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Results for “gene expression evolution”

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At least 199 records · Page 11Linked to original sources
PubMed2005

[Dynamic evolution of MMP-2 gene expression and its enzymatic activities in experimental liver fibrosis].

OBJECTIVES: To explore the dynamic changes and interactions between MMP-2 and TIMP-2 during experimental liver fibrosis. METHODS: Wistar rats were randomly allocated into a normal group and a model group. To induce liver fibrosis, rats were injected intraperitoneally with dimethylnitrosamine (DMN) three consecutive times in the first week, then two consecutive times per week, totally for 6 weeks. In the normal control group, rats were injected with saline by the same method as the model group. Animals were sacrificed 1, 4, 10, 17, 28, 42, 56 days after starting DMN injections. Conventional histological examinations of the livers were performed with hematoxylin and eosin and Masson staining. The fibrosis was classified into 0 to 4 stages. Hydroxyproline content was determined after liver tissues were hydrolyzed in HCl at 160 degree C for 2 hrs and then measured with spectrometry at 560 nm wavelength. mRNA levels of MMP-2 and TIMP-2 were determined by semi-quantitive RT-PCR. Gelatinase activity of MMP-2 was examined by zymography using gelatin substrate. RESULTS: In the model group the hepatic MMP-2 mRNA expression started to increase 10 days after DMN administration and remained at a much higher level than in the normal group throughout the study period, while TIMP-2 mRNA expression started to be lower than in the normal group 17 days after DMN administration and reached the lowest level on the 28th day. Then it rapidly rebounded and remained higher than that in the normal group from the 42nd day to the end of the study period. TIMP-2/MMP-2 began to be lower by several days than that of the normal group after DMN administration through the remaining study period. Zymography showed that the enzymatic activities of both latent MMP-2 and active MMP-2 were increased during the process of liver fibrosis. CONCLUSION: In liver fibrosis, MMP-2 expression increases, while TIMP-2 expression relatively decreases. The enzymatic activities of MMP-2 increase as the liver fibrosis develops.

Animals↗
PubMed2006

Expression profiling in primates reveals a rapid evolution of human transcription factors.

Although it has been hypothesized for thirty years that many human adaptations are likely to be due to changes in gene regulation, almost nothing is known about the modes of natural selection acting on regulation in primates. Here we identify a set of genes for which expression is evolving under natural selection. We use a new multi-species complementary DNA array to compare steady-state messenger RNA levels in liver tissues within and between humans, chimpanzees, orangutans and rhesus macaques. Using estimates from a linear mixed model, we identify a set of genes for which expression levels have remained constant across the entire phylogeny (approximately 70 million years), and are therefore likely to be under stabilizing selection. Among the top candidates are five genes with expression levels that have previously been shown to be altered in liver carcinoma. We also find a number of genes with similar expression levels among non-human primates but significantly elevated or reduced expression in the human lineage, features that point to the action of directional selection. Among the gene set with a human-specific increase in expression, there is an excess of transcription factors; the same is not true for genes with increased expression in chimpanzee.

Animals↗
PubMed2004

Divergence in gene expression related to variation in host specificity of an ectomycorrhizal fungus.

Ectomycorrhizae are formed by mutualistic interactions between fungi and the roots of woody plants. During symbiosis the two organisms exchange carbon and nutrients in a specific tissue that is formed at the contact between a compatible fungus and plant. There is considerable variation in the degree of host specificity among species and strains of ectomycorrhizal fungi. In this study, we have for the first time shown that this variation is associated with quantitative differences in gene expression, and with divergence in nucleotide sequences of symbiosis-regulated genes. Gene expression and sequence evolution were compared in different strains of the ectomycorrhizal fungus Paxillus involutus; the strains included Nau, which is not compatible with birch and poplar, and the two compatible strains Maj and ATCC200175. On a genomic level, Nau and Maj were very similar. The sequence identity was 98.9% in the 16 loci analysed, and only three out of 1075 genes analysed by microarray-based hybridizations had signals indicating differences in gene copy numbers. In contrast, 66 out of the 1075 genes were differentially expressed in Maj compared to Nau after contact with birch roots. Thirty-seven of these symbiosis-regulated genes were also differentially expressed in the ATCC strain. Comparative analysis of DNA sequences of the symbiosis-regulated genes in different strains showed that two of them have evolved at an enhanced rate in Nau. The sequence divergence can be explained by a decreased selection pressure, which in turn is determined by lower functional constraints on these proteins in Nau as compared to the compatible strains.

