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PubMed2005

Identification of transcriptional regulatory elements in chemosensory receptor genes by probabilistic segmentation.

Genome sequencing has allowed many gene regulatory elements to be identified through cross-species comparisons . However, the expression of genes in multigene families can diverge rapidly between related species . An alternative approach to characterizing multigene families utilizes the fact that genes within the group are likely to share aspects of their regulation. Here, we use a statistical approach, probabilistic segmentation , to identify sequences that are overrepresented in the regions upstream of C. elegans chemosensory receptor genes. Although each of these elements is present in only a subset of the genes, their distribution across and within the promoters of chemosensory receptor genes makes it possible to detect them. Many of the motifs show positional preference with respect to the translational start site and correspond to the binding sites of known families of transcription factors. We verified one motif, the E-box sequence WWYCACSTGYY, by showing that it directs expression of reporter genes to the ADL chemosensory neurons. Thus, probabilistic segmentation can be used to identify functional regulatory elements with no previous knowledge of gene expression or regulation. This approach may be of particular value for rapidly evolving genes in the immune system and the nervous system.

Amino Acid Motifs↗

PubMed2006

Expression analysis of the Epha1 receptor tyrosine kinase and its high-affinity ligands Efna1 and Efna3 during early mouse development.

Interaction of Eph receptor tyrosine kinases with their membrane bound ephrin ligands initiates bidirectional signaling events that regulate cell migratory and adhesive behavior. Whole-mount in situ hybridization revealed overlapping expression of the Epha1 receptor and its high-affinity ligands ephrin A1 (Efna1) and ephrin A3 (Efna3) in the primitive streak and the posterior paraxial mesoderm during early mouse development. These results show complex and dynamic expression for all three genes with expression domains that are successively complementary, overlapping, and divergent.

Animals↗

PubMed1997

Sequence divergence of measles virus haemagglutinin during natural evolution and adaptation to cell culture.

Phylogenetic analysis of the sequence of the H gene of 75 measles virus (MV) strains (32 published and 43 new sequences) was carried out. The lineage groups described from comparison of the nucleotide sequences encoding the C-terminal regions of the N protein of MV were the same as those derived from the H gene sequences in almost all cases. The databases document a number of distinct genotype switches that have occurred in Madrid (Spain). Well-documented is the complete replacement of lineage group C2, the common European genotype at that time, with that of group D3 around the autumn of 1993. No further isolations of group C2 took place in Madrid after this time. The rate of mutation of the H gene sequences of MV genotype D3 circulating in Madrid from 1993 to 1996 was very low (5 x 10(-4) per annum for a given nucleotide position). This is an order of magnitude lower than the rates of mutation observed in the HN genes of human influenza A viruses. The ratio of expressed over silent mutations indicated that the divergence was not driven by immune selection in this gene. Variations in amino acid 117 of the H protein (F or L) may be related to the ability of some strains to haemagglutinate only in the presence of salt. Adaptation of MV to different primate cell types was associated with very small numbers of mutations in the H gene. The changes could not be predicted when virus previously grown in human B cell lines was adapted to monkey Vero cells. In contrast, rodent brain-adapted viruses displayed a lot of amino acid sequence variation from normal MV strains. There was no convincing evidence for recombination between MV genotypes.

Animals↗

PubMed1989

Genetic basis of the antibody repertoire in Xenopus: analysis of the Vh diversity.

