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PubMed1997

Divergent expression of regional metabolic topographies in Parkinson's disease and normal ageing.

We have used [18F]fluorodeoxyglucose (FDG) with PET to identify regional metabolic covariance patterns associated with Parkinson's disease and normal ageing. In this study we utilized these patterns as metabolic markers to assess the relative roles of these processes in the progression of parkinsonism. We studied 37 Parkinson's disease patients and 20 normal volunteer subjects with FDG/PET to calculate regional metabolic rates for glucose. We applied the Parkinson's disease and normal ageing regional covariance patterns separately to these data to compute the expression of both these markers in each subject on an individual case basis. The measured expression of the normal ageing pattern provided an estimate of subject age, based entirely upon the FDG/PET data. The normalized difference between this metabolic estimate and chronological age (delta) was then computed, where delta = (metabolic age - real age)/(real age). We found that delta values were negative and significantly reduced in the Parkinson's disease cohort compared with normal subjects (P < 0.005) indicating a consistent underestimation of chronological age by FDG/PET in parkinsonism. In the Parkinson's disease group, delta correlated negatively with disease duration (r = -0.38, P < 0.04); extrapolation of this linear relationship to delta = 0 yielded an estimate of the mean preclinical period of 4.5 years. These findings suggest that the Parkinson's disease process is likely to be associated with a progressive disruption of the normal age-metabolism relationship, rather than with an exaggeration of the normal ageing process. Our metabolic data also suggest that the preclinical period in Parkinson's disease is of relatively short duration.

Aging↗
PubMed1985

Normal and transformed human prokeratinocytes express divergent effects of a tumor promoter on cell cycle-mediated control of proliferation and differentiation.

The tumor promoter, 12-O-tetradecanoylphorbol-13-acetate (TPA), is shown to be a potent inhibitor of growth of normal human prokeratinocytes (HPK) cultured in serum-free medium. More specifically TPA inhibits the clonal growth of low density HPK cultures in a dose-dependent manner and the anti-proliferative effect of TPA is selective in that the inactive phorbol diester, 4-alpha-12,13-phorbol didecanoate, does not exert a similar effect. One-hour pulse exposure of HPK to TPA also has an effect comparable with continuous exposure to TPA; both treatments induce rapid growth arrest. Flow cytofluorometric analysis of DNA content shows that in TPA-treated HPK growth arrest is associated with accumulation of cells in both the G1 and G2/M phases of the cell cycle. Most interestingly, the data establish that the growth arrest of HPK induced by TPA is irreversible in that treated cells lose their colony-forming potential and that such cells are committed to differentiate without further cell cycle progression when placed in differentiation-promoting medium. In contrast, a human squamous carcinoma cell line, designated SCC-25, is insensitive to the anti-proliferative effect of TPA regardless of whether these cells are cultured in either serum-containing or serum-free medium. These data are interpreted to suggest that transformed human epithelial cells SCC-25 are defective in their ability to regulate their proliferation and differentiation by TPA-sensitive cell cycle-dependent mechanisms.

Adult↗
PubMed1998

Divergent expression of alpha1-protease inhibitor genes in mouse and human.

The alpha1-protease inhibitor proteins of laboratory mice are homologous in sequence and function to human alpha1-antitrypsin and are encoded by a highly conserved multigene family comprised of five members. In humans, the inhibitor is expressed in liver and in macrophages and decreased expression or inhibitory activity is associated with a deficiency syndrome which can result in emphysema and liver disease in affected individuals. It has been proposed that macrophage expression may be an important component of the function of human alpha1-antitrypsin. Clearly, it is desirable to develop a mouse model of this deficiency syndrome, however, efforts to do this have been largely unsuccessful. In this paper, we report that aside from the issues of potentially redundant gene function, the mouse may not be a suitable animal for such studies, because there is no significant expression of murine alpha1-protease inhibitor in the macrophages of mice. This difference between the species appears to result from an absence of a functional macrophage-specific promoter in mice.

Animals↗
PubMed2006

Divergent expression and function of glucocorticoid receptor beta in human monocytes and T cells.