Base Sequence↗
PubMed2005

Toward a neutral evolutionary model of gene expression.

We introduce a stochastic model that describes neutral changes of gene expression over evolutionary time as a compound Poisson process where evolutionary events cause changes of expression level according to a given probability distribution. The model produces simple estimators for model parameters and allows discrimination between symmetric and asymmetric distributions of evolutionary expression changes along an evolutionary lineage. Furthermore, we introduce two measures, the skewness of expression difference distributions and relative difference of evolutionary branch lengths, which are used to quantify deviation from clock-like behavior of gene expression distances. Model-based analyses of gene expression profiles in primate liver and brain samples yield the following results: (1) The majority of gene expression changes are consistent with a neutral model of evolution; (2) along evolutionary lineages, upward changes in expression are less frequent but of greater average magnitude than downward changes; and (3) the skewness measure and the relative branch length difference confirm that an acceleration of gene expression evolution occurred on the human lineage in brain but not in liver. We discuss the latter result with respect to a neutral model of transcriptome evolution and show that a small number of genes expressed in brain can account for the observed data.

Animals↗
PubMed1995

Differential evolution and expression of murine peroxisomal membrane protein genes.

Gene segments encoding the 70 and 22-kDa peroxisomal membrane proteins (PMP) have been characterized in mice and compared with other peroxisomal proteins in terms of evolution and expression. The mouse PMP22 gene sequence predicts A16G and I136V substitutions that agree with those defined by cyanogen bromide cleavage analysis, providing additional evidence that this gene encodes the major 22-kDa membrane protein visualized by SDS-polyacrylamide electrophoresis. Mammalian PMP22 genes exhibit high evolutionary rates (0.17% amino acid substitution per million years) than PMP35 (0.14%), PMP70 (0.07%), or catalase genes (0.13%). PMP70 gene regions are conserved throughout vertebrate phylas based on Southern analysis, while PMP22 sequences were only detected in rodents. Amino acid substitutions are clustered in both PMP22 and PMP70 genes, and their pattern supports membrane topologies derived from hydropathy profiles. Northern blot analysis identifies single mRNAs of 4.6 kb (PMP70), 1.4 kb (PMP22), and 2.3 kb (catalase) in several rodent tissues. Quantitative or competitive RT-PCR assays detected two- to three-fold greater numbers of catalase mRNA molecules relative to PMP mRNA molecules in brain, liver, and kidney; PMP22 and PMP35 mRNAs were two-fold more abundant than PMP70 mRNA in these tissues. Steady-state levels of PMP22 mRNA were highest in rodent liver kidney, spinal cord, and duodenum with low levels in colon, adrenal, thymus, and spleen. We conclude that PMP genes exhibit independent evolutionary rates and tissue regulation, suggesting that they have unique roles in peroxisome biogenesis and tissue differentiation.

ATP-Binding Cassette Transporters↗
PubMed1993

A proteolipid protein gene family: expression in sharks and rays and possible evolution from an ancestral gene encoding a pore-forming polypeptide.

The myelin proteolipid proteins (PLP and DM20) are believed to act as "adhesive struts" in the extracellular apposition of the CNS myelin sheath. These proteins have been considered late evolutionary developments, which arose de novo in the antecedents of early tetrapods. However, PCR primed with degenerate oligonucleotides corresponding to common segments of rat PLP/DM20 revealed three novel mRNAs in the brains of two elasmobranchs. These mRNAs are closely related to each other and to mammalian DM20, but lack the sequence that distinguishes PLP from DM20. We term the novel proteolipid proteins DM alpha, DM beta, and DM gamma. At least DM alpha and DM gamma are highly expressed in white matter in myelinating shark brain. The DMs not only are highly homologous to each other, but also contain regions bearing similarities with segments of channel-forming regions of the nicotinic acetylcholine receptor and the glutamate receptor macromolecular complexes. Significantly, we find that across these segments, DM alpha and DM gamma are more similar to the channel proteins than the two channel proteins are to each other.

