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Most prokaryotic proteins consist of a single structural domain (SD) with little intrinsically disordered regions (IDRs) that by themselves do not adopt stable structures, whereas the typical eukaryotic protein comprises multiple SDs and IDRs. How eukaryotic proteins evolved to differ from prokaryotic proteins has not been fully elucidated. Here, we found that the longer the internal exons are, the more frequently they encode IDRs in eight eukaryotes including vertebrates, invertebrates, a fungus, and plants. Based on this observation, we propose the "small bang" model from the proteomic viewpoint: the protoeukaryotic genes had no introns and mostly encoded one SD each, but a majority of them were subsequently divided into multiple exons (step 1). Many exons unconstrained by SDs elongated to encode IDRs (step 2). The elongated exons encoding IDRs frequently facilitated the acquisition of multiple SDs to make the last common ancestor of eukaryotes (step 3). One prediction of the model is that long internal exons are mostly unconstrained exons. Analytical results of the eight eukaryotes are consistent with this prediction. In support of the model, we identified cases of internal exons that elongated after the rat–mouse divergence and discovered that the expanded sections are mostly in unconstrained exons and preferentially encode IDRs. The model also predicts that SDs followed by long internal exons tend to have other SDs downstream. This prediction was also verified in all the eukaryotic species analyzed. Our model accounts for the dichotomy between prokaryotic and eukaryotic proteins and proposes a selective advantage conferred by IDRs. [ABSTRACT FROM AUTHOR]

Schwann cell-specific knockdown of PTP4A1 in mice increases signals related to cytohesin-2 and myelin marker expression.(A) The transgene units composed of the Schwann cell-specific MSE, shPTP4A1mir, and polyA sequences were injected into fertilized C57BL/6J oocytes and Tg mice were generated. Phosphorylated cytohesin-2 was detected in control mouse Schwann cells but not in knockin mouse Schwann cells or neuronal cells (Fig. Further studies will promote our understanding of not only the detailed mechanism by which SH2B1 and PTP4A1, centering on cytohesin-2, regulate Schwann cell myelination in mice but also how they contribute to coupling yet unidentified upstream signals from receptors and their adaptor proteins to downstream signals leading to myelination. Cytohesin-2 Y381F knockin mice show decreased signals related to cytohesin-2 and myelin marker expression.(A) Amino acid sequences corresponding to Tyr 381 of human and mouse cytohesin-2 and Tyr 380 of rat cytohesin-2 molecules were compared to those of human cytohesins-1, -3, and -4. [Extracted from the article]

Epithelial cell polarity regulator Crumbs3 (Crb3), a mammalian homolog within the Drosophila Crb gene family, was initially identified as an essential embryonic development factor. It is recently implicated in tumor suppression, though its specific functions are controversial. We here demonstrate that Crb3 strongly promotes tumor invasion and metastasis of human colon adenocarcinoma cells. Crb3 centrality to tumor migration was supported by strong expression at invasive front and metastatic foci of colonic adenocarcinoma of the patient tissues. Accordingly, two different Crb3‐knockout (KO) lines, Crb3‐KO (Crb3 −/−) DLD‐1 and Crb3‐KO WiDr from human colonic adenocarcinomas, were generated by the CRISPR‐Cas9 system. Crb3‐KO DLD‐1 cells exhibited loss of cellular mobility in vitro and dramatic suppression of liver metastases in vivo in contrast to the wild type of DLD‐1. Unlike DLD‐1, Crb3‐KO WiDr mobility and metastasis were unaffected, which were similar to wild‐type WiDr. Proteome analysis of Crb3‐coimmunopreciptated proteins identified different respective fibroblast growth factor receptor (FGFR) isotypes specifically bound to Crb3 isoform a through their intracellular domain. In DLD‐1, Crb3 showed membranous localization of FGFR1 leading to its functional activation, whereas Crb3 bound to cytoplasmic FGFR4 in WiDr without FGFR1 expression, leading to cellular growth. Correlative expression between Crb3 and FGFR1 was consistently detected in primary and metastatic colorectal cancer patient tissues. Taking these together, Crb3 critically accelerates cell migration, namely invasion and metastasis of human colon cancers, through specific interaction to FGFR1 on colon cancer cells. What's new? Epithelial cell polarity regulator Crumbs3 (Crb3) was initially identified as an essential embryonic development factor. More recently, it has been implicated in tumor suppression, though its specific functions remain controversial. Here, the authors demonstrate that Crb3 strongly promotes tumor invasion and metastasis of human colon adenocarcinoma cells. They identify among the binding partners of Crb3 the FGF receptors family, which is pivotal to tumor cell dynamics including proliferation, migration, and differentiation. Crb3 colocalizes with FGFR1 to activate downstream signaling and critically accelerate tumor migration and metastasis of human colon cancers. [ABSTRACT FROM AUTHOR]

