Antisense suppression of the putative ribosomal protein S3A gene disrupts ovarian development in Drosophila melanogaster

The Drosophila melanogaster homologue of the Anopheles gambiae C3 cDNA has been isolated and characterized by sequence analysis. The encoded protein was localized by immunochemical and immunocytochemical methods. The Drosophila C3 protein is highly similar to homologues of disputed function, which have previously been identified in fungi, plants and animals. The protein is ubiquitous and localized in the cytoplasm. Cell fractionation followed by detection with a specific antibody preparation shows that the protein is associated with the 40S ribosomal subunit. The C3 gene is located in section 101F of chromosome 4. Antisense transgenic analysis shows that this gene is essential for oogenesis. The most prominent phenotype resulting from antisense depletion of C3 RNA is disappearance of the follicular cells of the ovary (where the concentration of C3 protein is normally high) and abnormalities of the associated germline derivatives, leading to failure of egg production. Received: 13 January 1997 / Accepted: 13 June 1997     

Golgi Phosphoprotein 3 Determines Cell Binding Properties under Dynamic Flow by Controlling Golgi Localization of Core 2 N-Acetylglucosaminyltransferase 1

Core 2 N-acetylglucosaminyltransferase 1 (C2GnT1) is a key enzyme participating in the synthesis of core 2-associated sialyl Lewis x (C2-O-sLe^x), a ligand involved in selectin-mediated leukocyte trafficking and cancer metastasis. To accomplish that, C2GnT1 needs to be localized to the Golgi and this step requires interaction of its cytoplasmic tail (CT) with a protein that has not been identified. Employing C2GnT1 CT as the bait to perform a yeast two-hybrid screen, we have identified Golgi phosphoprotein 3 (GOLPH3) as a principal candidate protein that interacts with C2GnT1 and demonstrated that C2GnT1 binds to GOLPH3 via the LLRRR⁹ sequence in the CT. Confocal fluorescence microscopic analysis shows substantial Golgi co-localization of C2GnT1 and GOLPH3. Upon GOLPH3 knockdown, C2GnT1 is found mainly in the endoplasmic reticulum and decorated with complex-type N-glycans, indicating that the enzyme has been transported to the Golgi but is not retained. Also, we have found that a recombinant protein consisting of C2GnT1 CT^1–16-Leu^17–32-Gly^33–42-GFP is localized to the Golgi although the same construct with mutated CT (AAAAA⁹) is not. The data demonstrate that the C2GnT1 CT is necessary and sufficient for Golgi localization of C2GnT1. Furthermore, GOLPH3 knockdown results in reduced synthesis of C2-O-sLe^x associated with P-selectin glycoprotein ligand-1, reduced cell tethering to and rolling on immobilized P- or E-selectin, and compromised E-selectin-induced activation of spleen tyrosine kinase and cell adhesion to intercellular adhesion molecule-1 under dynamic flow. Our results reveal that GOLPH3 can regulate cell-cell interaction by controlling Golgi retention of C2GnT1.     

Identification and characterization of an immunologically conserved adenovirus early region 11,000 Mr protein and its association with the nuclear matrix

Antisera from some hamsters bearing adenovirus-induced tumors contain antibodies to an 11,000 M_r adenovirus-induced protein. In adenovirus-infected HeLa cells, this early viral protein was specifically associated with the nuclear matrix fraction. After two-dimensional gel electrophoresis, two forms of the 11,000 M_r protein at pI 5.6 and pI 5.4 were found. Only the pI 5.4 form of this protein was associated with the nuclear matrix fraction. Adenoviruses from groups A, B, C, D and E all produced an early viral protein (10,000 to 12,000 M_r) that reacted with group C antibody to the 11,000 M_r protein. To date, this is the only known early viral protein that is immunologically conserved in all of the human adenovirus groups.The positions of two methionine and seven leucine residues were determined by sequencing the first 35 amino acids from the N terminus of the adenovirus serotype 2 group C 11,000 M_r protein. The positions of these amino acid residues were compared to the adenovirus serotype 2 nucleotide sequence, which uniquely localized the structural gene of the 11,000 M_r protein to region E4, subregion 3 in type 2 adenovirus. A frameshift mutant, which contained a deletion of one base-pair in the structural gene of the 11,000 M_r protein, was isolated and mapped by marker rescue and nucleotide sequence analysis. This mutant failed to produce immunologically detectable 11,000 M_r protein. The mutant had a viable phenotype, producing normal levels of infectious virus in both HeLa cells and WI38 cells in culture. These experiments identify the first adenovirus early region 4 protein detected in virus-infected cells.     