Amino Acid Sequence↗
PubMed2005

Rewiring of the yeast transcriptional network through the evolution of motif usage.

Recent experiments revealed large-scale differences in the transcription programs of related species, yet little is known about the genetic basis underlying the evolution of gene expression and its contribution to phenotypic diversity. Here we describe a large-scale modulation of the yeast transcription program that is connected to the emergence of the capacity for rapid anaerobic growth. Genes coding for mitochondrial and cytoplasmic ribosomal proteins display a strongly correlated expression pattern in Candida albicans, but this correlation is lost in the fermentative yeast Saccharomyces cerevisiae. We provide evidence that this change in gene expression is connected to the loss of a specific cis-regulatory element from dozens of genes following the apparent whole-genome duplication event. Our results shed new light on the genetic mechanisms underlying the large-scale evolution of transcriptional networks.

Aerobiosis↗
PubMed2000

Evolution, structure, and expression of GNPI/Oscillin orthologous genes.

Oscillin was identified from hamster sperm as a factor responsible for oocyte calcium oscillations. However, its high level of homology with the bacterial glucosamine-6-phosphate isomerase suggests that it may play more fundamental roles. In the current study, we identified Oscillin orthologs from Caenorhabditis elegans, Drosophila melanogaster, mouse, and human. Their amino acid identities with hamster oscillin were 67.0, 72.3, 97.6, and 95.5%, respectively. No Oscillin orthologs were found in Saccharomyces cerevisiae. The human Oscillin gene (HGMW-approved symbol GNPI) spans 12.4 kb and consists of eight exons. The position of the fourth intron was conserved in other species. The human Oscillin promoter has features characteristic of housekeeping genes, including a GC-rich content, multiple SP1 binding sites, and the absence of a TATA motif. Human and mouse Oscillin genes were ubiquitously expressed in all tissues examined. These data showed that Oscillin is a housekeeping gene conserved throughout evolution and do not support the notion that Oscillin is the sperm-specific factor responsible for calcium oscillations.

Aldose-Ketose Isomerases↗
PubMed2003

Rapid evolution of male-biased gene expression in Drosophila.

A number of genes associated with sexual traits and reproduction evolve at the sequence level faster than the majority of genes coding for non-sex-related traits. Whole genome analyses allow this observation to be extended beyond the limited set of genes that have been studied thus far. We use cDNA microarrays to demonstrate that this pattern holds in Drosophila for the phenotype of gene expression as well, but in one sex only. Genes that are male-biased in their expression show more variation in relative expression levels between conspecific populations and two closely related species than do female-biased genes or genes with sexually monomorphic expression patterns. Additionally, elevated ratios of interspecific expression divergence to intraspecific expression variation among male-biased genes suggest that differences in rates of evolution may be due in part to natural selection. This finding has implications for our understanding of the importance of sexual dimorphism for speciation and rates of phenotypic evolution.

Animals↗
PubMed2003

4-coumarate:CoA ligase gene family in Rubus idaeus: cDNA structures, evolution, and expression.

The enzyme 4-coumarate:CoA ligase (4CL) activates cinnamic acid and its hydroxylated derivatives by forming the corresponding CoA thioesters. These serve as substrates for biosynthesis of phenylpropanoid-derived end-products that are important determinants of fruit quality in raspberry (Rubus idaeus L.). In higher plants, 4CL is typically encoded by a gene family. To investigate the participation of distinct 4CL genes in the process of fruit ripening, we have characterized this gene family in raspberry. By complementing a PCR-based homology search with low-stringency cDNA library screening, we have isolated three classes of raspberry 4CL cDNAs (Ri4CL1, Ri4CL2, and Ri4CL3). Phylogenetic analysis places the three raspberry 4CL gene family members into two distinct groups, a pattern consistent with an ancient divergence from an ancestral progenitor. Quantitative RT-PCR assay reveals a differential pattern of transcription of each of the three genes in various organs, as well as distinct temporal patterns of expression during flower and fruit development. The regulatory elements thus appear to have evolved independently of the genes themselves. Based on phylogenetic classification, expression patterns and recombinant protein activities the different Ri4CL genes are likely to participate in different biosynthetic pathways leading to the various phenylpropanoid-derived metabolites that help create flavor and color in raspberry fruit.

