, lower lipid peroxidation levels, increased peroxidase activities, and higher levels of proline and soluble sugars, all of which contributed to increased salt and drought stress tolerance. However, transgenic cotton plants in which the expression of GhAnn1 was suppressed showed the opposite results compared to the overexpressing plants. These findings demonstrated that GhAnn1 plays an important role in the abiotic stress response, and that overexpression of GhAnn1 in transgenic cotton improves salt and drought tolerance.

Exogenous fatty acid binding protein 4 promotes human prostate cancer cell progression.

Epidemiologic studies have found that obesity is associated with malignant grade and mortality in prostate cancer. Several adipokines have been implicated as putative mediating factors between obesity and prostate cancer. Fatty acid binding protein 4 (FABP4), a member of the cytoplasmic fatty acid binding protein multigene family, was recently identified as a novel adipokine. Although FABP4 is released from adipocytes and mean circulating concentrations of FABP4 are linked with obesity, effects of exogenous FABP4 on prostate cancer progression are unclear. In this study, we examined the effects of exogenous FABP4 on human prostate cancer cell progression. FABP4 treatment promoted serum-induced prostate cancer cell invasion in vitro. Furthermore, oleic acid promoted prostate cancer cell invasion only if FABP4 was present in the medium. These promoting effects were reduced by FABP4 inhibitor, which inhibits FABP4 binding to fatty acids. Immunostaining for FABP4 showed that exogenous FABP4 was taken up into DU145 cells in three-dimensional culture. In mice, treatment with FABP4 inhibitor reduced the subcutaneous growth and lung metastasis of prostate cancer cells. Immunohistochemical analysis showed that the number of apoptotic cells, positive for cleaved caspase-3 and cleaved PARP, was increased in subcutaneous tumors of FABP4 inhibitor-treated mice, as compared with control mice. These results suggest that exogenous FABP4 might promote human prostate cancer cell progression by binding with fatty acids. Additionally, exogenous FABP4 activated the PI3K/Akt pathway, independently of binding to fatty acids. Thus, FABP4 might be a key molecule to understand the mechanisms underlying the obesity-prostate cancer progression link.

N-Acetylglucosaminylation of Serine-Aspartate Repeat Proteins Promotes Staphylococcus aureus Bloodstream Infection

Staphylococcus aureus secretes products that convert host fibrinogen to fibrin and promote its agglutination with fibrin fibrils, thereby shielding bacteria from immune defenses. The agglutination reaction involves ClfA (clumping factor A), a surface protein with serine-aspartate (SD) repeats that captures fibrin fibrils and fibrinogen. Pathogenic staphylococci express several different SD proteins that are modified by two glycosyltransferases, SdgA and SdgB. Here, we characterized three genes of S. aureus, aggA, aggB (sdgA), and aggC (sdgB), and show that aggA and aggC contribute to staphylococcal agglutination with fibrin fibrils in human plasma. We demonstrate that aggB (sdgA) and aggC (sdgB) are involved in GlcNAc modification of the ClfA SD repeats. However, only sdgB is essential for GlcNAc modification, and an sdgB mutant is defective in the pathogenesis of sepsis in mice. Thus, GlcNAc modification of proteins promotes S. aureus replication in the bloodstream of mammalian hosts.

Calcium-Dependent Protein Kinases in Plants: Evolution, Expression and Function

Calcium-dependent protein kinases (CPKs) are plant proteins that directly bind calcium ions before phosphorylating substrates involved in metabolism, osmosis, hormone response and stress signaling pathways. CPKs are a large multigene family of proteins that are present in all plants studied to date, as well as in protists, oomycetes and green algae, but are not found in animals and fungi. Despite the increasing evidence of the importance of CPKs in developmental and stress responses from various plants, a comprehensive genome-wide analysis of CPKs from algae to higher plants has not been undertaken. This paper describes the evolution of CPKs from green algae to plants using a broadly sampled phylogenetic analysis and demonstrates the functional diversification of CPKs based on expression and functional studies in different plant species. Our findings reveal that CPK sequence diversification into four major groups occurred in parallel with the terrestrial transition of plants. Despite significant expansion of the CPK gene family during evolution from green algae to higher plants, there is a high level of sequence conservation among CPKs in all plant species. This sequence conservation results in very little correlation between CPK evolutionary groupings and functional diversity, making the search for CPK functional orthologs a challenge.