The article focuses on the BRCA1/2 genetic testing in patients with gastric cancer (GC). Topics discussed include an overview of the BRCA1/2 mutations, the determination of pathogenic germline BRCA1/2 mutations with familial GC component, and the association of BRCA1/2 mutations with GC familial predisposition.

Protein-protein interactions (PPI) play key roles in various biological processes. The bimolecular fluorescence complementation (BiFC) assay is an excellent tool for routine PPI analyses in living cells. We developed new Gateway vectors for a high-throughput BiFC analysis of plants, adopting a monomeric Venus split just after the tenth β-strand, and analyzed the interaction between Arabidopsis thaliana coated vesicle coatmers, the clathrin heavy chain (CHC), and the clathrin light chain (CLC). In competitive BiFC tests, CLC interacted with CHC through a coiled-coil motif in the middle section of CLC. R1340, R1448, and K1512 in CHC and W94 in CLC are potentially key amino acids underlying the inter-chain interaction, consistent with analyses based on homology modeling. Our Gateway BiFC system, the V10-BiFC system, provides a useful tool for a PPI analysis in living plant cells. The CLC-CHC interaction identified may facilitate clathrin triskelion assembly needed for cage formation. [ABSTRACT FROM AUTHOR]

The relationship between sequence polymorphisms and human disease has been studied mostly in terms of effects of single nucleotide polymorphisms (SNPs) leading to single amino acid substitutions that change protein structure and function. However, less attention has been paid to more drastic sequence polymorphisms which cause premature termination of a protein's sequence or large changes, insertions, or deletions in the sequence. We have analyzed a large set (n = 512) of insertions and deletions (indels) and single nucleotide polymorphisms causing premature termination of translation in disease-related genes. Prediction of protein-destabilization effects was performed by graphical presentation of the locations of polymorphisms in the protein structure, using the Genomes TO Protein (GTOP) database, and manual annotation with a set of specific criteria. Protein-destabilization was predicted for 44.4% of the nonsense SNPs, 32.4% of the frameshifting indels, and 9.1% of the non-frameshifting indels. A prediction of nonsense-mediated decay allowed to infer which truncated proteins would actually be translated as defective proteins. These cases included the proteins linked to diseases inherited dominantly, suggesting a relation between these diseases and toxic aggregation. Our approach would be useful in identifying potentially aggregation-inducing polymorphisms that may have pathological effects. [ABSTRACT FROM AUTHOR]

O-glycosylation of mammalian proteins is one of the important posttranslational modifications. We applied a support vector machine (SVM) to predict whether Ser or Thr is glycosylated, in order to elucidate the O-glycosylation mechanism. O-glycosylated sites were often found clustered along the sequence, whereas other sites were located sporadically. Therefore, we developed two types of SVMs for predicting clustered and isolated sites separately. We found that the amino acid composition was effective for predicting the clustered type, whereas the site-specific algorithm was effective for the isolated type. The highest prediction accuracy for the clustered type was 74%, while that for the isolated type was 79%. The existence frequency of amino acids around the O-glycosylation sites was different in the two types: namely, Pro, Val and Ala had high existence probabilities at each specific position relative to a glycosylation site, especially for the isolated type. Independent component analyses for the amino acid sequences around O-glycosylation sites showed the position-specific existences of the identified amino acids as independent components. The O-glycosylation sites were preferentially located within intrinsically disordered regions of extracellular proteins: particularly, more than 90% of the clustered O-GalNAc glycosylation sites were observed in intrinsically disordered regions. This feature could be the key for understanding the non-conservation property of O-glycosylation, and its role in functional diversity and structural stability. [ABSTRACT FROM AUTHOR]

