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Cell adhesion molecules act as tumor suppressors primarily by cell attachment activity, but additional mechanisms modifying signal transduction are suggested in some cases. Cell adhesion molecule 1 (CADM1), a membrane-spanning immunoglobulin superfamily, mediates intercellular adhesion by trans-homophilic interaction and acts as a tumor suppressor. Here, we investigated CADM1-associated proteins comprehensively using proteomic analysis of immune-precipitates of CADM1 by mass spectrometry and identified a transmembrane adaptor protein, Csk-binding protein (Cbp), known to suppress Src-mediated transformation, as a binding partner of CADM1. CADM1 localizes to detergent-resistant membrane fractions and co-immunoprecipitated with Cbp and c-Src. Suppression of CADM1 expression using siRNA reduces the amount of co-immunoprecipitated c-Src with Cbp and activates c-Src in colon cancer cells expressing both CADM1 and Cbp. On the other hand, co-replacement of CADM1 and Cbp in colon cancer cells lacking CADM1 and Cbp expression suppresses c-Src activation, wound healing and tumorigenicity in nude mice. Furthermore, expression of Cbp and CADM1 was lost in 55% and 83% of human colon cancer, respectively, preferentially in tumors with larger size and/or lymph node metastasis. CADM1 would act as a colon tumor suppressor by intervening oncogenic c-Src signaling through binding with Cbp besides its authentic cell adhesion activity., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

We investigated differences in the feeding habits of the starspotted smooth-hound, Mustelus manazo, in Tokyo Bay between the mid-1990s (low stock size) and the late 2000s (high stock size). The frequency of M. manazo with empty stomachs increased from 5.9% in the mid-1990s to 16.1% in the late 2000s. A decrease in the relative weight of the stomach contents was evident from the mid-1990s to the late 2000s, especially in the small size classes, along with changes in the species composition in the stomach contents. Although crustaceans were the main constituents of the stomach contents, the proportion of crabs increased while those of shrimps and hermit crabs decreased. Changes in the feeding habits of M. manazo may be associated with shifts in the benthic community structure in Tokyo Bay., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Trinucleotide repeat-containing gene 6A protein (TNRC6A) is an essential protein for microRNA-mediated gene silencing. TNRC6A functions in the cytoplasm as a platform protein interacting with Argonaute protein, on which microRNA is loaded for RNA silencing, and decapping enzymes or deadenylation protein complexes to induce mRNA degradation. We previously revealed that TNRC6A shuttles between the cytoplasm and nucleus. However, the function of TNRC6A in the nucleus is unclear. Here, we performed a comprehensive identification of the nuclear and cytoplasmic interacting proteins of TNRC6A protein by mass spectrometry and identified multiple proteins involved in the nuclear and cytoplasmic complexes. We found that many RNA degradation pathway proteins were involved in both nuclear and cytoplasmic TNRC6A complexes, suggesting that RNA silencing may occur via TNRC6A in both nucleus and cytoplasm or that they were involved in other important function in the nucleus. Furthermore, proteins identified in the nuclear TNRC6A complex were categorized into the spliceosomal pathway. This may mean that TNRC6A regulates splicing in the nucleus. In contrast, pathogen infection- and RNA transport-associated proteins were identified in the cytoplasmic TNRC6A complex. Thus, TNRC6A may be also involved in these pathways in the cytoplasm., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