Characterization of the human NIPSNAP1 gene from 22q12: a member of a novel gene family

Rapid progress in sequencing of human and other genomes allows high-resolution analysis of their gene content on the basis of comparison between species. We have used a combined computer and biochemical approach to characterize 135 kb of human genomic sequence from 22q12 and discovered a new 10 exon gene, termed NIPSNAP1, located between the neurofibromatosis type 2 and the pK1.3 genes. The NIPSNAP1 gene spans 26 kb of genomic sequence and shows two large introns in the 5′-region. All exon–intron junctions contain the gt/ag consensus splice site. The putative promoter of the NIPSNAP1 gene is TATA-less and resides in a GC-rich island characteristic of housekeeping genes. The NIPSNAP1 mRNA is 2.1 kb, is expressed ubiquitously at variable levels, with the highest expression in liver, is terminated by an uncommon ATTAAA polyadenylation site, and is capable of encoding a 284-amino-acid protein. This NIPSNAP1 protein has a strong sequence similarity limited to the central portion of a hypothetical protein (acc. P34492) from chromosome III of C. elegans, in which the other portions resemble a 4-nitrophenylphosphatase domain and non-neuronal SNAP25-like protein. Thus, the NIPSNAP1 gene is a member of an evolutionarily well conserved, novel gene family with two members in human and mouse that have now been characterized, and one member in C. elegans. The second human gene, NIPSNAP2, is localized in the vicinity of marker D7S499 on chromosome 7. Although the function of the NIPSNAP protein family is unknown, clues about its role may reside in the co-expression of the C. elegans orthologue, within an operon encoding protein motifs known to be involved in vesicular transport.     

Intrastrain and interstrain genetic variation within a paralogous gene family in Chlamydia pneumoniae

Background

Chlamydia pneumoniae causes human respiratory diseases and has recently been associated with atherosclerosis. Analysis of the three recently published C. pneumoniae genomes has led to the identification of a new gene family (the Cpn 1054 family) that consists of 11 predicted genes and gene fragments. Each member encodes a polypeptide with a hydrophobic domain characteristic of proteins localized to the inclusion membrane.

Results

Comparative analysis of this gene family within the published genome sequences provided evidence that multiple levels of genetic variation are evident within this single collection of paralogous genes. Frameshift mutations are found that result in both truncated gene products and pseudogenes that vary among isolates. Several genes in this family contain polycytosine (polyC) tracts either upstream or within the terminal 5' end of the predicted coding sequence. The length of the polyC stretch varies between paralogous genes and within single genes in the three genomes. Sequence analysis of genomic DNA from a collection of 12 C. pneumoniae clinical isolates was used to determine the extent of the variation in the Cpn 1054 gene family.

Conclusions

These studies demonstrate that sequence variability is present both among strains and within strains at several of the loci. In particular, changes in the length of the polyC tract associated with the different Cpn 1054 gene family members are common within each tested C. pneumoniae isolate. The variability identified within this newly described gene family may modulate either phase or antigenic variation and subsequent physiologic diversity within a C. pneumoniae population.     

Characterization of the endonuclease SSO2001 from Sulfolobus solfataricus P2

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) have been suggested to act as an immune system in archaea and bacteria mimicking the eukaryotic RNA interference (RNAi) system. We have investigated the properties of the protein SSO2001 from Sulfolobus solfataricus (Sso) P2, which is part of the cas gene cluster. This study shows that SSO2001 is an endonuclease specifically digesting double-stranded oligonucleotides and preferably cleaving at G:C pairs. Point mutations identify both highly conserved aspartate and glutamate residues as being crucial for the nuclease activity. The catalytic activity shows an optimum at neutral pH and pH 3.     