Abstract: A systematic survey of intrinsically disordered (ID) regions was carried out in 2109 human plasma membrane proteins with full assignment of the transmembrane topology with respect to the lipid bilayer. ID regions with 30 consecutive residues or more were detected in 41.0% of the human proteins, a much higher percentage than the corresponding figure (4.7%) for inner membrane proteins of Escherichia coli. The domain organization of each of the membrane protein in terms of transmembrane helices, structural domains, ID, and unassigned regions as well as the distinction of inside or outside of the cell was determined. Long ID regions constitute 13.3 and 3.5% of the human plasma membrane proteins on the inside and outside of the cell, respectively, showing that they preferentially occur on the cytoplasmic side. We interpret this phenomenon as a reflection of the general scarcity of ID regions on the extracellular side and their relative abundance on the cytoplasmic side in multicellular eukaryotic organisms. [Copyright &y& Elsevier]

Human transcriptional regulation factors, such as activators, repressors, and enhancer-binding factors are quite different from their prokaryotic counterparts in two respects: the average sequence in human is more than twice as long as that in prokaryotes, while the fraction of sequence aligned to domains of known structure is 31% in human transcription factors (TFs), less than half of that in bacterial TFs (72%). Intrinsically disordered (ID) regions were identified by a disorder-prediction program, and were found to be in good agreement with available experimental data. Analysis of 401 human TFs with experimental evidence from the Swiss-Prot database showed that as high as 49% of the entire sequence of human TFs is occupied by ID regions. More than half of the human TFs consist of a small DNA binding domain (DBD) and long ID regions frequently sandwiching unassigned regions. The remaining TFs have structural domains in addition to DBDs and ID regions. Experimental studies, particularly those with NMR, revealed that the transactivation domains in unbound TFs are usually unstructured, but become structured upon binding to their partners. The sequences of human and mouse TF orthologues are 90.5% identical despite a high incidence of ID regions, probably reflecting important functional roles played by ID regions. In general ID regions occupy a high fraction in TFs of eukaryotes, but not in prokaryotes. Implications of this dichotomy are discussed in connection with their functional roles in transcriptional regulation and evolution. [Copyright &y& Elsevier]

Much attention has been paid recently to proteins with partially or fully disordered structures, which are found to exist mostly in eukaryotes and are involved mainly in pivotal cellular processes such as transcriptional regulation, translation and cellular signal transduction. Long disordered sequences are sometimes inserted within the single structural domains of proteins, forming loops from the molecular surface. Such intrinsically disordered loops (IDLs) either are invisible in X-ray crystallography, or hamper protein crystallization itself due to great flexibility. Perhaps because of this, such long disordered sequences have not been characterized adequately. Here, we propose an informational method that stringently identifies IDLs in the structural domains of proteins using the amino acid sequence alone. A genome-wide survey of human proteins conducted with the method identified 50 IDL-containing proteins, several of which have experimentally determined 3D structures. Similar searches in other entirely sequenced organisms revealed that IDLs are prevalent in eukaryotes, while they are much less so in prokaryotes. As there is a statistically significant coincidence between the boundaries of IDLs and those of exons, we suggest that IDLs were produced mainly by exon addition in eukaryotes. IDLs are almost always located at the surface of proteins and are enriched with hydrophilic residues, and IDL-containing proteins tend to be intracellular. Some of the well-characterized proteins with IDLs illustrate that IDLs play pivotal roles in the switching of intracellular signaling or regulatory functions, suggesting that IDL insertion is an effective way to create functionally different domain variants. [Copyright &y& Elsevier]