The Xenopus IgH locus includes various variable (VH) families, several putative diversity (DH) and at least seven joining (JH) elements, but--although structurally very similar to the mammalian locus--it contributes to a restricted antibody repertoire. The largest three VH families contain 15-30 VH elements which are interspersed at the VHI-VHII and VHII-VHIII boundaries. Twenty-nine genomic and eight expressed VH regions have been sequenced. Each VH family has distinct promoter elements with up to three octamers (ATGCCTAAAT) in either orientation. The incidence of pseudogenes ranges from less than 15% in VHI and VHII to approximately 50% in VHIII, consistent with their relative expression. CDR1 and CDR2 show low overall diversity with nucleotide divergence limited to parts of the CDRs. Randomly selectedly VH elements share CDR1 and CDR2, in some cases also with expressed VH regions. Thus, the complexity of VH elements is not maximal. Patterns of sequence similarities or identities indicate recombination or gene conversion events; sets of direct and inverted repeats flank the sites of, or lie within FR or CDR sequences where these genetic events may occur. Restricted antibody diversity in Xenopus seems therefore to be at least partially related to low complexity of VH elements, frequence of pseudogenes and expression regulated by specific promoter elements; diversity may potentially be increased by (non)homologous recombination events.

Amino Acid Sequence↗

PubMed2003

Codon optimization of Caenorhabditis elegans GluCl ion channel genes for mammalian cells dramatically improves expression levels.

Organisms use synonymous codons in a highly non-random fashion. These codon usage biases sometimes frustrate attempts to express high levels of exogenous genes in hosts of widely divergent species. The Caenorhabditis elegans GluClalpha1 and GluClbeta genes form a functional glutamate and ivermectin-gated chloride channel when expressed in Xenopus oocytes, but expression is weak in mammalian cells. We have constructed synthetic genes that retain the amino acid sequence of the wild-type GluCl channel proteins, but use codons that are optimal for mammalian cell expression. We have tagged the native and codon-optimized GluCl cDNAs with enhanced yellow fluorescent protein (EYFP, GluClalpha1 subunit) and enhanced cyan fluorescent protein (EFCP, GluClbeta subunit), expressed the channels in E18 rat hippocampal neurons and measured the relative expression levels of the two genes with fluorescence microscopy as well as with electrophysiology. Codon optimization provides a 6- to 9-fold increase in expression, allowing the conclusions that the ivermectin-gated channel has an EC(50) of 1.2 nM and a Hill coefficient of 1.9. We also confirm that the Y182F mutation in the codon-optimized beta subunit results in a heteromeric channel that retains the response to ivermectin while reducing the response to 100 microM glutamate by 7-fold. The engineered GluCl channel is the first codon-optimized membrane protein expressed in mammalian cells and may be useful for selectively silencing specific neuronal populations in vivo.

Animals↗

PubMed1999

Distribution of AP-2 subtypes in the adult mouse brain.

In the mammalian central nervous system (CNS), transcription factor activator protein 2 (AP-2) is one of the critical regulatory factors for neural gene expression and neural development. As AP-2 has diverged into several subtypes, i.e. AP-2alpha, -2beta, and 2.2, we investigated the distribution of the AP-2 subtypes in the adult mouse brain by in situ hybridization using subtype-specific probes. Though AP-2 was essentially expressed in most regions of the brain, the hippocampus and cerebellum Purkinje cells exhibited a relatively high concentration of transcripts of any of the AP-2 subtypes. Among AP-2alpha variants, the expression of variant 1 was considerably lower than that of variant 3. Hence, the expression pattern of AP-2alpha variant 3 is suggested to represent the major gene expression of AP-2alpha. On the other hand, the expression of AP-2beta messenger RNA (mRNA) was higher than that of AP-2alpha in many regions. Especially, the olfactory bulb, hippocampus, cerebellum, and cerebral cortex contained an abundance of these mRNAs. Different from those of AP-2alpha, AP-2beta mRNAs were detected in considerable amounts in the glanular cells as well as in Purkinje cells. AP-2.2 gene expression was weak throughout the brain. Consequently, we found that various AP-2 subtypes and variants were expressed in a similar distribution pattern with each having its own specific intensity but that their precise distribution profiles were not exactly the same. In the mature brain, AP-2 is thought to regulate neural gene expression through specific and redundant association with a target gene.

Animals↗

PubMed1989

Cytokeratin patterns of tissues related to cholesteatoma pathogenesis.