In silicoanalysis of the germinlike protein multigene family members of tomato with predicted oxalate oxidase activity

Germins and germin like proteins (GLPs) have been reported as plant glycoproteins belonging to the ‘cupin’ superfamily. They have been documented to possess enzymatic activities leading to the generation of H2O2, a reactive oxygen species (ROS). Hence, members of the GLP family have been proposed to play major role in plant disease resistance through ROS-mediated signaling. Interestingly, the functional characterization of GLP(s) in terms of their suitability as a key player in plant disease resistance has remained under-explored in case of tomato (Solanumlycopersicum L.). In the present study, 15 tomato GLPs, predicted to have oxalate oxidase activity, have been investigated in silico. Deduced multiple amino acid sequence alignment-based clustering of these proteins was carried out to classify them into 3 sub-families. All the proteins were found to contain the conserved amino acid stretches, representing the BoxA, B and C, and an inter-motif region of variable length. It was observed through homology modeling and structural alignment that the active sites of all except 3 of these proteins have Mn2+ bound at the active site involving the three conserved histidine and one conserved glutamate residue(s). The active site architecture was analyzed with a comparative view in order to examine the metal binding capacity of tomato GLPs. Thus the present work makes a platform for further genetic, molecular biological and functional genomics studies in the field of tomato GLPs, the possible key players for conferring biotic and/or abiotic stress tolerance, in future.

Light-inducible stress plastid proteins of phototrophs

The review summarizes the current understanding of light-inducible proteins of plants, wide-spread among prokaryotic and eukaryotic photosynthetic organisms. The greatest attention is paid to the Early light-inducible proteins of plastids (Elip) and their photoprotective role under light stress. Data are presented on structure and functions of Elip-related proteins such as Ohp/Hlip, Sep, and on the family of Cab proteins, chlorophyll a/b-binding proteins of photosystems I and II, which are in many properties similar to Elip proteins. The multigene family of proteins of light-harvesting complexes (LHC) are discussed together with the possible ways of their evolution.

The Mycobacterium tuberculosis PE Proteins Rv0285 and Rv1386 Modulate Innate Immunity and Mediate Bacillary Survival in Macrophages

The unique PE/PPE multigene family of proteins occupies almost 10% of the coding sequence of Mycobacterium tuberculosis (M.tb), the causative agent of human tuberculosis. Although some members of this family have been shown to be involved in pathways essential to M.tb pathogenesis, their precise physiological functions remain largely undefined. Here, we investigate the roles of the conserved members of the ‘PE only’ subfamily Rv0285 (PE5) and Rv1386 (PE15) in mediating host-pathogen interactions. Recombinant Mycobacterium smegmatis strains expressing PE5 and PE15 showed enhanced survival vs controls in J774.1 and THP-1 macrophages - this increase in viable counts was correlated with a reduction in transcript levels of inducible nitric oxide synthase. An up-regulation of anti- and down-regulation of pro-inflammatory cytokine levels was also observed in infected macrophages implying an immuno-modulatory function for these proteins. Induction of IL-10 production upon infection of THP-1 macrophages was associated with increased phosphorylation of the MAP Kinases p38 and ERK1/2, which was abolished in the presence of the pharmacological inhibitors SB203580 and PD98059. The PE5-PPE4 and PE15-PPE20 gene pairs were observed to be co-operonic in M.tb, hinting at an additional level of complexity in the functioning of these proteins. We conclude that M.tb exploits the PE proteins to evade the host immune response by altering the Th1 and Th2 type balance thereby favouring in vivo bacillary survival.

The plaque protein myozap identified as a novel major component of adhering junctions in endothelia of the blood and the lymph vascular systems.

Recently the protein myozap, a 54-kD polypeptide which is not a member of any of the known cytoskeletal and junctional protein multigene families, has been identified as a constituent of the plaques of the composite junctions in the intercalated disks connecting the cardiomyocytes of mammalian hearts. Using a set of novel, highly sensitive and specific antibodies we now report that myozap is also a major constituent of the cytoplasmic plaques of the adherens junctions (AJs) connecting the endothelial cells of the mammalian blood and lymph vascular systems, including the desmoplakin-containing complexus adhaerentes of the virgultar cells of lymph node sinus. In light and electron microscopic immunolocalization experiments we show that myozap colocalizes with several proteins of desmosomal plaques as well as with AJ-specific transmembrane molecules, including VE-cadherin. In biochemical analyses, rigorous immunoprecipitation experiments have revealed N-cadherin, desmoplakin, desmoglein-2, plakophilin-2, plakoglobin and plectin as very stably bound complex partners. We conclude that myozap is a general component of cell–cell junctions not only in the myocardium but also in diverse endothelia of the blood and lymph vascular systems of adult mammals, suggesting that this protein not only serves a specific role in the heart but also a broader set of functions in the vessel systems. We also propose to use myozap as an endothelial cell type marker in diagnoses.