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At least 235 records · Page 13Linked to original sources
PubMed2025

The evolutionary trajectories and gene regulatory roles of nuclear-integrated plastid DNA: clues for enhancing environmental adaptation in Caryophyllales.

Environmental stimuli can induce the transfer of chloroplast DNA to the nuclear genome, resulting in nuclear-integrated plastid DNAs (NUPTs). However, their role in plant adaptability remains unclear. Species within the Caryophyllales order, known for their adaptation to extreme environments, provide an ideal model for studying the evolutionary dynamics and functions of NUPTs. In this study, we analyzed NUPTs in 24 Caryophyllales species to investigate their evolution and regulatory roles in gene expression, particularly in response to environmental stimuli. We found significant interspecies variation in NUPT abundance, ranging from 566 insertions in Amaranthus cruentus to 3585 in Beta vulgaris, with sizes spanning from 100 bp to over 100 kb. Approximately 62% of NUPTs were inserted within the last 20 million years, while some species exhibit insertion peaks dating back 49 million years. NUPT presence/absence polymorphisms in six related species suggest that NUPT insertions and deletions are dynamic processes influenced by phylogeny. NUPTs predominantly integrate into intergenic regions but also insert into genes and promoters, with certain regions acting as hotspots. Notably, NUPTs introduce numerous environmental-responsive cis-acting elements in promoter regions. Genes with NUPT insertions in their promoters are significantly enriched for functions related to environmental response. Further luciferase assays in Spinacia oleracea demonstrated that NUPT insertions can regulate the expression of genes related to environmental responses, indicating their potential role in adaptive evolution. Overall, our study provides insights into NUPT evolution and their influence on gene function and plant adaptability to environmental stimuli.

Plastids↗
PubMed1995

The gene for pyruvate, orthophosphate dikinase in C4 plants: structure, regulation and evolution.

Pyruvate, orthophosphate dikinase (PPDK; EC 2.7.9.1) is a key enzyme in photosynthesis in plants that exploit the C4 photosynthetic pathway for the fixation of CO2. This review focuses on the structure, regulation and evolution of the C4-type ppdk gene in the maize genome. The C4-ppdk gene in maize consists of 19 exons spanning about 12 kbp. The gene is transcribed from two different initiation sites under the control of two promoters to produce two mRNAs of different sizes. The larger one contains the exon 1 sequence that encodes the chloroplast transit peptide and its product acts as C4-PPDK in chloroplasts, while the smaller one does not contain the sequence and its product may function as a C3-enzyme in the cytosol. This unusual dual promoter system is not unique to the maize C4-type ppdk gene since the same organization is also observed in the rice (C3 plant) ppdk gene and in Flaveria. Thus, the two-promoter system is common to plant ppdk genes from C3 and C4, monocot and dicot plants. A discussion is also presented of the generation of a system for regulation of the expression of the C4-type ppdk gene. A chimeric gene consisting of a reporter gene under the control of the promoter of maize C4-ppdk is exclusively expressed in photosynthetic tissues and not in roots or stems of transgenic rice. The expression of the introduced gene is also regulated by light: it is low in etiolated leaves and is enhanced by illumination. These results indicate that the regulatory system that controls ppdk expression in maize is not unique to C4 plants.

Amino Acid Sequence↗
PubMed1987

[Adaptive significance of the limited gene expression of the immune system].

Evolutionary development of immunity multigene systems seems to involve host-parasite molecular coevolution, as evidenced by comparison of metasoans and unicellular organisms in fixation rates of neutral and adaptive point mutations per one pair of corresponding genes. The estimations we attempted revealed that organisms with maximal restriction of Ig-like gene repertoire expression by an individual immune cell are more adaptive in formation of competent antigen-induced immune response, provided that the magnitude of potential repertoire of functional Ig-like receptors exceeds lymphoid cell population size. In contrast, when phage and bacteria populations are in coevolution, there is no need to limit the repertoire of expressive genes encoding bacteria surface receptor proteins which are recognized by a phage adsorption system. Other hypotheses of evolutionary premises and stimulus of immune genes expression limitation (allelic, isotypic etc.) are critically discussed.

Adaptation, Physiological↗
PubMed2005

Remembering the cell fate during cellular differentiation.

Higher eukaryote contains several hundreds of different cell types, each with a distinctive set of property defined by a unique gene expression pattern, even though every cell (with minor exception) shares the common genome. During cellular differentiation, the committed gene expression pattern is set up and propagated through numerous cell divisions. Therefore, cells must have evolved some elegant and inherent mechanisms to remember their expression states for the requirement of the stability of differentiation and development. Here we speculate a hypothetically cellular memory mechanism. In this hypothesis, the cell-cell variation during cellular differentiation may result from the inherent stochastic gene expression. The evolution of histone and distant regulatory sequences change the parameters of expression stochasticity. S-phase-dependent gene activation and epigenetic marks on chromatin provide means to discriminate transcriptionally active and repressive states. Eventually, mitotic memory mechanisms have been developed through which these expression states are transmitted through numerous cell divisions.

