39 research outputs found

    The evolution of BIR domain and its containing proteins

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    AbstractBIR domain and its containing proteins play critical roles in cell apoptosis and cell division. Here several lines of novelty were revealed based on a comprehensive evolutionary analysis of BIR domains in 11 representative organisms. First, the type II BIR domains in Survivin and Bruce showed more conservation compared with the type I BIR domains in the inhibitors of apoptosis proteins (IAPs). Second, cIAP was derived from a XIAP duplicate and emerged just after the divergence of invertebrates and vertebrates. Third, the three BIR domains of NAIP displayed significantly elevated evolutionary rates compared with the BIR domains in other IAPs

    Phylogenetic and evolutionary analysis of the septin protein family in metazoan

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    AbstractSeptins, a conserved family of cytoskeletal GTP-binding proteins, were presented in diverse eukaryotes. Here, a comprehensive phylogenetic and evolutionary analysis for septin proteins in metazoan was carried out. First, we demonstrated that all septin proteins in metazoan could be clustered into four subgroups, and the representative homologue of every subgroup was presented in the non-vertebrate chordate Ciona intestinalis, indicating that the emergence of the four septin subgroups should have occurred prior to divergence of vertebrates and invertebrates, and the expansion of the septin gene number in vertebrates was mainly by the duplication of pre-existing genes rather than by the appearance of new septin subgroup. Second, the direct orthologues of most human septins existed in zebrafish, which suggested that human septin gene repertoire was mainly formed by as far as before the split between fishes and land vertebrates. Third, we found that the evolutionary rate within septin family in mammalian lineage varies significantly, human SEPT1, SEPT 10, SEPT 12, and SEPT 14 displayed a relative elevated evolutionary rate compared with other septin members. Our data will provide new insights for the further function study of this protein family

    The ancient function of RB-E2F Pathway: insights from its evolutionary history

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    <p>Abstract</p> <p>Background</p> <p>The RB-E2F pathway is conserved in most eukaryotic lineages, including animals and plants. E2F and RB family proteins perform crucial functions in cycle controlling, differentiation, development and apoptosis. However, there are two kinds of E2Fs (repressive E2Fs and active E2Fs) and three RB family members in human. Till now, the detail evolutionary history of these protein families and how RB-E2F pathway evolved in different organisms remain poorly explored.</p> <p>Results</p> <p>We performed a comprehensive evolutionary analysis of E2F, RB and DP (dimerization partners of E2Fs) protein family in representative eukaryotic organisms. Several interesting facts were revealed. First, orthologues of RB, E2F, and DP family are present in several representative unicellular organisms and all multicellular organisms we checked. Second, ancestral E2F, RB genes duplicated before placozoans and bilaterians diverged, thus E2F family was divided into E2F4/5 subgroup (including repressive E2Fs: E2F4 and E2F5) and E2F1/2/3 subgroup (including active E2Fs: E2F1, E2F2 and E2F3), RB family was divided into RB1 subgroup (including RB1) and RBL subgroup (including RBL1 and RBL2). Third, E2F4 and E2F5 share more sequence similarity with the predicted E2F ancestral sequence than E2F1, E2F2 and E2F3; E2F4 and E2F5 also possess lower evolutionary rates and higher purification selection pressures than E2F1, E2F2 and E2F3. Fourth, for RB family, the RBL subgroup proteins possess lower evolutionary rates and higher purification selection pressures compared with RB subgroup proteins in vertebrates,</p> <p>Conclusions</p> <p>Protein evolutionary rates and purification selection pressures are usually linked with protein functions. We speculated that function conducted by E2F4/5 subgroup and RBL subgroup proteins might mainly represent the ancient function of RB-E2F pathway, and the E2F1/2/3 subgroup proteins and RB1 protein might contribute more to functional diversification in RB-E2F pathway. Our results will enhance the current understanding of RB-E2F pathway and will also be useful to further functional studies in human and other model organisms.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Pierre Pontarotti, Dr. Arcady Mushegian and Dr. Zhenguo Lin (nominated by Dr. Neil Smalheiser).</p

    Customers’ Mode Choice Behaviors of Express Service Based on Latent Class Analysis and Logit Model

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    As the parcel delivery service is booming in China, the competition among express companies intensifies. This paper employed multinomial logit model (MNL) and latent class model (LCM) to investigate customers’ express service choice behavior, using data from a SP survey. The attributes and attribute levels that matter most to express customers are identified. Meanwhile, the customers are divided into two segments (penny pincher segment and high-end segment) characterized by their taste heterogeneity. The results indicate that the LCM performs statistically better than MNL in our sample. Therefore, more attention should be paid to the taste heterogeneity, especially for further academic and policy research in freight choice behavior