We investigated factors that might have disturbed the stock recovery of marbled flounder in Tokyo Bay by focusing on the early life stages. Field surveys in Tokyo Bay from 2006 to 2011 revealed that mature adult biomass increased from 2006 to 2008 and decreased thereafter. Meanwhile, larval and juvenile densities were high in 2006 and 2008 but low in other years. Discrepancies in the yearly trends of these parameters suggest that mortality during life stages between spawning and early larval phases might have affected the abundance of the subsequent life stages. Monthly mean water temperature between January and February, in which hatching and pelagic larvae occur in the bay, was lower in 2006 (8.6 °C) and 2008 (9.6 °C) than was observed in other years (10.4-11.4 °C). Significant negative correlation between water temperature and larval density implies that mortality during pre- and post-larval stages would be higher in warmer winter years (>10 °C). To test this hypothesis, we examined the effects of water temperature on mortality and development in egg and larval stages under controlled laboratory conditions. Hatching rate was high in a water temperature range of 9.2-12.7 °C (66.6-82.5%), whereas it decreased in cooler (3.7% at 5.9 °C) or warmer (33.9% at 14.8 °C) conditions. Meanwhile, days from fertilization to hatching, size of larvae at hatching and survival rate of larvae after 18 d from hatching were monotonically and significantly decreased as water temperature was elevated. Combined evidence of the field and laboratory studies suggests that a warmer reproductive season (>10 °C) might induce mortalities of marbled flounder larvae in Tokyo Bay., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

To develop oral antibody therapy against rotavirus infection, we previously produced a recombinant fragment of llama heavy-chain antibody to rotavirus (ARP1) in rice seeds (MucoRice-ARP1). We intend to use a purification-free rice powder for clinical application but needed to check whether MucoRice-ARP1 had increased levels of known allergen proteins. For this purpose, we used two-dimensional fluorescence difference gel electrophoresis to compare the allergen protein levels in MucoRice-ARP1 and wild-type rice. We detected no notable differences, except in the levels of α-amylase/trypsin inhibitor-like family proteins. Because by this approach we could not completely separate ARP1 from the proteins of this family, we confirmed the absence of changes in the levels of these allergens by using shotgun mass spectrometry as well as immunoblot. By using immunoelectron microscopy, we also showed that RAG2, a member of the α-amylase/trypsin inhibitor-like protein family, was relocated from protein bodies II to the plasma membrane or cell wall in MucoRice-ARP1 seed. The relocation did not affect the level of RAG2. We demonstrated that most of the known rice allergens were not considerably upregulated by the genetic modification in MucoRice-ARP1. Our data suggest that MucoRice-ARP1 is a potentially safe oral antibody for clinical application., (Copyright © 2016 Elsevier Inc. All rights reserved.)

This study demonstrated the spatiotemporal patterns of the environmental conditions and benthic macrofauna in Tokyo Bay, Japan, and investigated the factors causing disturbances in the assemblage structure. In the north-central areas, the density and species diversity of the macrobenthos was low. Although hypoxia appeared in July, defaunation occurred in August. The delayed defaunation and recolonization soon after the abatement of hypoxia were attributed to several polychaete and bivalve species that were tolerant to the hypoxic environment. In the southeastern areas, however, the density and species diversity of the macrobenthos was high throughout the year, and no defaunation was recorded. Multivariate analyses showed that the disturbance in the macrofauna correlated with organic enrichment in the sediment and bottom-water hypoxia. There is a concern about further impairment of the macrofauna in the bay due to the expansion of sediment with high levels of organic matter towards the southern regions that could cause hypoxia and subsequent defaunation., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Tob belongs to the anti-proliferative Tob/BTG protein family. The expression level of Tob family proteins is strictly regulated both transcriptionally and through post-translational modification. Ubiquitin (Ub)/proteosome-dependent degradation of Tob family proteins is critical in controlling cell cycle progression and DNA damage responses. Various Ub ligases (E3s) are responsible for degradation of Tob protein. Here, we show that Tob family proteins undergo monoubiquitination even in the absence of E3s in vitro. Determination of the ubiquitination site(s) in Tob by mass spectrometric analysis revealed that two lysine residues (Lys48 and Lys63) located in Tob/BTG homology domain are ubiquitinated. A mutant Tob, in which both Lys48 and Lys63 are substituted with alanine, is more strongly polyubiquitinated than wild-type Tob in vivo. These data suggest that monoubiquitination of Tob family proteins confers resistance against polyubiquitination, which targets proteins for degradation. The strategy for regulating the stability of Tob family proteins suggests a novel role for monoubiquitination., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Cell signaling pathways are essentially organized through the distribution of various types of binding domains in signaling proteins, with each domain binding to specific target molecules. Although identification of these targets is crucial for mapping the pathways, affinity-based or copurification methods are insufficient to distinguish between direct and indirect interactions in a cellular context. In the present study, we developed another approach involving the genetic encoding of a photo-crosslinkable amino acid. p-Trifluoromethyl-diazirinyl-l-phenylalanine was thus incorporated at a defined site in the Src homology 2 (SH2) domain of the adaptor protein GRB2 in human embryonic kidney cells. These cells were exposed to 365-nm light after an epidermal growth factor stimulus, and the crosslinkable GRB2-SH2 domain exclusively formed covalent bonds with directly interacting proteins. Proteomic mass spectrometry analysis identified these direct binders of GRB2-SH2 separately from the proteins noncovalently bound to the Src homology 3 domains of GRB2. In addition to two signaling-associated proteins (GIT1 and AF6), the heterogeneous nuclear ribonucleoproteins F, H1, and H2 were thus identified as novel direct binders. The results revealed a connection between the cell signaling protein and the nuclear machinery involved in mRNA processing, and demonstrated the usefulness of genetically encoded photo-crosslinkers for mapping protein-protein interactions in cells., (Copyright © 2010 Elsevier Ltd. All rights reserved.)