Glucocorticoid (GC) insensitivity is a significant problem in the treatment of immune-mediated diseases. The current study examined whether T cells and monocytes differed in their response to GC and the potential molecular basis for their variation in response to steroids. Functional studies revealed that dexamethasone (DEX) inhibited phorbol 12-myristate 13-acetate/ionomycin-induced tumor necrosis factor alpha and interleukin-6 production to a significantly lesser extent in monocytes than T cells. In parallel, a significantly longer period of time was required for DEX to induce the steroid-responsive gene, mitogen-activated protein kinase phosphatase-1 (MKP-1), in human monocytes as compared with T cells. It is interesting that such differences were not observed between murine T cells and monocytes. GC receptor beta (GCRbeta) is a splicing variant of the classic GCR, GCRalpha, which functions as a dominant-negative inhibitor of GCRalpha in humans, not mice (as mice do not express GCRbeta mRNA as a result of a difference in the murine GCR 9b exon sequence). It was found that human monocytes had a significantly higher level of GCRbeta than T cells. Furthermore, GCRbeta was found in the cytoplasm and nucleus of monocytes, and GCRbeta was localized to the nucleus of T cells. This raised the possibility that GCRbeta in the cytoplasm could affect GCRalpha cellular shuttling in response to DEX. Indeed, we found that DEX-induced nuclear translocation of GCRalpha was decreased in monocytes as compared with T cells. Specific RNA silencing of GCRbeta in human monocytes resulted in enhanced steroid-induced GCRalpha transactivation and transrepression. Our data suggest that GCRbeta contributes to variation in the GC responses of monocytes versus T cells.

Animals↗
PubMed2003

Divergent expression of type 2 deiodinase and the putative thyroxine-binding protein p29, in rat brain, suggests that they are functionally unrelated proteins.

Deiodinases (D1, D2, and D3) are selenoproteins involved in thyroid hormone metabolism. Generation of the active hormone T(3), from T(4), is carried out by D1 and D2, whereas D3 degrades both hormones. The identity of the cloned D2 as a selenoprotein is well supported by biochemical and physiological data. However, an alternative view has proposed that type 2 deiodinase is a nonselenoprotein complex containing a putative T(4) binding subunit called p29, with an almost identity in sequence with the Dickkopf protein Dkk3. To explore a possible functional relationship between p29 and D2, we have compared their mRNA expression patterns in the rat brain. In brain, parenchyma p29 was expressed in neurons. High expression levels were found in all the regions of the blood-cerebrospinal fluid (CSF) barrier. p29 was present in different types of cells than D2, with the exception of the tanycytes. Our data do not support that p29 has a functional relationship with D2. On the other hand, expression of p29 in the blood-CSF barrier suggests that it might be involved in T(4) transport to and from the CSF, but further studies are needed to substantiate this hypothesis.

Animals↗
PubMed1995

Conserved and divergent expression aspects of the Drosophila segmentation gene hunchback in the short germ band embryo of the flour beetle Tribolium.

The segmentation gene hunchback (hb) plays a central role in determining the anterior-posterior pattern in the Drosophila embryo. We have cloned the homologue of hb from the flour beetle Tribolium and show that, on the basis of its expression pattern, most of its functions seem to be conserved between these two species. Like Drosophila, Tribolium has a maternal hb expression that appears to be under translational control by a factor at the posterior pole of the embryo. The maternal expression is followed by a zygotic expression in the region of the developing head and thoracic segments. During germ band extension, a posterior expression domain appears that is likely to be homologous to the posterior blastoderm expression of hb in Drosophila. These observations suggest that hb may have the same functions in early Drosophila and Tribolium development, despite the different types of embryogenesis in these two species (long versus short germ development). One differing aspect of hb expression in Tribolium concerns a structure that is not present in Drosophila, namely the serosa. An hb expression domain at the anterior pole precisely demarcates the border between the extraembryonic serosa and the embryonic field in the Tribolium embryo at an early stage, and hb protein remains expressed in the serosa cells until the end of embryogenesis.

Amino Acid Sequence↗
PubMed2001

Two tomato expansin genes show divergent expression and localization in embryos during seed development and germination.

Expansins are plant proteins that can induce extension of isolated cell walls and are proposed to mediate cell expansion. Three expansin genes were expressed in germinating tomato (Lycopersicon esculentum Mill.) seeds, one of which (LeEXP4) was expressed specifically in the endosperm cap tissue enclosing the radicle tip. The other two genes (LeEXP8 and LeEXP10) were expressed in the embryo and are further characterized here. LeEXP8 mRNA was not detected in developing or mature seeds but accumulated specifically in the radicle cortex during and after germination. In contrast, LeEXP10 mRNA was abundant at an early stage of seed development corresponding to the period of rapid embryo expansion; it then decreased during seed maturation and increased again during germination. When gibberellin-deficient (gib-1) mutant seeds were imbibed in water, LeEXP8 mRNA was not detected, but a low level of LeEXP10 mRNA was present. Expression of both genes increased when gib-1 seeds were imbibed in gibberellin. Abscisic acid did not prevent the initial expression of LeEXP8 and LeEXP10, but mRNA abundance of both genes subsequently decreased during extended incubation. The initial increase in LeEXP8, but not LeEXP10, mRNA accumulation was blocked by low water potential, but LeEXP10 mRNA amounts fell after longer incubation. When seeds were transferred from abscisic acid or low water potential solutions to water, abundance of both LeEXP8 and LeEXP10 mRNAs increased in association with germination. The tissue localization and expression patterns of both LeEXP8 and LeEXP10 suggest developmentally specific roles during embryo and seedling growth.

