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PubMed1992

Transgenic animal studies on the evolution of genetic regulatory circuitries.

The ability to transfer genes from one species to another provides a powerful method to study genetic regulatory differences between species in a homogeneous genetic background. A survey of several transgenic animal experiments indicates that the vast majority of regulatory differences observed between species are due to differences in the cis-acting elements associated with the genes under study. A corollary is that in almost all cases the host species provides the necessary regulatory proteins for expression of the transgenes in specific tissues in which the endogenous homolog is not expressed. Although the details of the cis-acting differences are unknown for most cases, it appears that these differences may consist of the acquisition or loss of unique elements or subtle variation of conserved elements. It is unknown whether much of this variation is directly related to adaptive evolution. The identification of the promoter/enhancer elements responsible for these differences is an important first step in examining the functional significance of this variation.

Animals↗
PubMed2006

Evolutionary transfers of mitochondrial genes to the nucleus in the Populus lineage and coexpression of nuclear and mitochondrial Sdh4 genes.

The transfer of mitochondrial genes to the nucleus is an ongoing evolutionary process in flowering plants. Evolutionarily recent gene transfers provide insights into the evolutionary dynamics of the process and the way in which transferred genes become functional in the nucleus. Genes that are present in the mitochondrion of some angiosperms but have been transferred to the nucleus in the Populus lineage were identified by searches of Populus sequence databases. Sequence analyses and expression experiments were used to characterize the transferred genes. Two succinate dehydrogenase genes and six mitochondrial ribosomal protein genes have been transferred to the nucleus in the Populus lineage and have become expressed. Three transferred genes have gained an N-terminal mitochondrial targeting presequence from other pre-existing genes and two of the transferred genes do not contain an N-terminal targeting presequence. Intact copies of the succinate dehydrogenase gene Sdh4 are present in both the mitochondrion and the nucleus. Both copies of Sdh4 are expressed in multiple organs of two Populus species and RNA editing occurs in the mitochondrial copy. These results provide a genome-wide perspective on mitochondrial genes that were transferred to the nucleus and became expressed, functional genes during the evolutionary history of Populus.

Active Transport, Cell Nucleus↗
PubMed2000

Comparison of Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, Spodoptera frugiperda, and COS7 cells for recombinant gene expression. Application to a rabbit liver carboxylesterase.

Expression of a rabbit liver carboxylesterase has been achieved in several different model systems including Escherichia coli, Pichia pastoris, Saccharomyces cerevisiae, Spodoptera frugiperda, and COS7 cells. Although, recombinant protein was observed in E. coli sonicates, little or no enzymatic activity was detected. Similarly, no activity was observed following expression in S. cerevisiae. In contrast, active protein was produced in P. pastoris, from S. frugiperda following baculoviral infection and in COS7 cells following transient transfection of plasmid DNA. For the preparation of small amounts of protein for kinetic and biochemical studies, enzyme expressed in P. pastoris has proved sufficient. However, to produce large amounts of carboxylesterase for structural studies, baculoviral-mediated expression of a secreted form of the protein in S. frugiperda was the most efficient. Using this system, we have generated and purified milligram quantities of essentially pure protein. These results demonstrate that the choice of in vitro system for the generation of large amounts of active carboxylesterase, and probably most endoplasmic reticulum processed proteins, is crucial for high level expression and subsequent purification.

Animals↗
PubMed1997

The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression.

The goal of the fungal mitochondrial genome project (FMGP) is to sequence complete mitochondrial genomes for a representative sample of the major fungal lineages; to analyze the genome structure, gene content, and conserved sequence elements of these sequences; and to study the evolution of gene expression in fungal mitochondria. By using our new sequence data for evolutionary studies, we were able to construct phylogenetic trees that provide further solid evidence that animals and fungi share a common ancestor to the exclusion of chlorophytes and protists. With a database comprising multiple mitochondrial gene sequences, the level of support for our mitochondrial phylogenies is unprecedented, in comparison to trees inferred with nuclear ribosomal RNA sequences. We also found several new molecular features in the mitochondrial genomes of lower fungi, including: (1) tRNA editing, which is the same type as that found in the mitochondria of the amoeboid protozoan Acanthamoeba castellanii; (2) two novel types of putative mobile DNA elements, one encoding a site-specific endonuclease that confers mobility on the element, and the other constituting a class of highly compact, structured elements; and (3) a large number of introns, which provide insights into intron origins and evolution. Here, we present an overview of these results, and discuss examples of the diversity of structures found in the fungal mitochondrial genome.

Base Sequence↗
PubMed1994

Microbes, enzymes and genes involved in dichloromethane utilization.