    Phylogenetic analysis of CDK and cyclin proteins in premetazoan lineages

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    BACKGROUND: The molecular history of animal evolution from single-celled ancestors remains a major question in biology, and little is known regarding the evolution of cell cycle regulation during animal emergence. In this study, we conducted a comprehensive evolutionary analysis of CDK and cyclin proteins in metazoans and their unicellular relatives. RESULTS: Our analysis divided the CDK family into eight subfamilies. Seven subfamilies (CDK1/2/3, CDK5, CDK7, CDK 20, CDK8/19, CDK9, and CDK10/11) are conserved in metazoans and fungi, with the remaining subfamily, CDK4/6, found only in eumetazoans. With respect to cyclins, cyclin C, H, L, Y subfamilies, and cyclin K and T as a whole subfamily, are generally conserved in animal, fungi, and amoeba Dictyostelium discoideum. In contrast, cyclin subfamilies B, A, E, and D, which are cell cycle-related, have distinct evolutionary histories. The cyclin B subfamily is generally conserved in D. discoideum, fungi, and animals, whereas cyclin A and E subfamilies are both present in animals and their unicellular relatives such as choanoflagellate Monosiga brevicollis and filasterean Capsaspora owczarzaki, but are absent in fungi and D. discoideum. Although absent in fungi and D. discoideum, cyclin D subfamily orthologs can be found in the early-emerging, non-opisthokont apusozoan Thecamonas trahens. Within opisthokonta, the cyclin D subfamily is conserved only in eumetazoans, and is absent in fungi, choanoflagellates, and the basal metazoan Amphimedon queenslandica. CONCLUSIONS: Our data indicate that the CDK4/6 subfamily and eumetazoans emerged simultaneously, with the evolutionary conservation of the cyclin D subfamily also tightly linked with eumetazoan appearance. Establishment of the CDK4/6-cyclin D complex may have been the key step in the evolution of cell cycle control during eumetazoan emergence

    The Correct Localization of Borealin in Midbody during Cytokinesis Depends on IQGAP1

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    Borealin is a key component of chromosomal passenger complex, which is vital in cytokinesis. IQ domain-containing GTPase-activating protein 1 (IQGAP1) also participates in cytokinesis. The correlation between Borealin and IQGAP1 during cytokinesis is not yet clear. Here, we used mass spectrometry and endogenous coimmunoprecipitation experiments to investigate the interaction between IQGAP1 and Borealin. Results of the current study showed that Borealin interacted directly with IQGAP1 both in vitro and in vivo. Knockdown of IQGAP1 resulted in an abnormal location of Borealin in the midbody. Knocking down Borealin alone, IQGAP1 alone, or Borealin and IQGAP1 at the same time inhibited the completion of cytokinesis and formed multinucleated cells. Our results indicated that IQGAP1 interacts with Borealin during cytokinesis, and the correct localization of Borealin in the midbody during cytokinesis is determined by IQGAP1, and IQGAP1 may play an important role in regulating Borealin function in cytokinesis

    Immuno-histochemistry analysis of Helicobacter pylori antigen in renal biopsy specimens from patients with glomerulonephritis

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    This study was conducted to investigate the relationship between Helicobacter pylori infection and three varieties of glomerulonephritis. Renal biopsy specimens from patients with Henoch Schonlein Purpura nephritis (HSPN; n = 10), membranous nephropathy (MN; n = 9) and lupus nephritis (LN; n = 27) were studied using immuno-histochemical labeling to clarify the etiological significance of H. pylori antigen in this disease. Immuno-histochemical labeling was performed using a mixture of anti-H. pylori-antibody-positive serum from nine volunteers; a mixture of anti-H. pylori-antibody-negative serum from nine volunteers was used as control. Staphylococci protein-A labeled by horseradish peroxidase was used as the second antibody in this study. A total of 34 of the 48 specimens revealed positive reaction with the anti-H. pylori-positive serum and five of the 48 specimens revealed positive reaction with the anti-H. pylori-negative serum. Positive reaction against anti-H. pylori-positive serum was seen in 10/10 patients with HSPN, six of nine patients with MN and 18/27 patients with LN. Statistical analysis showed that the difference of the positive reaction between anti-H. pylori-positive and negative sera was significant (χ 2 = 36.318, P = 0.000). Our study indicates that H. pylori infection may be associated with the development and/or progression of HSPN, MN and LN

    UNC50 Prompts G1/S Transition and Proliferation in HCC by Regulation of Epidermal Growth Factor Receptor Trafficking

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    <div><p>Background</p><p>UNC50 has long been recognized as a Golgi apparatus protein in yeast, and is involved in nicotinic receptor trafficking in <i>Caenorhabditis elegans</i>, but little is known about <i>UNC50</i> gene function in human biology despite it being conserved from yeast to high eukaryotes.</p><p>Objectives</p><p>We investigated the relation between UNC50 and human hepatocellular carcinoma (HCC) and the potential mechanisms underlying HCC development.</p><p>Methods</p><p><i>UNC50</i> mRNA expression patterns in 12 HCC and adjacent non-cancerous tissues determined using northern blotting were confirmed by real-time PCR in another 44 paired tissues. Microarray experiments were used to screen for global effects of UNC50 knockdown in the Hep3B cell line, and were confirmed by real-time PCR, western blotting, flow cytometry, and tetrazolium assay in both UNC50 overexpression and knockdown Hep3B cells.</p><p>Results</p><p>UNC50 expression levels were upregulated in HCC tissues in comparison with the adjacent non-cancerous tissues. UNC50 knockdown reduced mRNA levels of the downstream targets of the epidermal growth factor receptor (EGFR) pathway: cyclin D1 (<i>CCND1</i>), <i>EGF</i>, matrix metalloproteinase-7 (<i>MMP7</i>), aldose reductase-like 1 (<i>AKR1B10</i>), cell surface–associated mucin 1 (<i>MUC1</i>), and gastrin (<i>GAST</i>). Moreover, UNC50 influenced EGF, inducing cell cycle entry by affecting cell surface EGFR amounts.</p><p>Conclusions</p><p><i>UNC50</i> may plays some roles in HCC progression by affecting the EGFR pathway.</p></div
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