Specimens of cholesteatoma matrix, meatal epidermis, and middle ear epithelium were removed during surgery, and immunohistochemical techniques were used to investigate cytokeratin expression. The use of five chain-specific anticytokeratin monoclonal antibodies and one broad specific anticytokeratin monoclonal antibody showed the divergent behavior of middle ear epithelium compared with the cytokeratin expression of the other two types of epithelium. Middle ear epithelium was characterized by the presence of cytokeratins 4, 8, 18, and 19, whereas in both cholesteatoma and meatal epidermis cytokeratin 10 predominated. Furthermore, cholesteatoma showed an infrequent focal presence of cytokeratins 4, 18, and 19. The similarity between cholesteatoma and meatal epidermis with respect to morphology, and the presence of cytokeratin 10 support an epidermal origin of cholesteatoma. However, a metaplastic origin cannot be excluded, because of the infrequent occurrence of a small amount of cytokeratins 4, 18, and 19 in cholesteatoma matrix that was not found in meatal epidermis but was a component of the cytokeratin pattern of middle ear epithelium.

Antibodies, Monoclonal↗

PubMedDate not supplied

Comparative gene expression of steroidogenic factor 1 in Chrysemys picta and Apalone mutica turtles with temperature-dependent and genotypic sex determination.

Characterizing the molecular network underlying temperature-dependent (TSD) and genotypic (GSD) sex determination, including patterns across closely related taxa, is crucial to elucidate the still enigmatic evolution of sex determining mechanisms in vertebrates. Here we examined the expression of an important gene for sexual differentiation common to both systems, Sf1, at male- and female-producing temperatures, in TSD (Chrysemys picta) and GSD turtles (Apalone mutica). We tested the hypotheses that Sf1 expression responds to temperature consistently across TSD turtles but is unaffected in GSD turtles, and that this differential expression starts no earlier than the onset of the thermosensitive period (TSP). As expected, Sf1 expression was thermally insensitive in A. mutica (GSD). Although Sf1 exhibited a differential expression by temperature in C. picta, the expression pattern differed from other TSD turtles (Trachemys scripta), perhaps reflecting divergence of the gene regulatory networks underlying sex determination over evolutionary time. Most notably, Sf1 was differentially expressed in C. picta (significantly higher at the male-producing temperature) before the onset of the TSP, implying that in TSD taxa significant thermal effects may occur early in development. This result may reconcile field observations where temperatures experienced prior to the TSP have an effect on sex ratios, thus challenging traditional TSP models. Importantly, the molecular factors that render TSD mechanisms thermosensitive remain unknown, and potential candidates are genes that express differentially before the onset of the TSP (genes shaping or opening the TSP-window rather those acting once the TSP window has opened). Therefore, our findings make Sf1 one such potential candidate.

Amino Acid Sequence↗

PubMed1996

Characterization of the expression of the thcB gene, coding for a pesticide-degrading cytochrome P-450 in Rhodococcus strains.

A cytochrome P-450 system in Rhodococcus strains, encoded by thcB, thcC, and thcD, participates in the degradation of thiocarbamates and several other pesticides. The regulation of the system was investigated by fusing a truncated lacZ in frame to thcB, the structural gene for the cytochrome P-450 monooxygenase. Analysis of the thcB-lacZ fusion showed that the expression of thcB was 10-fold higher in the presence of the herbicide EPTC (s-ethyl dipropylthiocarbamate). Similar enhancement of the thcB-lacZ expression was found with other thiocarbamate pesticides. Atrazine, simazine, or carbofuran, although metabolized by the system, had no effect on the thcB-lacZ expression. The presence of glucose slightly increased the expression of thcB-lacZ, indicating no catabolic repression of the thcB-lacZ expression. The expression of thcB-lacZ was decreased more than twofold in Luria-Bertani medium. This was due in part to cysteine, which repressed thcB-lacZ expression. It was confirmed that the thcR gene, which is transcribed divergently from thcB, codes for a positive regulatory protein which is essential for the thcB-lacZ expression. Studies of the thcR-lacZ protein fusion showed that the thcR gene is expressed constitutively.

Atrazine↗

PubMedDate not supplied

Prognostic significance of blood group antigen expression of tumor tissue in lung cancer patients.