Dichloromethane (DCM) is efficiently utilized as a carbon and energy source by aerobic, Gram-negative, facultative methylotrophic bacteria. It also serves as a sole carbon and energy source for a nitrate-respiring Hyphomicrobium sp. and for a strictly anaerobic co-culture of a DCM-fermenting bacterium and an acetogen. The first step of DCM utilization by methylotrophs is catalyzed by DCM dehalogenase which, in a glutathione-dependent substitution reaction, forms inorganic chloride and S-chloromethyl glutathione. This unstable intermediate decomposes to glutathione, inorganic chloride and formaldehyde, a central metabolite of methylotrophic growth. Genetic studies on DCM utilization are beginning to shed some light on questions pertaining to the evolution of DCM dehalogenases and on the regulation of DCM dehalogenase expression. DCM dehalogenase belongs to the glutathione S-transferase supergene family. Analysis of the amino acid sequences of two bacterial DCM dehalogenases reveals 56% identity, and comparison of these sequences to those of glutathione S-transferases indicates a closer relationship to class Theta eukaryotic glutathione S-transferases than to a number of bacterial glutathione S-transferases whose sequences have recently become available. dcmA, the structural gene of the highly substrate-inducible DCM dehalogenase, is carried in most DCM utilizing methylotrophs on large plasmids. In Methylobacterium sp. DM4 its expression is governed by dcmR, a regulatory gene located upstream of dcmA, dcmR encodes a trans-acting factor which negatively controls DCM dehalogenase formation at the transcriptional level. Our working model thus assumes that the dcmR product is a repressor which, in the absence of DCM, binds to the promoter region of dcmA and thereby inhibits initiation of transcription.

Amino Acid Sequence↗
PubMed1985

Highly conserved sequences in the 3' untranslated region of mRNAs coding for homologous proteins in distantly related species.

Comparison of the nucleotide sequence of mRNAs coding for several vertebrate actins revealed a high degree of sequence homology in the 3' untranslated region (3' UTR) between those mRNAs coding for homologous (isotypic) actins in different organisms but not between mRNAs coding for very similar isoforms differing in their function or tissue specificity. A similar pattern of sequence conservation in the 3' UTR is also found in several other genes. Furthermore, while there is a great variation in the size of the 3' UTR of mRNAs coding for different proteins, mRNA coding for isotypic proteins in distantly related organisms often have 3' UTR of similar size. The data suggest that the 3' UTR may play an important role in the regulation of expression of at least some genes at the transcriptional or posttranscriptional level.

Actins↗
PubMed1992

Evolutionary adaptation to different thermal environments via transcriptional regulation.

Populations of the teleost fish Fundulus heteroclitus are subjected to the clinical variation in environmental temperatures that occurs along the eastern seacoast of North America. In concordance with this change in temperature is the clinal variation in the enzyme concentration of the heart-type lactate dehydrogenase (LDH-B; E.C.1.1.1.27). Previously we have shown that the compensating change in the LDH-B enzyme concentration is due to a change in the amount of LDH-B mRNA, but we did not define whether this was due to differences in mRNA stability or to differences in rate of transcription. The results presented here help clarify the molecular mechanism responsible for the variation in Ldh-B gene expression: the rate of transcription from the Ldh-B locus is significantly different between populations, and this difference is responsible for the compensatory change in LDH-B enzyme concentration.

Adaptation, Biological↗
PubMed1988

Evolutionary implication of genetic code deviations.

We formulate the following hypothesis: Life's origin may have occurred during the lower Archaean at a time when the environmental temperature was higher than it is at present. Preliminary consequences of this hypothesis are studied from the point of view of molecular evolution. We restrict our attention to implications regarding the genetic code. We conclude that alternative assignment of termination codons may be understood in terms of: (a) the elevated temperatures to which the progenote may initially have been exposed; and (b) the subsequent response of its genome to the opportunity provided by the eventual loss of hyperthermal genetic expression during a thermal transition (TT) period, which was triggered off by the evolution of the dynamic Earth.

Biological Evolution↗
PubMedDate not supplied

Evolution of regulatory elements producing a conserved gene expression pattern in Caenorhabditis.

Natural selection acts at the level of function, not at the logistical level of how organisms achieve a particular function. Consequently, significant DNA sequence and regulatory differences can achieve the same function, such as a particular gene expression pattern. To investigate how regulatory features underlying a conserved function can evolve, we compared the regulation of a conserved gene expression pattern in the related species Caenorhabditis elegans and C. briggsae. We find that both C. elegans and C. briggsae express the ovo-related zinc finger gene lin-48 in the same pattern in hindgut cells. However, the regulation of this gene by the Pax-2/5/8 protein EGL-38 differs in two important ways. First, specific differences in the regulatory sequences of lin-48 result in the presence of two redundant EGL-38 response elements in C. elegans, whereas the redundancy is absent in C. briggsae. Second, there is a single egl-38 gene in C. briggsae. In contrast, the gene is duplicated in C. elegans, with only one copy retaining the ability to regulate lin-48 in vivo. These results illustrate molecular changes that can occur despite maintenance of conserved gene function in different species.