Cell Wall↗
PubMed2000

Control of expression of divergent Pseudomonas putida put promoters for proline catabolism.

Pseudomonas putida KT2440 uses proline as the sole C and N source. Utilization of this amino acid involves its uptake, which is mediated by the PutP protein, and its conversion into glutamate, mediated by the PutA protein. Sequence analysis revealed that the putA and putP genes are transcribed divergently. Expression from the putP and putA genes was analyzed at the mRNA level in different host backgrounds in the absence and presence of proline. Expression from the put promoters was induced by proline. The transcription initiation points of the putP and putA genes were precisely mapped via primer extension, and sequence analysis of the upstream DNA region showed well-separated promoters for these two genes. The PutA protein acts as a repressor of put gene expression in P. putida because expression from the put promoters is constitutive in a host background with a knockout putA gene. This regulatory activity is independent of the catabolic activity of PutA, because we show that a point mutation (Glu896-->Lys) that prevents catalytic activity allowed the protein to retain its regulatory activity. Expression from the put promoters in the presence of proline in a putA-proficient background requires a positive regulatory protein, still unidentified, whose expression seems to be sigma(54) dependent because the put genes were not expressed in a sigma(54)-deficient background. Expression of the putA and putP genes was equally high in the presence of proline in sigma(38)- and ihf-deficient P. putida backgrounds.

Amino Acid Transport Systems, Neutral↗
PubMed2006

Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution.

Evolutionary rates provide important information about the pattern and mechanism of evolution. Although the rate of gene sequence evolution has been well studied, the rate of gene expression evolution is poorly understood. In particular, it is unclear whether the gene expression level and tissue specificity influence the divergence of expression profiles between orthologous genes. Here we address this question using a microarray data set comprising the expression signals of 10,607 pairs of orthologous human and mouse genes from over 60 tissues per species. We show that the level of gene expression and the degree of tissue specificity are generally conserved between the human and mouse orthologs. The rate of gene expression profile change during evolution is negatively correlated with the level of gene expression, measured by either the average or the highest level among all tissues examined. This is analogous to the observation that the rate of gene (or protein) sequence evolution is negatively correlated with the gene expression level. The impacts of the degree of tissue specificity on the evolutionary rate of gene sequence and that of expression profile, however, are opposite. Highly tissue-specific genes tend to evolve rapidly at the gene sequence level but slowly at the expression profile level. Thus, different forces and selective constraints must underlie the evolution of gene sequence and that of gene expression.

Animals↗
PubMed2006

Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana.

BACKGROUND: Genome analyses have revealed that gene duplication in plants is rampant. Furthermore, many of the duplicated genes seem to have been created through ancient genome-wide duplication events. Recently, we have shown that gene loss is strikingly different for large- and small-scale duplication events and highly biased towards the functional class to which a gene belongs. Here, we study the expression divergence of genes that were created during large- and small-scale gene duplication events by means of microarray data and investigate both the influence of the origin (mode of duplication) and the function of the duplicated genes on expression divergence. RESULTS: Duplicates that have been created by large-scale duplication events and that can still be found in duplicated segments have expression patterns that are more correlated than those that were created by small-scale duplications or those that no longer lie in duplicated segments. Moreover, the former tend to have highly redundant or overlapping expression patterns and are mostly expressed in the same tissues, while the latter show asymmetric divergence. In addition, a strong bias in divergence of gene expression was observed towards gene function and the biological process genes are involved in. CONCLUSION: By using microarray expression data for Arabidopsis thaliana, we show that the mode of duplication, the function of the genes involved, and the time since duplication play important roles in the divergence of gene expression and, therefore, in the functional divergence of genes after duplication.

Amino Acid Substitution↗
PubMed2001

CD40 and CD86 upregulation with divergent CMRF44 expression on blood dendritic cells in inflammatory bowel diseases.