Toll-like receptor (TLR) signaling in macrophages is essential for anti-pathogen responses such as cytokine production and antigen presentation. Although numerous reports suggest that protein tyrosine kinases (PTKs) are involved in cytokine induction in response to lipopolysaccharides (LPS; TLR4 ligand) in macrophages, the PTK-mediated signal transduction pathway has yet to be analyzed in detail. Here, we carried out a comprehensive and quantitative dynamic tyrosine phosphoproteomic analysis on the TLR4-mediated host defense system in RAW264.7 macrophages using stable isotope labeling by amino acids in cell culture (SILAC). We determined the temporal profiles of 25 proteins based on SILAC-encoded peptide(s). Of these, we focused on the tyrosine phosphorylation of B-cell adaptor for phosphatidylinositol 3-kinase (BCAP) because the function of BCAP remains unknown in TLR signaling in macrophages. Furthermore, Bcap has two distinct transcripts, a full-length (Bcap-(L)) and an alternatively initiated or spliced (Bcap-(S)) mRNA, and little is known about the differential functions of the BCAP-(L) and BCAP-(S) proteins. Our study showed, for the first time, that RNAi-mediated selective depletion of BCAP-(L) enhanced IL-6 and IL-10 production but not TNF-α production in TLR ligand-stimulated macrophages. We propose that BCAP-(L) (but not BCAP-(S)) is a negative regulator of the TLR-mediated host defense system in macrophages., (Copyright © 2010 Elsevier Inc. All rights reserved.)

In insects, specific proteins and physiologically active molecules whose functions are related to their lifestyles are secreted from the salivary system. To investigate proteins/molecules related to the sociality of the European honeybee (Apis mellifera L.), we performed a proteomic analysis of the honeybee salivary system. The honeybee salivary system comprises two secretory glands: the postcerebral gland (PcG) and the thoracic gland (TG), both of which are connected to a common duct that opens in the mouthpart. Although most (31 out of 35) of the major proteins identified from the PcG and TG were housekeeping proteins, the spot intensities for aldolase and acetyl-CoA acyltransferase 2 were stronger in the PcG than in the TG in the 2-dimensional gel electrophoresis. Immunoblotting confirmed that the expression of these proteins was stronger in the PcG than in the TG, whereas expression was almost not detectable in the hypopharyngeal gland (HpG), suggesting that carbohydrate metabolism is enhanced in the honeybee PcG. In addition, imaginal disc growth factor 4 (IDGF4) was synthesized in the honeybee salivary system. Immunoblotting indicated IDGF4 expression was very strong in the PcG, moderate in the TG, and very weak in the HpG. A considerable amount of IDGF4 was detected in the royal jelly, while less was detected in honey, strongly suggesting that the honeybee salivary system secretes IDGF4 into the royal jelly and honey. The secreted IDGF4 might therefore affect growth and physiology of the other colony members., (Copyright 2010 Elsevier Inc. All rights reserved.)