Amino Acid Sequence↗
PubMed1997

Genes coding for mouse activin beta C and beta E are closely linked and exhibit a liver-specific expression pattern in adult tissues.

Five activin beta subunits have been isolated to date, and a comparative analysis of amino acid identity has suggested that the activin beta C, beta D and beta E subunits represent a distinct subset. Based on genomic cloning studies, we now report that the mouse activin beta C and beta E genetic loci are closely linked-i.e, the coding sequences are separated by 5.5-kbp. These genes also show similarities in structural organization as well as a unique liver-restricted pattern of expression in adult mice. Our results suggest that tandem duplication of an ancestral gene generated the mouse activin beta C and beta E genetic loci, and they provide further evidence for the postulate that the beta C-beta E subunits form a distinct subset of related activins. To our knowledge, this report is the first to demonstrate close chromosomal linkage between members of the TGF-beta superfamily as well as a liver-restricted expression pattern for a TGF-beta-like gene.

Activins↗
PubMed1992

A common gene regulates pigmentation pattern in diverse plant species.

The delila (del) gene regulates the pattern of red anthocyanin pigmentation in Antirrhinum majus plants. We describe the cloning of the del locus by transposon tagging and show that it encodes a protein with extensive homology to products of the R gene family, which regulates pigmentation in maize. This shows that in spite of the many differences in morphology and coloration between maize and Antirrhinum, the control of pigmentation pattern is mediated by a common regulator. The del and R products contain a region similar to the conserved domain of the helix-loop-helix family of transcription factors. In situ hybridization and RNA analysis show that the expression of del correlates with the distribution of anthocyanins in the flowers. We discuss the implications of these findings for the evolution of regulatory networks.

Amino Acid Sequence↗
PubMed1982

Intron-exon splice junctions map at protein surfaces.

There have been several suggested explanations for the presence of noncoding intervening sequences in many eukaryotic structural genes. They may be examples of 'selfish DNA, conferring little phenotypic advantage, or they may have some importance in gene expression and/or evolution. It has been suggested that each exon (coding sequence) may represent a structural or functional unit of the encoded protein, for which there is good evidence in the case of immunoglobulin and haemoglobin genes. Exon modification, duplication and recombination may thus be general mechanisms for the rapid evolution of eukaryotic structural genes. In many cases, however, it is not apparent that an exon corresponds to some specific feature of the encoded protein. We describe here evidence that intron-exon junctions usually map to amino acid residues located at the protein surface, suggesting a restriction on the permitted positions of introns within a gene.

Amino Acids↗
PubMed1994

LDH-B enzyme expression: the mechanisms of altered gene expression in acclimation and evolutionary adaptation.

The temperature-dependent expression of lactate dehydrogenase-B (LDH-B) was compared between two environmentally distinct populations of Fundulus heteroclitus acclimated to 10 degrees C and 20 degrees C. The variability in LDH-B protein expression both within and between populations is consistent with a model of thermal compensation. The northern population from the colder environment expresses a twofold greater amount of LDH-B protein than the warmer southern population at both acclimation temperatures. Correspondingly, both populations have 1.3-fold greater levels of the enzyme at an acclimation temperature of 10 degrees C in comparison to 20 degrees C. In 20 degrees C-acclimated individuals there is a similar twofold difference between populations for LDH-B mRNA concentrations, and LDH-B protein and mRNA are highly correlated (r = 0.81). After acclimation to 10 degrees C, this difference between populations is not seen and in the northern population there is no relationship between LDH-B mRNA and protein levels. Thus the molecular mechanism regulating LDH-B enzyme expression changes in response to temperature acclimation and is different between populations.

Acclimatization↗
PubMed1988

Studies on the expression and evolution of the glycogen phosphorylase gene family in the rat.