OBJECTIVE: Dendritic cells (DC) are the only antigen-presenting cells that can activate naïve T lymphocytes and initiate a primary immune response. They are also thought to have a role in immune tolerance. DC traffic from the blood to peripheral tissue where they become activated. They then present antigen and the costimulating signals necessary to initiate an immune response. In this study, we investigated the number, subsets, and activation pattern of circulating and intestinal DC from patients with clinically mild ulcerative colitis (UC) or Crohn's disease. METHODS: Patients were recruited, if they were not taking immunosuppressive therapy, and were assessed for clinical severity of their disease using for UC, the Clinical Activity Index, and for Crohn's disease, the Crohn's Disease Activity Index. Blood CD11c+ and CD11c- DC subsets, expression of costimulatory antigens, CD86 and CD40, and the early differentiation/activation antigen, CMRF44, were enumerated by multicolor flow cytometry of lineage negative (lin- = CD3-, CD19-, CD14-, CD16-) HLA-DR+ DC. These data were compared with age-matched healthy and the disease control groups of chronic noninflammatory GI diseases (cGI), acute noninflammatory GI diseases (aGI), and chronic non-GI inflammation (non-GI). In addition, cryostat sections of colonoscopic biopsies from healthy control patients and inflamed versus noninflamed gut mucosa of inflammatory bowel disease (IBD) patients were examined for CD86+ and CD40+ lin- cells. RESULTS: Twenty-one Crohn's disease and 25 UC patients, with mean Crohn's Disease Activity Index of 98 and Clinical Activity Index of 3.1, and 56 healthy controls, five cGI, five aGI, and six non-GI were studied. CD11c+ and CD11c- DC subsets did not differ significantly between Crohn's, UC, and healthy control groups. Expression of CD86 and CD40 on freshly isolated blood DC from Crohn's patients appeared higher (16.6%, 31%) and was significantly higher in UC (26.6%, 46.3%) versus healthy controls (5.5%, 25%) (p = 0.004, p = 0.012) and non-GI controls (10.2%, 22.8%) (p = 0.012, p = 0.008), but not versus cGI or aGI controls. CD86+ and CD40+ DC were also present in inflamed colonic and ileal mucosa from UC and Crohn's patients but not in noninflamed IBD mucosa or normal mucosa. Expression of the CMRF44 antigen was low on freshly isolated DC, but it was upregulated after 24-h culture on DC from all groups, although significantly less so on DC from UC versus Crohn's or healthy controls (p = 0.024). The CMRF44+ antigen was mainly associated with CD11c+ DC, and in UC was inversely related to the Clinical Activity Index (r = -0.69, p = 0.0002). CONCLUSIONS: There is upregulation of costimulatory molecules on blood DC even in very mild IBD but surprisingly, there is divergent expression of the differentiation/activation CMRF44 antigen. Upregulation of costimulatory molecules and divergent expression of CMRF44 in blood DC was also apparent in cGI and aGI but not in non-GI or healthy controls, whereas intestinal CD86+ and CD40+ DC were found only in inflamed mucosa from IBD patients. Persistent or distorted activation of blood DC or divergent regulation of costimulatory and activation antigens may have important implications for gut mucosal immunity and inflammation.

Adolescent↗
PubMed2006

Discovery of eight novel divergent homologs expressed in cattle placenta.

Ten divergent homologs were identified using a subtractive bioinformatic analysis of 12,614 cattle placenta expressed sequence tags followed by comparative, evolutionary, and gene expression studies. Among the 10 divergent homologs, 8 have not been identified previously. These were named as follows: cattle cerebrum and skeletal muscle-specific transcript 1 (CSSMST1), cattle intestine-specific transcript 1 (CIST1), hepatitis A virus cellular receptor 1 amino-terminal domain-containing protein (HAVCRNDP), prolactin-related proteins 8, 9, and 11 (PRP8, PRP9, and PRP11, respectively) and secreted and transmembrane protein 1A and 1B (SECTM1A and SECTM1B, respectively). In addition, two previously known divergent genes were identified, trophoblast Kunitz domain protein 1 (TKDP1) and a new splice variant of TKDP4. Nucleotide substitution analysis provided evidence for positive selection in members of the PRP gene family, SECTM1A and SECTM1B. Gene expression profiles, motif predictions, and annotations of homologous sequences indicate immunological and reproductive functions of the divergent homologs. The genes identified in this study are thus of evolutionary and physiological importance and may have a role in placental adaptations.