Assignment of all transcription factors (TFs) from genome sequence data is not a straightforward task due to the wide variation in TFs among different species. A DNA binding domain (DBD) and a contiguous non-DBD with a characteristic SCOP or Pfam domain combination are observed in most members of TF families. We found that most of the experimentally verified TFs in prokaryotes are detectable by a combination of SCOP or Pfam domains assigned to DBDs and non-DBDs. Based on this finding, we set up rules to detect TFs and classify them into 52 TF families. Application of the rules to 154 entirely sequenced prokaryotic genomes detected >18 000 TFs classified into families, which have been made publicly available from the ‘GTOP_TF’ database. Despite the rough proportionality of the number of TFs per genome with genome size, species with reduced genomes, i.e. obligatory parasites and symbionts, have only a few if any TFs, reflecting a nearly complete loss. Also the number of TFs is significantly lower in archaea than in bacteria. In addition, all but 1 of the 19 TF families present in archaea is present in bacteria, whereas 33 TF families are found exclusively in bacteria. This observation indicates that a number of new TF families have evolved in bacteria, making the transcription regulatory system more divergent in bacteria than in archaea. [ABSTRACT FROM PUBLISHER]

Alternative splicing has been recognized as a major mechanism by which protein diversity is increased without significantly increasing genome size in animals and has crucial medical implications, as many alternative splice variants are known to cause diseases. Despite the importance of knowing what structural changes alternative splicing introduces to the encoded proteins for the consideration of its significance, the problem has not been adequately explored. Therefore, we systematically examined the structures of the proteins encoded by the alternative splice variants in the HUGE protein database derived from long (>4kb) human brain cDNAs. Limiting our analyses to reliable alternative splice junctions, we found alternative splice junctions to have a slight tendency to avoid the interior of SCOP domains and a strong statistically significant tendency to coincide with SCOP domain boundaries. These findings reflect the occurrence of some alternative splicing events that utilize protein structural units as a cassette. However, 50 cases were identified in which SCOP domains are disrupted in the middle by alternative splicing. In six of the cases, insertions are introduced at the molecular surface, presumably affecting protein functions, while in 11 of the cases alternatively spliced variants were found to encode pairs of stable and unstable proteins. The mRNAs encoding such unstable proteins are much less abundant than those encoding stable proteins and tend not to have corresponding mRNAs in non-primate species. We propose that most unstable proteins encoded by alternative splice variants lack normal functions and are an evolutionary dead-end. [Copyright &y& Elsevier]

The authors reviewed Niigata Cancer Center Hospital's experience treating patients with lumpectomy to evaluate the utility of three-dimensional helical computed tomography (3D-CT) image-guided made-to-order lumpectomy and determine a positive margin rate. From April 1993 to September 2000, 251 breasts in 248 patients were treated with lumpectomy with a 1 cm macroscopic free margin. In 213 breasts (85%), 3D-CT image-guided made-to-order lumpectomy was performed. Thirty-eight breasts (15%) underwent a lumpectomy without 3D-CT. The lumpectomy specimen was sectioned at 5 mm intervals. Margin status was classified as negative (no invasive or ductal carcinoma in situ (DCIS) within 2 mm from the cut surface) or positive. Positive margins were classified as focally positive (invasive or DCIS transected at the margin within 5 mm or one slide) or massively positive. With 3D-CT image-guided Iumpectomy, 21% (45/213) of lesions had a positive margin and 42% (16/38) of lesions without 3D-CT image-guided lumpectomy had a positive margin ( p = 0.0055). For lesions with massively positive margins, the rates were 9% (4/45) for 3D-CT image-guided lumpectomy and 38% (6/16) for lumpectomy without 3D-CT ( p = 0.0152). 3D-CT image-guided made-to-order lumpectomy decreased the positive surgical margin rate. Among patients with positive margins, those with 3D-CT image-guided lumpectomy have less residual cancer than those without 3D-CT. [ABSTRACT FROM AUTHOR]