Animals↗
PubMed1996

Heterochrony and neotenic salamanders: possible clues for understanding the animal development and evolution.

A synthesis of developmental genetics with evolutionary genetics is now making possible to understand significant evolutionary changes in multicellular organisms. The key concept for unifying the two must be heterochrony. Heterochrony causes evolutionary modifications due to changes in timing and/or rate of development. The heterochrony is conventionally categorized into three patterns as neoteny (retardation in somatic development), progenesis (acceleration in gonadal development), and direct development (acceleration in somatic development, resulting in lack of larval or tadpole stages). A lot of species showing neoteny are known in urodeles, but not in anurans. Neotenic urodeles are also divided into three categories; permanent or obligate, "inducible" obligate and facultative neotenies. Hynobius retardatus, a specific population of which had been reported to show neoteny but is believed to be extinct at present, has become to be used for experimental analysis of heterochronic expression of several adult characters during its ontogeny. Gonadal maturation and a transition of globin subunits from larval to adult types have been shown to occur independently on the morphological metamorphosis in H. retardatus. Mechanisms underlying the heterochrony, including morphogenetic clock, heterochronic genes in Drosophila and C. elegans, temporal colinearity in Hox gene complex in mice, and atavistic transformation induced by altered expression of Hox genes are discussed in terms of current molecular biology.

Animals↗
PubMed2025

The release of sexual conflict after sex loss is associated with evolutionary changes in gene expression.

Sexual conflict can arise because males and females, while sharing most of their genome, can have different phenotypic optima. Sexually dimorphic gene expression may help reduce conflict, but the expression of many genes may remain sub-optimal owing to unresolved tensions between the sexes. Asexual lineages lack such conflict, making them relevant models for understanding the extent to which sexual conflict influences gene expression. We investigate the evolution of sexual conflict subsequent to sex loss by contrasting the gene expression patterns of sexual and asexual lineages in the pea aphid Acyrthosiphon pisum. Although asexual lineages of this aphid produce a small number of males in autumn, their mating opportunities are limited because of geographic isolation between sexual and asexual lineages. Therefore, gene expression in parthenogenetic females of asexual lineages is no longer constrained by that of other morphs. We found that the expression of genes in males from asexual lineages tended towards the parthenogenetic female optimum, in agreement with theoretical predictions. Surprisingly, males and parthenogenetic females of asexual lineages overexpressed genes normally found in the ovaries and testes of sexual morphs. These changes in gene expression in asexual lineages may arise from the relaxation of selection or the dysregulation of gene networks otherwise used in sexual lineages.

Animals↗
PubMed2001

Five Nkx5 genes show differential expression patterns in anlagen of sensory organs in medaka: insight into the evolution of the gene family.

We report the identification and characterisation of five different Nkx5-related genes in medaka fish (Oryzias latipes). They constitute homologues of genes previously isolated in higher vertebrates, Nkx5--1, Nkx5--2, Hmx1/Nkx5--3 and SOHo-1, and were named accordingly: OlNkx5--1.1, OlNkx5--2, OlNkx5--3 and OlSOHo. For the Nkx5--1 gene a new, second homologue, OlNkx5--1.2, was isolated. In medaka, Nkx5 and SOHo genes are differentially expressed in three developing sensory organs: eye, ear and lateral line and later in defined brain regions. Phylogenetic analyses of the entire Nkx5 family revealed that four paralogous Nkx5 groups, Nkx5--1, Nkx5--2, Hmx1/Nkx5--3/GH6 and SOHo, are present in vertebrates. Only some of the Nkx5 family members have been identified in singular vertebrate species so far. Here we present, for the first time, the isolation of representatives of each Nkx5 subgroup in one species, the medaka fish. Based on similarities in sequence and expression patterns, and genomic organisation we propose a model of the evolutionary history of the Nkx5 family. The model predicts that the four vertebrate Nkx5 genes arose by a tandem duplication, followed by chromosomal duplication. The two Nkx5--1 genes identified so far exclusively in medaka most probably result from an additional genome duplication in the fish lineage.

Amino Acid Sequence↗
PubMed2005

Analysis of 101 nuclear transcriptomes reveals 23 distinct regulons and their relationship to metabolism, chromosomal gene distribution and co-ordination of nuclear and plastid gene expression.