西伯利亚蓼rd22基因的克隆与序列分析

以3% NaHCO₃溶液胁迫处理48 h的西伯利亚蓼为试材,利用RACE技术,从其茎部组织克隆了脱水应答蛋白RD22的全长cDNA序列。测序后的结果分析表明,该cDNA序列全长为1 302 bp,5′非翻译区为59 bp,3′非翻译区为25 bp,开放读码框为1 218 bp,编码405个氨基酸。在氨基酸序列的C端含有一个比较保守的BURP结构域,N端含有5个重复序列THV-VGKGGV-V。信号肽检测证明该蛋白为分泌性蛋白,前21个氨基酸区域为信号肽结构。其推演的氨基酸序列与葡萄的同源性最高,达到60%。该基因已在GenBank上注册,基因序列登录号为DQ836050。     

Complement component 1, q subcomponent binding protein is a marker for proliferation in breast cancer

Complement component 1, q subcomponent binding protein (C1QBP), is a multi-compartmental protein with higher mRNA expression reported in breast cancer tissues. This study evaluated the association between immunohistochemical expression of the C1QBP protein in breast cancer tissue microarrays (TMAs) and clinicopathological parameters, in particular tumor size. In addition, an in vitro study was conducted to substantiate the breast cancer TMA findings. Breast cancer TMAs were constructed from pathological specimens of patients diagnosed with invasive ductal carcinoma. C1QBP protein and proliferating cell nuclear antigen (PCNA) immunohistochemical analyses were subsequently performed in the TMAs. C1QBP immunostaining was detected in 131 out of 132 samples examined. The C1QBP protein was predominantly localized in the cytoplasm of the breast cancer cells. Univariate analysis revealed that a higher C1QBP protein expression was significantly associated with older patients (P = 0.001) and increased tumor size (P = 0.002). Multivariate analysis showed that C1QBP is an independent predictor of tumor size in progesterone-positive tumors. Furthermore, C1QBP was also significantly correlated with expression of PCNA, a known marker of proliferation. Inhibition of C1QBP expression was performed by transfecting C1QBP siRNA into T47D breast cancer cells, a progesterone receptor-positive breast cancer cell line. C1QBP gene expression was analyzed by real-time RT-PCR, and protein expression by Western blot. Cell proliferation assays were also performed by commercially available assays. Down-regulation of C1QBP expression significantly decreased cell proliferation and growth in T47D cells. Taken together, our findings suggest that the C1QBP protein could be a potential proliferative marker in breast cancer.     

A Family with Atypical Hailey Hailey Disease- Is There More to the Underlying Genetics than ATP2C1?

The autosomal dominant Hailey Hailey disease (HHD) is caused by mutations in the ATP2C1 gene encoding for human secretory pathway Ca2+/Mn2+ ATPase protein (hSPCA1) in the Golgi apparatus. Clinically, HHD presents with erosions and hyperkeratosis predominantly in the intertrigines. Here we report an exome next generation sequencing (NGS) based analysis of ATPase genes in a Greek family with 3 HHD patients presenting with clinically atypical lesions mainly localized on the neck and shoulders. By NGS of one HHD-patient and in silico SNP calling and SNP filtering we identified a SNP in the expected ATP2C1 gene and SNPs in further ATPase genes. Verification in all 3 affected family members revealed a heterozygous frameshift deletion at position 2355_2358 in exon 24 of ATP2C1 in all three patients. 7 additional SNPs in 4 ATPase genes (ATP9B, ATP11A, ATP2B3 and ATP13A5) were identified. The SNPs rs138177421 in the ATP9B gene and rs2280268 in the ATP13A5 gene were detected in all 3 affected, but not in 2 non affected family members. The SNPs in the ATP2B3 and ATP11A gene as well as further SNPs in the ATP13A5 gene could not be confirmed in all affected family members. One may speculate that besides the level of functional hSPCA1 protein, levels of other ATPase proteins may influence expressivity of the disease and might also contribute, as in this case, to atypical presentations.     