Cloning, Molecular↗
PubMed2005

Structure, evolution, and expression of the two invertase gene families of rice.

Invertases catalyze the irreversible hydrolysis of sucrose to glucose and fructose. Plants contain two unrelated families of these enzymes: acid forms that derive from periplasmic invertases of eubacteria and are found in cell wall and vacuole, and neutral/alkaline forms evolved from the cytosolic invertases of cyanobacteria. Genomes of rice (Oryza sativa) and thale cress (Arabidopsis thaliana) contain multiple genes encoding these two families. Here for rice we identify the member genes of a cell-wall group (designated OsCIN1-9), a vacuolar group (OsVIN1-2), and two ancient neutral/alkaline groups: alpha (OsNIN1-4) and beta (OsNIN5-8). In Arabidopsis these groups contain six, two, four and five members, respectively. It is believed that the vacuolar group evolved from the cell-wall group. We provide evidence that the N-terminal signal peptide that directs cell-wall invertases co-translationally into the endoplasmic reticulum for secretion was replaced in the vacuolar group by a sequence similar to the complex N-terminal motif that targets alkaline phosphatase post-translationally to the vacuolar membrane of yeast. Since the last common ancestor of Arabidopsis and rice, the two invertase families evolved equally rapidly via gene duplication and gene loss, but the acid invertase family underwent approximately 10 events of intron loss compared with a single event of intron gain in the neutral/alkaline invertase family. Transcripts were detected for all rice invertase genes except OsCIN9. The acid invertase genes showed greater spatial and temporal diversity of expression than the neutral/alkaline genes.

Amino Acid Sequence↗
PubMed2006

Expression of the AmphiTcf gene in amphioxus: insights into the evolution of the TCF/LEF gene family during vertebrate evolution.

T-cell factor (TCF) and lymphoid enhancer factors (LEF) genes encode proteins that are transcription factors mediating beta-catenin/Wnt signaling. Whereas mammals have four such genes, the Florida amphioxus (Branchiostoma floridae) apparently has only one such gene (AmphiTcf). From cleavage through early gastrula, cytoplasmic maternal transcripts of this gene are localized toward the animal pole. In gastrulae, AmphiTcf expression begins in the mesendoderm. In neurulae, there is expression in the pharynx, hindgut, anterior notochord, somites, and at the anterior end of the neural plate. In early larvae, expression is detectable in the floor of the diencephalon, notochord, tail bud, forming somites, pharynx, and ciliated pit (a presumed homolog of the vertebrate adenohypophysis). Phylogenetic analysis of TCF/LEF proteins placed AmphiTcf as the sister group of a clade comprising vertebrate Tcf1, Lef1, Tcf3, and Tcf4. Comparison of developmental expression for amphioxus AmphiTcf and vertebrate TCF/LEF genes indicates that this gene family has undergone extensive subfunctionalization and neofunctionalization during vertebrate evolution.

Animals↗
PubMed2006

Diversity and evolution of conotoxins based on gene expression profiling of Conus litteratus.

Cone snails are attracting increasing scientific attention due to their unprecedented diversity of invaluable channel-targeted peptides. As arguably the largest and most successful evolutionary genus of invertebrates, Conus also may become the model system to study the evolution of multigene families and biodiversity. Here, a set of 897 expressed sequence tags (ESTs) derived from a Conus litteratus venom duct was analyzed to illuminate the diversity and evolution mechanism of conotoxins. Nearly half of these ESTs represent the coding sequences of conotoxins, which were grouped into 42 novel conotoxin cDNA sequences (seven superfamilies), with T-superfamily conotoxins being the dominant component. The gene expression profile of conotoxin revealed that transcripts are expressed with order-of-magnitude differences, sequence divergence within a superfamily increases from the N to the C terminus of the open reading frame, and even multiple scaffold-different mature peptides exist in a conotoxin gene superfamily. Most excitingly, we identified a novel conotoxin superfamily and three novel cysteine scaffolds. These results give an initial insight into the C. litteratus transcriptome that will contribute to a better understanding of conotoxin evolution and the study of the cone snail genome in the near future.