Amino Acid Sequence↗
PubMed2006

Adaptive protein evolution and regulatory divergence in Drosophila.

Two recent studies demonstrated a positive correlation between divergence in gene expression and protein sequence in Drosophila. This correlation could be driven by positive selection or variation in functional constraint. To distinguish between these alternatives, we compared patterns of molecular evolution for 1,862 genes with two previously reported estimates of expression divergence in Drosophila. We found a slight negative trend (nonsignificant) between positive selection on protein sequence and divergence in expression levels between Drosophila melanogaster and Drosophila simulans. Conversely, shifts in expression patterns during Drosophila development showed a positive association with adaptive protein evolution, though as before the relationship was weak and not significant. Overall, we found no strong evidence for an increase in the incidence of positive selection on protein-coding regions in genes with divergent expression in Drosophila, suggesting that the previously reported positive association between protein and regulatory divergence primarily reflects variation in functional constraint.

Amino Acid Sequence↗
PubMed2006

BMP2/4 and BMP5-8 in jellyfish development and transdifferentiation.

Bone morphogenetic proteins (BMPs) have key roles in gastrulation, mesoderm induction and axial patterning. The multitude of bilaterian BMPs employed in these morphogenetic processes contrasts starkly with the scarcity of BMPs in Cnidaria, the most basal eumetazoan phylum. In coral, sea anemone and hydra species, BMPs have been found to be associated with larval and polyp axial patterning. In the hydrozoan jellyfish Podocoryne (Hydractinia) carnea the BMP2/4 and BMP5-8 genes are expressed unilaterally in the larva, corroborating a possible role in larval axial development. With the focal area of BMP expression in the anterior region, however, the jellyfish larva may have a developmental reversal of spatial polarity compared to the anthozoan larva. In medusa development, BMP genes are expressed in divergent expression territories within the presumptive radial canals and in various parts of the endoderm, indicative of an involvement in mesoderm patterning and gastrovascular system formation reminiscent of bilaterian BMP functions. In addition, the BMP2/4 and BMP5-8 genes may play roles in wound response and dedifferentiation or S-phase re-entry, respectively, as the former is expressed in striated muscle cells immediately after excision from the bell and the latter in the initial phase of muscle cell transdifferentiation.

Amino Acid Sequence↗
PubMed1990

Tissue-specific expression of divergent actins in soybean root.

It has been proposed that the evolution of distinct classes of genes encoding the kappa-, lambda-, and mu-actins in soybean is the result of an ancient divergence in patterns of actin gene expression. In this study, antisera against a family of synthetic actin peptides from a divergent region within the predicted actin polypeptide sequences have been used to explore the differential expression of plant actins. Antiserum elicited against a 16-residue synthetic lambda-actin peptide SAc4:257 reacted with a 46-kilodalton protein in soybean extracts, showed specificity for the lambda-peptide over the divergent kappa- and mu-actin peptides in enzyme-linked immunosorbent assays, and reacted strongly and preferentially with root protoderm in apical roots and in lateral root primordia. Antiserum elicited against the synthetic kappa-actin peptide SAc1:257 reacted with 46-kilodalton protein on protein gel blots, showed partial specificity toward the immunogenic kappa-peptide over the divergent lambda- and mu-peptides, and reacted strongly with all root tissues with the exception of root cap. These data support the hypothesis that ancient classes of plant actin genes may have been preserved because of their role in developmentally controlled differences in tissue-specific actin expression and/or function. The possibility that other diverse actin classes have unique patterns of regulation is discussed.

Actins↗
PubMed2004

A neutral model of transcriptome evolution.

Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues.

Animals↗
PubMed2006

Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states.

Variation in gene expression levels on a genomic scale has been detected among different strains, among closely related species, and within populations of genetically identical cells. What are the driving forces that lead to expression divergence in some genes and conserved expression in others? Here we employ flux balance analysis to address this question for metabolic genes. We consider the genome-scale metabolic model of Saccharomyces cerevisiae, and its entire space of optimal and near-optimal flux distributions. We show that this space reveals underlying evolutionary constraints on expression regulation, as well as on the conservation of the underlying gene sequences. Genes that have a high range of optimal flux levels tend to display divergent expression levels among different yeast strains and species. This suggests that gene regulation has diverged in those parts of the metabolic network that are less constrained. In addition, we show that genes that are active in a large fraction of the space of optimal solutions tend to have conserved sequences. This supports the possibility that there is less selective pressure to maintain genes that are relevant for only a small number of metabolic states.

Cell Proliferation↗