Post-endosymbiotic evolution of the proto-chloroplast was characterized by gene transfer to the nucleus. Hence, most chloroplast proteins are nuclear-encoded and the regulation of chloroplast functions includes nuclear transcriptional control. The expression profiles of 3292 nuclear Arabidopsis genes, most of them encoding chloroplast proteins, were determined from 101 different conditions and have been deposited at the GEO database (http://www.ncbi.nih.gov/geo/) under . The 1590 most-regulated genes fell into 23 distinct groups of co-regulated genes (regulons). Genes of some regulons are not evenly distributed among the five Arabidopsis chromosomes and pairs of adjacent, co-expressed genes exist. Except regulons 1 and 2, regulons are heterogeneous and consist of genes coding for proteins with different subcellular locations or contributing to several biochemical functions. This implies that different organelles and/or metabolic pathways are co-ordinated at the nuclear transcriptional level, and a prototype for this is regulon 12 which contains genes with functions in amino acid and carbohydrate metabolism, as well as genes associated with transport or transcription. The co-expression of nuclear genes coding for subunits of the photosystems or encoding proteins involved in the transcription/translation of plastome genes (particularly ribosome polypeptides) (regulons 1 and 2, respectively) implies the existence of a novel mechanism that co-ordinates plastid and nuclear gene expression and involves nuclear control of plastid ribosome abundance. The co-regulation of genes for photosystem and plastid ribosome proteins escapes a previously described general control of nuclear chloroplast proteins imposed by a transcriptional master switch, highlighting a mode of transcriptional regulation of photosynthesis which is different compared to other chloroplast functions. From the evolutionary standpoint, the results provided indicate that functional integration of the proto-chloroplast into the eukaryotic cell was associated with the establishment of different layers of nuclear transcriptional control.

Arabidopsis↗
PubMed2006

No accelerated rate of protein evolution in male-biased Drosophila pseudoobscura genes.

Sexually dimorphic traits are often subject to diversifying selection. Genes with a male-biased gene expression also are probably affected by sexual selection and have a high rate of protein evolution. We used SAGE to measure sex-biased gene expression in Drosophila pseudoobscura. Consistent with previous results from D. melanogaster, a larger number of genes were male biased (402 genes) than female biased (138 genes). About 34% of the genes changed the sex-related expression pattern between D. melanogaster and D. pseudoobscura. Combining gene expression with protein divergence between both species, we observed a striking difference in the rate of evolution for genes with a male-biased gene expression in one species only. Contrary to expectations, D. pseudoobscura genes in this category showed no accelerated rate of protein evolution, while D. melanogaster genes did. If sexual selection is driving molecular evolution of male-biased genes, our data imply a radically different selection regime in D. pseudoobscura.

Amino Acid Substitution↗
PubMed1981

Comparison of mouse immunoglobulin gamma 2a and gamma 2b chain genes suggests that exons can be exchanged between genes in a multigenic family.

A 23-kilobase EcoRI DNA fragment coding for the BALB/c immunoglobulin gamma 2a chain was cloned from mouse embryo DNA in the cosmid pJC74, and a nucleotide sequence of 1904 bases was determined for the entire constant region (CH1, CH2, and CH3), the three intervening sequences (IVS 1, IVS 2, and IVS 3) and the 5' and 3' flanking sequences. When the gamma 2a chain nucleotide sequence was compared with the gamma 2b chain nucleotide sequence, the percent homology of corresponding segments (excluding deletion and insertion) was 82% for the 5' flanking sequence, 87% for CH1, 84% for IVS 1, 96% for the hinge, 95% for IVS 2, 94.6% for CH2, 86% for IVS 3, 74% for CH3, 89% for the 3' untranslated region, and 92% for the 3' flanking region. These findings show that different domains of gamma 2a and gamma 2b have independent rates of evolution and that some of the noncoding segments of the gene are more conserved than are adjacent coding segments. Hypotheses on the possible role of IVS is gene evolution and expression are discussed.

Animals↗
PubMed1991

Structure, evolution, expression and regulation of insulin-like growth factors I and II.

Insulin-like growth factors (IGF) I and II are chemically-related single-chain peptides with diverse actions on cellular growth and metabolism. This review will focus on recent information pertinent to the biochemical and molecular biological aspects of these peptides. Three areas will be examined: The structure of the two IGF molecules and their precursors will be analyzed; the complicated anatomy of the IGF genes and their mRNAs will be described; and the multiple ways in which the expression of IGF-I and IGF-II can be regulated will be discussed. Gaps in our understanding of these peptides will be highlighted in the context of opportunities for further investigation in this field.

Amino Acid Sequence↗
PubMed2006

Synthesizing cellular networks from evolved ribosome-mRNA pairs.

We describe cellular engineering for the creation of multiple new cellular modules each composed of an orthogonal ribosome and orthogonal mRNA. These modules operate independently of the endogenous ribosome and mRNA. We discuss some of the applications of orthogonal pairs and highlight the expression of Boolean logic in gene regulation using multiple orthogonal pairs.

Biological Evolution↗