AIMS AND BACKGROUND: Many prognostic factors have been evaluated both for SCLC and NSCLC. The prognostic significance of blood group antigen expression of tumor tissues has been studied particularly in NSCLC, yielding divergent results. The aim of the present study was to investigate the prognostic value of the tumoral expression of blood group antigens ABH in lung cancer. METHODS: The presence of blood group antigens was assessed immunohistochemically in paraffin-embedded tumor samples from 92 patients diagnosed between 1996 and 1997. Monoclonal antibodies were used to detect blood group antigens. RESULTS: The median survival was longer in NSCLC patients whose tumors were positive for blood group antigen A (P = 0.009). Since the expression of blood group antigen A in tumor cells was limited to patients with type A or AB blood, survival analysis of these patients showed survival to be longer in non-small cell lung cancer patients with blood group antigen A-positive tumors (P= 0.0019). CONCLUSIONS: Expression of blood group antigen A in tumor cells is an important, favorable prognostic factor in patients with non-small cell lung cancer, which could be useful to stratify patients with blood group A or AB according to possible outcome, and to guide therapeutic decision-making. The expression of blood group antigens ABH should be evaluated in larger series of lung cancer patients (including small and non-small cell lung cancer) with all blood types.

ABO Blood-Group System↗

PubMed1994

Codon use and the rate of divergence of land plant chloroplast genes.

Codon fitnesses for chloroplast genes were estimated using the relative synonymous codon use of psbA, which has a different pattern of codon use than other chloroplast genes and is the major translation product of the chloroplast. These estimates were used to calculate the codon adaptation index (CAI) of chloroplast genes from Marchantia polymorpha, Nicotiana tabacum, and Chlamydomonas reinhardtii. The genes with the highest CAI values in M. polymorpha correspond to those that are expressed at the highest levels. The rate of divergence between M. polymorpha and both C. reinhardtii and N. tabacum is inversely related to the CAI value of the M. polymorpha gene. The data suggest that selection is acting on the synonymous codon use of the highly expressed genes of the M. polymorpha chloroplast genome. The data set is inconclusive about N. tabacum genes, but, as there is a weaker correspondence between CAI value and expression level, it suggests that selection is not operating in this lineage.

Animals↗

PubMed2002

Regulation of neurotrophic peptide expression in sympathetic neurons: quantitative analysis using radioimmunoassay and real-time quantitative polymerase chain reaction.

The regulated expression of the peptide and transcript levels of the neurotrophic peptides, pituitary adenylate cyclase-activating polypeptide (PACAP), galanin and vasoactive intestinal peptide (VIP) were examined in sympathetic neurons of the rat superior cervical ganglion (SCG). Real-time quantitative PCR methods were developed to assess modulation of neuronal peptide precursor protein transcript levels following experimental paradigms of neuropeptidergic plasticity. Oligonucleotide primer, fluorogenic probe and amplification conditions were optimized for maximal assay sensitivity. Depolarization of primary cultured sympathetic neurons stimulated PACAP, galanin, and VIP peptide contents and releases with differing magnitudes and temporal profiles. The rank order of increased neuronal peptide content paralleled the augmented peptide release (VIP>galanin>PACAP). Maximal cellular PACAP and VIP levels were achieved by 72 and 96 h, respectively; galanin levels did not plateau during the treatment period. PACAP transcript elevation was rapid and transient; PACAP mRNA expression diminished at longer depolarization times, which diverged markedly from the sustained high peptide production levels. By contrast, VIP and galanin mRNAs reached maximal levels at later times, and appeared to correlate more closely with peptide production. We previously described multiple proPACAP mRNA variants resulting from alternative 3' untranslated region cleavage and polyadenylation. The shorter depolarization-induced PACAP transcripts exhibit longer half-lives, suggesting that the short proPACAP mRNA variant may function to impart PACAP translational efficiency and sustain PACAP peptide production.