Amino Acid Sequence↗
PubMed2006

Comparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolution.

Group B1 Sox genes encode HMG domain transcription factors that play major roles in neural development. We have identified six zebrafish B1 sox genes, which include pan-vertebrate sox1a/b, sox2, and sox3, and also fish-specific sox19a/b. SOX19A/B proteins show a transcriptional activation potential that is similar to other B1 SOX proteins. The expression of sox19a and sox3 begins at approximately the 1,000-cell stage during embryogenesis and becomes confined to the future ectoderm by the shield stage. This is reminiscent of the epiblastic expression of Sox2 and/or Sox3 in amniotes. As development progresses, these six B1 sox genes display unique expression patterns that overlap distinctly from one region to another. sox19a expression is widespread in the early neuroectoderm, resembling pan-neural Sox2 expression in amniotes, whereas zebrafish sox2 shows anterior-restricted expression. Comparative genomics suggests that sox19a/b and mammalian Sox15 (group G) have an orthologous relationship and that the B1/G Sox genes arose from a common ancestral gene through two rounds of genome duplication. It seems likely, therefore, that each B1/G Sox gene has gained a distinct expression profile and function during vertebrate evolution.

Animals↗
PubMed1998

Nuclear calcium: a key regulator of gene expression.

Through the evolution of multicellular organisms, calcium has emerged as the preferred ion for intracellular signalling. It now occupies a pivotal role in many cell types and nowhere is it more important than in neurons, where it mediates both the relaying and long-term storage of information. The latter is a process that enables learning and memory to be formed and requires the activation of gene expression by calcium signals. Evidence from a number of diverse organisms shows that transcription mediated by the transcription factor CREB is critical for learning and memory. Here we review the features of CREB activation by calcium signals in mammalian cells. In contrast to other transcription factors, its regulation is dependent on an elevation of nuclear calcium concentration, potentially placing this spatially distinct pool of calcium as an important mediator of information storage.

Animals↗
PubMed1998

Hemoglobins from bacteria to man: evolution of different patterns of gene expression.

The discovery of hemoglobins in virtually all kingdoms of organisms has shown (1) that the ancestral gene for hemoglobin is ancient, and (2) that hemoglobins can serve additional functions besides transport of oxygen between tissues, ranging from intracellular oxygen transport to catalysis of redox reactions. These different functions of the hemoglobins illustrate the acquisition of new roles by a pre-existing structural gene, which requires changes not only in the coding regions but also in the regulatory elements of the genes. The evolution of different regulated functions within an ancient gene family allows an examination of the types of biosequence data that are informative for various types of issues. Alignment of amino acid sequences is informative for the phylogenetic relationships among the hemoglobins in bacteria, fungi, protists, plants and animals. Although many of these diverse hemoglobins are induced by low oxygen concentrations, to date none of the molecular mechanisms for their hypoxic induction shows common regulatory proteins; hence, a search for matches in non-coding DNA sequences would not be expected to be fruitful. Indeed, alignments of non-coding DNA sequences do not reveal significant matches even between mammalian alpha- and beta-globin gene clusters, which diverged approximately 450 million years ago and are still expressed in a coordinated and balanced manner. They are in very different genomic contexts that show pronounced differences in regulatory mechanisms. The alpha-globin gene is in constitutively active chromatin and is encompassed by a CpG island, which is a dominant determinant of its regulation, whereas the beta-globin gene is in A+T-rich genomic DNA. Non-coding sequence matches are not seen between avian and mammalian beta-globin gene clusters, which diverged approximately 250 million years ago, despite the fact that regulation of both gene clusters requires tissue-specific activation of a chromatin domain regulated by a locus control region. The cis-regulatory sequences needed for domain opening and enhancement do show common binding sites for transcription factors. In contrast, alignments of non-coding sequences from species representing multiple eutherian mammalian orders, some of which diverged as long as 135 million years ago, are reliable predictors of novel cis-regulatory elements, both proximal and distal to the genes. Examples include a potential target for the hematopoietic transcription factor TAL1.

Amino Acid Sequence↗