Muscle, liver, and brain glycogen phosphorylases in mammals comprise a family of closely related isozymes that are differentially expressed in a wide variety of cell types. Towards obtaining a better understanding of the mechanisms governing the tissue-specific control of expression of this isozyme family, we used an antibody generated against bovine liver phosphorylase to obtain quantitative estimates of the concentrations of the three isozymes in rat tissues by Western blot analysis. This analysis indicated that expression of these isozymes at the protein level, although widespread, was tissue-specific and each isozyme exhibited variations in expression throughout the tissues where it was produced. We also began a preliminary analysis of the evolution of the genes encoding these three isozymes. Towards this end, we isolated and sequenced a partial cDNA to the rat brain isozyme that encompassed the coding region from amino acids 569 to 729. Using known phosphorylase gene sequences, we reconstructed a phylogeny spanning three kingdoms. This phylogeny indicated that brain and muscle isozymes are more closely related to each other than to the liver isozyme and that gene duplications that give rise to the family predate the mammalian radiation. Differences in the relative rates of change of the three isozymes were observed and this may reflect different constraints on their evolution perhaps related to their functional roles and (or) tissue-specific expression.

Amino Acid Sequence↗
PubMed1988

Evolution and expression of the Sgs-3 glue gene of Drosophila.

A cluster of three glue genes is present at chromosomal site 68C in the Drosophila melanogaster genome. In this study, we have used a comparative approach to investigate both the regulation and the evolution of the largest of these three genes, Sgs-3. The homologous genes from two related Drosophila species (D. erecta and D. yakuba) have been introduced into the D. melanogaster genome by P-factor-mediated transformation. When the resulting transformant lines were assayed for expression of the introduced genes, near-normal patterns of expression were seen. This demonstrates that the cis-acting regulatory sequences of the introduced Sgs-3-homologous glue genes are capable of interacting effectively with the transcriptional machinery of D. melanogaster. We have also determined the sequences of the Sgs-3-homologous glue genes from D. simulans, D. erecta and D. yakuba. These sequences were compared and used in two ways. The first was to locate conserved sequence elements in regions known to be involved in regulation of the gene. Several such elements were found; they represent potential sites of cis-acting regulatory sequences. Second, we looked at the evolution of the glue gene protein-coding regions. A very rapidly evolving central region of the protein-coding sequences was found; this region contains a striking series of tandem repeats of a five amino acid residue sequence in all four species. Also a number of conserved aspects of the Sgs-3-homologous proteins were found; these features may be essential to their function as a glue.

Amino Acid Sequence↗
PubMed1986

Sequence, evolution and differential expression of the two genes encoding variant small subunits of ribulose bisphosphate carboxylase/oxygenase in Chlamydomonas reinhardtii.

We have sequenced the two genes for the small subunit of ribulose bisphosphate carboxylase/oxygenase (Rubisco) in Chlamydomonas reinhardtii and analyzed their expression. The two genes encode variant small subunits that differ by four amino acid residues. Both genes are expressed and each is transcribed into an RNA of distinct size. The accumulation of the two RNAs changes depending on the growth conditions, so the small subunit composition of Rubisco may be expected to differ in response to the environment. The C. reinhardtii small subunit sequence is homologous to those of vascular plants or cyanobacteria, but is longer at the amino terminus and in internal positions. The number and location of the intervening sequences in the genes from C. reinhardtii and from other plants differ. In several cases, internal length differences in the polypeptide coincide with the positions of introns in the coding sequence. Thus, changes in the exon structure of the genes during evolution may have been accompanied by substantial changes in the encoded protein. The translation and splicing signals in C. reinhardtii are similar to those of other eukaryotes, but the transcription signals are less conserved and the highly biased codon usage is very unusual.

Amino Acid Sequence↗
PubMed2026

Expression patterns of risk genes associated with three evolutionarily relevant syndromes in rhesus macaque and human brains.

Depressive disorder (DD), Alzheimer's disease (AD), and schizophrenia (SZ) are evolutionarily relevant traits that disrupt neural networks supporting affect and cognition. While genome-wide association studies have identified risk-related genes for these diseases, how the expression of these genes compare across species remains unclear. In this study, we examined the spatial and temporal expression of ~2000 disease-associated genes in human and rhesus macaque brains. Distinct cross-species signatures emerged. DD-linked genes showed broad cortical-subcortical expression in humans but were confined to subcortical regions in macaques. The divergent subset was enriched for neuron differentiation, migration, synaptic signalling, and cognition. SZ-linked genes were expressed across cortical-subcortical-cerebellar structures in humans. AD-linked genes showed postnatal cortical-hippocampal macaque expression, and broader cortical-subcortical human expression. Cross-species spatial comparisons revealed a significant negative correlation for DD genes, suggesting a broader spatial distribution of DD-related gene expression in humans, extending to distributed emotion-cognition networks, compared to affective hubs in macaques. SZ genes exhibited a similar, though non-significant, negative trend, while AD genes showed a weak, non-significant correlation, indicating an absence of systematic expression shifts. Together, evolutionary shifts in gene expression may have shaped emotional and cognitive functions in humans, and susceptibility to psychiatric and neurodegenerative disorders.

Animals↗