Animals↗

PubMed2000

Molecular characterization of a novel gene family (PHTF) conserved from Drosophila to mammals.

PHTF1 (putative homeodomain transcriptional factor; HGMW-approved symbol PHTF1) is a putative homeobox gene located at band 1p11-p13 of the human genome. We report here the cloning and sequencing of its mouse and Drosophila orthologs. The conservation between mouse and human proteins extends over the entire protein and is localized at the putative homeodomain and at the N- and C-terminal regions of Drosophila protein sequence. Blast searches allowed us to identify another member of the PHTF family, PHTF2, located at 7q11.23-q21 of the human genome. The strongest homologies between human PHTF1 and PHTF2 are localized to the domains that we already described in Drosophila, i.e., the putative homeodomain and the N- and C-terminal regions. The human and mouse genes display 98% similarity to one another, 56% similarity with the Drosophila gene, and 67% similarity with PHTF2, suggesting that phtf might define a novel gene family of highly divergent homeobox genes. Finally, Northern blot analysis showed that while PHTF1 is expressed mainly in testis, PHTF2 is predominantly expressed in muscle, suggesting that these two genes may have acquired different functions after their duplication and divergence.

5' Untranslated Regions↗

PubMed1999

FOG-2: A novel GATA-family cofactor related to multitype zinc-finger proteins Friend of GATA-1 and U-shaped.

GATA factors are transcriptional regulatory proteins that play critical roles in the differentiation of multiple cell types in both vertebrates and invertebrates. Recent evidence suggests that the biological activities of both mammalian and Drosophila GATA factors are controlled in part by physical interaction with multitype zinc-finger proteins, Friend of GATA-1 (FOG) and U-shaped (Ush), respectively. Here we describe a new FOG-related polypeptide, designated FOG-2, that is likely to participate in differentiation mediated by GATA factors in several tissues. Expression of FOG-2 mRNA differs from that of FOG and is largely restricted to heart, neurons, and gonads in the adult. Somewhat broader expression is evident during mouse embryonic development. Similar to FOG and Ush, FOG-2 protein interacts specifically with the amino finger of GATA factors in the yeast two-hybrid system and in mammalian cells. Remarkably, though FOG-2 is quite divergent from FOG in its primary sequence, forced expression of FOG-2 rescues terminal erythroid maturation of FOG-/- hematopoietic cells. Thus, members of the FOG family of cofactors share highly specific association with GATA factors and are substantially interchangeable with respect to some aspects of function in vivo. The interaction of GATA and FOG family members constitutes an evolutionarily conserved paradigm for transcriptional control in differentiation and organogenesis.

Amino Acid Sequence↗

PubMed2005

Dissecting functional similarities of ribosome-associated chaperones from Saccharomyces cerevisiae and Escherichia coli.

Ribosome-tethered chaperones that interact with nascent polypeptide chains have been identified in both prokaryotic and eukaryotic systems. However, these ribosome-associated chaperones share no sequence similarity: bacterial trigger factors (TF) form an independent protein family while the yeast machinery is Hsp70-based. The absence of any component of the yeast machinery results in slow growth at low temperatures and sensitivity to aminoglycoside protein synthesis inhibitors. After establishing that yeast ribosomal protein Rpl25 is able to recruit TF to ribosomes when expressed in place of its Escherichia coli homologue L23, the ribosomal TF tether, we tested whether such divergent ribosome-associated chaperones are functionally interchangeable. E. coli TF was expressed in yeast cells that lacked the endogenous ribosome-bound machinery. TF associated with yeast ribosomes, cross-linked to yeast nascent polypeptides and partially complemented the aminoglycoside sensitivity, demonstrating that ribosome-associated chaperones from divergent organisms share common functions, despite their lack of sequence similarity.

Amino Acid Sequence↗

PubMed2001

Divergent Pseudomonas exotoxin A sensitivity in normal and transformed liver cells is correlated with low-density lipoprotein receptor-related protein expression.