Pseudogenes are open reading frames (ORFs) encoding dysfunctional proteins with high homology to known protein-coding genes. Although pseudogenes were reported to exist in the genomes of many eukaryotes and bacteria, no systematic search for pseudogenes in the Escherichia coli genome has been carried out. Genome comparisons of E. coli strains K-12 and O157 revealed that many protein-coding sequences have prematurely terminated orthologs encoding unstable proteins. To systematically screen for pseudogenes, we selected ORFs generated by premature termination of the orthologous protein-coding genes and subsequently excluded those possibly arising from sequence errors. Lastly we eliminated those with close homologs in this and other species, as these shortened ORFs may actually have functions. The process produced 95 and 101 pseudogene candidates in K-12 and O157, respectively. The assigned three-dimensional structures suggest that most of the encoded proteins cannot fold properly and thus are dysfunctional, indicating that they are probably pseudogenes. Therefore, the existence of a significant number of probable pseudogenes in E. coli is predicted, awaiting experimental verification. Most of them were found to be genes with paralogs or horizontally transferred genes or both. We suggest that pseudogenes constitute a small fraction of the genomes of free-living bacteria in general, reflecting the faster elimination than production of pseudogenes. [Copyright &y& Elsevier]

In the first cycle following transfer from a 12 h light-12 h dark cycle (LD12:12) to constant darkness (DD), the standard deviation in circadian phase among individual clocks in populations of Gonyaulax polyedra is approximately 60 min. When a culture is transferred to constant light conditions (LL) from an LD 12:12 cycle, the standard deviation increases in the first 2-3 d, but then remains unchanged, suggesting a lack of observable desynchronization in LL after the transient period. The synchrony in a cell population is preserved even after several cell divisions. The results indicate that variations in period among cells are small, that the period of an individual clock does not fluctuate randomly from day to day, and that the circadian phase of a mother cell is faithfully passed to the clocks of the daughter cells. [ABSTRACT FROM AUTHOR]

Because of the long term persistence of free-running circadian rhythms in populations of unicells, several investigators have considered, but not demonstrated, a possible role for intercellular interaction in maintaining synchrony between individual cells. The experiments described here were designed to test more critically the possibility that there is interaction between cells, including those possessing only small phase differences. None was detected; the bioluminescent glow of the mixed cultures matched the algebraic sum of the independent control cultures. [ABSTRACT FROM AUTHOR]

A size filtration method to synchronize cultures of the dinoflagellate Gonyaulax polyedra to the beginning of the G1 phase has been developed. This technique selects newly born cells by two sequential filtrations, based on the fact that cell division is restricted to the beginning of the day, so that a decrease in cell volume occurs at this time. The fraction of synchronized cells immediately after the second filtration is about 90%; the procedures do not alter the free-running period or phase of glow rhythm, and the selected cells divide again in a few days. Applying this method, we have found that the generation times of this species in a light-dark cycle (LD 12:12) are indeed quantized to multiples of 24 hr, but are variable from generation to generation. [ABSTRACT FROM PUBLISHER]

Eukaryotic proteins consist of structural domains (SDs) and intrinsically disordered regions (IDRs), i.e., regions that by themselves do not assume unique three-dimensional structures. IDRs are generally subject to less constraint and evolve more rapidly than SDs. Proteins with a lower number of protein-to-protein interactions (PPIs) are also less constrained and tend to evolve fast. Extracellular proteins of mammals, especially immune-related extracellular proteins, on average have relatively high evolution rates. This article aims to examine if a high evolution rate in IDRs or that in SDs accounts for the rapid evolution of extracellular proteins. To this end, we classified eukaryotic proteins based on their cellular localizations and analyzed them. Moreover, we divided proteins into SDs and IDRs and calculated the respective evolution rate. Fractional IDR content is positively correlated with evolution rate. For their fractional IDR content, immune-related extracellular proteins show an aberrantly high evolution rate. IDRs evolve more rapidly than SDs in most subcellular localizations. In extracellular proteins, however, the difference is diminished. For immune-related proteins in mammals in particular, the evolution rates in SDs come close to those in IDRs. Thus high evolution rates in both IDRs and SDs account for the rapid evolution of immune-related proteins. [ABSTRACT FROM AUTHOR]