Chlamydomonas reinhardii gene for the 32 000 mol. wt. protein of photosystem II contains four large introns and is located entirely within the chloroplast inverted repeat

The chloroplast psbA gene from the green unicellular alga Chlamydomonas reinhardii has been localized, cloned and sequenced. This gene codes for the rapidly-labeled 32-kd protein of photosystem II, also identified as as herbicide-binding protein. Unlike psbA in higher plants which is found in the large single copy region of the chloroplast genome and is uninterrupted, psbA in C. reinhardii is located entirely within the inverted repeat, hence present in two identical copies per circular chloroplast genome, and contains four large introns. These introns range from 1.1 to 1.8 kb in size and fall into the category of Group I introns. Two of the introns contain open reading frames which are in-frame with the preceding exon sequences. We present the nucleotide sequence for the C. reinhardii psbA 5'-and 3' -flanking sequences, the coding region contained in five exons and the deduced amino acid sequence. The algal gene codes for a protein of 352 amino acid residues which is 95% homologous, excluding the last eight amino acid residues, with the higher plant protein.     

Subcellular localization of different regions of porcine Six1 gene and its expression analysis in C2C12 myoblasts

Six1 protein belongs to the Six homeoproteins family, exposing typical domain structure. Although the functions of Six1 have been drawn much attention, the roles of its individual domains are not completely elucidated. Here, we first detected the expression patterns of myogenin, MyoD, Myf5, and Six1 genes using real-time PCR in differentiating C2C12 cells cultured in differentiation medium for 2 or 6?days. The results showed that Six1 gene had the similar expression pattern with myogenin, MyoD, and Myf5 genes, which suggests that it may affect the myogenic differentiation. In order to evaluate the role of distinct domains of Six1 protein in subcellular localization, we constructed a series of truncated vectors tagged with green fluorescent proteins expressing various regions of porcine Six1 protein for subcellular localization analysis. Fluorescence confocal microscopy analysis showed that the different regions of Six1 protein displayed discrete distributions throughout the nucleus and the cytoplasm. The full-length CDS was exclusively localized in the nucleus and the individual HD domain was preferentially distributed to the nucleus both in C2C12 cells and in PK cells. However, the SD domain was diffusely distributed to the cytoplasm and the nucleus, and the localization of SD domain was biased to cytoplasm in C2C12 cells. Taken together, we conclude that the HD domain is important for the nuclear localization of porcine Six1 protein.     

A search for growth related genes in Kalanchoë blossfeldiana

Differential display of mRNA from four sets of contrasting phenotypes were carried out in order to identify and isolate genes associated with elongating growth of Kalanchoë blossfeldiana. A total of 17 unique differential expressed cDNA fragments were sequenced and 12 showed homology to genes in other plant species. Three genes were subsequently tested for growth related activity by Virus Induced Gene Silencing (VIGS) in Nicotiana benthamiana. One gene fragment (13C) resulted in plants with significantly reduced growth (N = 20, P = 0.05, one-tailed students t-test) from day 25 after virus infection. Full-length cDNA and genomic DNA sequences were obtained by inverse PCR and thermal asymmetric interlaced (TAIL) PCR and the gene was named KbORF1. The predicted gene is 2244 bp long with three exons of 411 bp in total encoding a protein of 137 amino acid residues with homologs widespread among plants. The protein has no known function, but its expression has been confirmed in a proteomic study of Arabidopsis. Southern blot analysis shows two hybridizing fragments in agreement with the tetraploid nature of K. blossfeldiana. Fragment 13C comprises 446 bp of the gene, and the portion of 13C conferring growth retardation by VIGS is located 10 bp into the second intron indicating a regulatory function of this part of the KbORF1 mRNA. Differential display in combination with VIGS as a screening method proved to be a good functional approach not only to search for genes of interest, but also to isolate expressed genetic regulatory domains.     

Enp1, a yeast protein associated with U3 and U14 snoRNAs,is required for pre-rRNA processing and 40S subunit synthesis

ENP1 is an essential Saccharomyces cerevisiae gene encoding a 483 amino acid polypeptide. Enp1 protein is localized in the nucleus and concentrated in the nucleolus. An enp1-1 temperature-sensitive mutant inhibited 35S pre-rRNA early processing at sites A₀, A₁ and A₂ as shown by northern analysis of steady state levels of rRNA precursors. Pulse-chase analysis further revealed that the enp1-1 strain was defective in the synthesis of 20S pre-rRNA and hence 18S rRNA, which led to reduced formation of 40S ribosomal subunits. Co-precipitation analysis revealed that Enp1 was associated with Nop1 protein, as well as with U3 and U14 RNAs, two snoRNAs implicated in early pre-rRNA processing steps. These results suggest a direct role for Enp1 in the early steps of rRNA processing.