Pseudomonas exotoxin A (PEA) is an extracellular virulence factor produced by the opportunistic human pathogen Pseudomonas aerguinosa. PEA intoxification begins when PEA binds to the low-density lipoprotein receptor-related protein (LRP). The liver is the primary target of systemic PEA, due largely to the high levels of functional LRP expressed by liver cells. Using a 3H-leucine incorporation assay to measure inhibition of protein synthesis we have demonstrated that normal (BNL CL.2) and transformed (BNL 1ME A7R.1) liver cells exhibit divergent PEA sensitivity; with BNL 1ME A7R.1 cells demonstrating greater PEA sensitivity than their non-transformed counterparts. The receptor-associated protein, a LRP antagonist, decreased PEA toxicity in BNL 1ME A7R.1 cells, confirming the importance of the LRP in PEA intoxification in this cell type. Increased PEA sensitivity in BNL 1ME A7R.1 cells was associated with increased functional cell surface LRP expression, as measured by alpha2-macroglobulin binding and internalization studies, and increased LRP mRNA levels, as determined by Northern blot analysis. Interestingly, BNL CL.2 cells were more sensitive than BNL 1ME A7R.1 cells to conjugate and mutant PEA toxins that do not utilize the LRP for cellular entry. These data demonstrate that increased LRP expression is an important mechanism by which PEA sensitivity is increased in BNL 1ME A7R.1 transformed liver cells.

ADP Ribose Transferases↗

PubMed2005

GABA receptors as broadcasters of sexually differentiating signals in the brain.

Epileptic seizures are more common in males than in females. One of the areas that has recently been implicated in the higher susceptibility of males to seizures is the substantia nigra reticulata (SNR). Several studies support the existence of phenotypic differences between male and female infantile SNR neurons, and particularly in several aspects of the GABAergic system, including its ability to control seizures. We have recently found that at postnatal day 14-17 (PN14-17) rats, which are equivalent to infants, activation of GABA(A) receptors has different physiological effects in male and female SNR neurons. This is likely due to the differences in the expression of the neuronal-specific potassium-chloride co-transporter KCC2, which regulates the intracellular chloride concentration. In male PN14-17 SNR neurons, GABA(A)-receptor activation with muscimol causes depolarization and increments in intracellular calcium concentration and the expression of calcium regulated genes, such as KCC2. Blockade of L-type voltage-sensitive calcium channels (L-VSCC) by nifedipine decreases KCC2 mRNA expression. However, in PN14-17 females, muscimol hyperpolarizes the SNR neurons, does not increase intracellular calcium, and decreases KCC2 mRNA expression. In PN15 females, nifedipine has no effect on KCC2 mRNA expression in the SNR. This sexually dimorphic function of GABA(A) receptors also creates divergent patterns of estradiol signaling. In male PN15 rats, estradiol decreases KCC2 mRNA expression in SNR neurons. Pretreatment with the GABA(A)-receptor antagonist bicuculline or with nifedipine, prevents the appearance of estradiol-mediated downregulation of KCC2 mRNA expression. In contrast, in PN15 females, estradiol does not influence KCC2 expression. These findings show that, in infantile rats, drugs or conditions that modulate the activity of GABA(A) receptors or L-VSCCs have different effects on the differentiation of the SNR. As a result, they have the potency of causing long-term changes in the function of the SNR in the control of seizures, movement, and the susceptibility to and course of epilepsy and movement disorders.

Animals↗

PubMed1987

A short 5'-flanking DNA region is sufficient for developmentally correct expression of moth chorion genes in Drosophila.

Fusions with the bacterial gene for chloramphenicol acetyltransferase followed by P-element-mediated germ-line transformation in Drosophila have permitted localization of the DNA sequence that confers a high degree of developmental specificity on a pair of silkmoth eggshell (chorion) genes. The short, 272-base-pair, 5'-flanking region shared by the divergently transcribed genes is sufficient for developmentally appropriate expression when placed upstream of the chloramphenicol acetyltransferase gene, in either orientation. A highly conserved motif within that region, TCACGT, is essential for chorion-specific expression.

Animals↗