Ectodomain shedding (shedding) is a post-translational modification, which liberates the extracellular domain of membrane proteins through juxtamembrane processing executed mainly by the ADAM (a disintegrin and metalloprotease) family of metalloproteases. Because shedding alters characteristics of cells in a rapid and irreversible manner, it should be strictly regulated. However, the molecular mechanisms determining membrane protein susceptibility to shedding (shedding susceptibility) are largely unknown. Here we report that alternative splicing can give rise to both shedding-susceptible and shedding-resistant CADM1 (cell adhesion molecule 1) variant proteins. We further show that O-glycans adjacent to the shedding cleavage site interfere with CADM1 shedding, and the only 33-bp alternative exon confers shedding susceptibility to CADM1 by inserting five non-glycosylatable amino acids between interfering O-glycans and the shedding cleavage site. These results demonstrate that shedding susceptibility of membrane protein can be determined at two different levels of its biosynthesis pathway, alternative splicing and O-glycosylation. [ABSTRACT FROM AUTHOR]

The molecular mechanisms by which neuronal processes grow are extremely complicated, involving fine-tuned regulation of extracellular and intracellular signals. It remains to be elucidated which molecules are contained in the regulation. Herein, we report for the first time that heat shock protein family A member 5 (HSPA5, also called immunoglobulin heavy chain binding endoplasmic reticulum [ER] protein [BiP]) is secreted from mouse primary dorsal neuronal ganglion (DRG) cells or neuronal cell line N1E-115, a frequently used neuronal differentiation model. Supporting these results, HSPA5 protein was co-localized not only with ER antigen KDEL but also with intracellular vesicles such as Rab11-positive secretory vesicles. Unexpectedly, addition of HSPA5 inhibited elongation of neuronal processes, whereas neutralization of extracellular HSPA5 with the antibodies elongated processes, characterizing extracellular HSPA5 as a negative regulator of neuronal differentiation. Treatment of cells with neutralizing antibodies for low-density lipoprotein receptor (LDLR) did not have significant effects on process elongation, whereas LDLR-related protein 1 (LRP1) antibodies promoted differentiation, implying that LRP1 may act as a receptor candidate for HSPA5. Interestingly, extracellular HSPA5 was greatly decreased following treatment with tunicamycin, an ER stress inducer, illustrating that the ability to form neuronal processes could be preserved, even under stress. These results suggest that neuronal HSPA5 itself is secreted to contribute to inhibitory effects on neuronal cell morphological differentiation and can be included on the list of extracellular signaling molecules negatively controlling differentiation. • HSPA5 is present in neuronal conditional medium. • Extracellular HSPA5 inhibits neuronal morphological differentiation. • HSPA5 interacts with LRP1, an LDL receptor family member. • HSPA5 expression is decreased following treatment with tunicamycin. [ABSTRACT FROM AUTHOR]

Highlights • Wild type AARS is localized in the cytoplasmic region. • The CMT2 N-associated AARS mutant is localized throughout the organelles. • The mutant inhibits differentiation in N1E-115 cells. • Valproic acid reverses the effect of the CMT2 N-associated AARS mutant. Abstract Charcot-Marie-Tooth (CMT) disease is composed of a heterogeneous group of hereditary peripheral neuropathies. The peripheral nervous system primarily comprises two types of cells: neuronal cells and myelinating glial Schwann cells. CMT2 N is an autosomal dominant disease and its responsible gene encodes alanyl-tRNA synthetase (AARS), which is a family of cytoplasmic aminoacyl-tRNA synthetases. CMT2 N is associated with the mutation, including a missense mutation, which is known to decrease the enzymatic activity of AARS, but whether and how its mutation affects AARS localization and neuronal process formation remains to be understood. First, we show that the AARS mutant harboring Asn71-to-Tyr (N71Y) is not localized in cytoplasm. The expression of AARS mutant proteins in COS-7 cells mainly leads to localization into lysosome, whereas the wild type is indeed localized in cytoplasm. Second, in N1E-115 cells as the neuronal cell model, cells expressing the N71Y mutant do not have the ability to grow processes. Third, pretreatment with antiepileptic valproic acid reverses the inhibitory effect of the N71Y mutant on process growth. Taken together, the N71Y mutation of AARS leads to abnormal intracellular localization, inhibiting process growth, yet this inhibition is reversed by valproic acid. [ABSTRACT FROM AUTHOR]