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PubMed1986

Anomalous placement of introns in a member of the intermediate filament multigene family: an evolutionary conundrum.

The origin of introns and their role (if any) in gene expression, in the evolution of the genome, and in the generation of new expressed sequences are issues that are understood poorly, if at all. Multigene families provide a favorable opportunity for examining the evolutionary history of introns because it is possible to identify changes in intron placement and content since the divergence of family members from a common ancestral sequence. Here we report the complete sequence of the gene encoding the 68-kilodalton (kDa) neurofilament protein; the gene is a member of the intermediate filament multigene family that diverged over 600 million years ago. Five other members of this family (desmin, vimentin, glial fibrillary acidic protein, and type I and type II keratins) are encoded by genes with six or more introns at homologous positions. To our surprise, the number and placement of introns in the 68-kDa neurofilament protein gene were completely anomalous, with only three introns, none of which corresponded in position to introns in any characterized intermediate filament gene. This finding was all the more unexpected because comparative amino acid sequence data suggest a closer relationship of the 68-kDa neurofilament protein to desmin, vimentin, and glial fibrillary acidic protein than between any of these three proteins and the keratins. It appears likely that an mRNA-mediated transposition event was involved in the evolution of the 68-kDa neurofilament protein gene and that subsequent events led to the acquisition of at least two of the three introns present in the contemporary sequence.

Amino Acid Sequence↗
PubMed2000

Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis.

The complete genome sequence has been reported for 24 microbial organisms. The genome organization and gene content of these organisms has revealed an incredible diversity. Nearly half of the open reading frames identified by these sequencing projects are for potential genes with no known biological function. Efforts to make evolutionary sense and biological sense of the gene content of these organisms have been initiated. The greatest future challenge of genomics will be to determine function for the unknown genes.

Bacteria↗
PubMedDate not supplied

Additional hox clusters in the zebrafish: divergent expression patterns belie equivalent activities of duplicate hoxB5 genes.

The evolution of metazoan body plans has involved changes to the Hox genes, which are involved in patterning the body axis and display striking evolutionary conservation of structure and expression. Invertebrates contain a single Hox cluster whereas tetrapods possess four clusters. The zebrafish has seven unlinked hox clusters, a finding that is difficult to reconcile with the notion that genomic complexity, reflected by Hox cluster number, and morphological complexity are causally linked, as the body plan of the zebrafish is not obviously more complex than that of the mouse or human. Why have the additional hox genes in zebrafish been conserved? To address the role of these additional zebrafish hox genes, we have examined the duplicate hoxB5 genes, hoxB5a, and hoxB5b. Conservation of gene duplicates can occur when one gene acquires a new function (neofunctionalization), or when the ancestral function is divided between the two duplicates (subfunctionalization). hoxB5a and hoxB5b are expressed in distinct domains, and their combined expression domain is strikingly similar to that of single Hoxb5 genes in other species. The biochemical functions encoded by the two genes were studied by overexpression, which resulted in identical developmental defects in the anterior hindbrain and cranial neural crest, suggesting strongly that hoxB5a and hoxB5b have equivalent biochemical properties with respect to early development. From these studies, we conclude that conservation of hoxB5a and hoxB5b is likely the result of division of the ancestral Hoxb5 function between the two genes, without significant changes in biochemical activity. These results suggest a resolution to the conundrum of the extra hox genes and clusters in the zebrafish, since if any of the additional hox genes in the zebrafish are similarly subfunctionalized, they are unlikely to supply novel genetic functions. Thus, the morphological complexity potentially conferred by the majority of additional zebrafish hox clusters may not be substantially greater than that conferred by the four tetrapod clusters.

3' Untranslated Regions↗
PubMed1998

Post-infarction heart failure in the rat is associated with distinct alterations in cardiac myocyte molecular phenotype.

The myocardial molecular and cellular responses to hemodynamic and other hypertrophic stimuli have been characterized extensively, but less is known of the alterations in gene expression during the evolution of heart failure following myocardial infarction, and specifically those affecting the cardiac myocytes. Therefore, the present study was undertaken to test the hypothesis that post-infarction heart failure and remodeling in the rat is associated with a distinct myocyte molecular phenotype. To address this question, hemodynamic measurements were performed in vivo; and myocytes isolated from the non-infarcted myocardium 1 day, 1 week, and 6 weeks post-coronary artery ligation in post-infarct rats and sham controls. Myocyte size, mRNA levels for immediate early genes, contractile proteins, and sarcoplasmic reticulum Ca2+-ATPase (SERCA) and phospholamban were assayed by Northern analyses, and SERCA and phospholamban proteins were examined by Western blotting. Hemodynamic evidence of heart failure was present at all post-infarct time points. Myocyte size was increased significantly at 6 weeks. c-myc expression was increased at 1 day and 1 week in the infarcted rats, but returned to baseline by 6 weeks. Atrial natriuretic peptide and VEGF mRNAs were elevated at 1 and 6 weeks. Both beta-myosin heavy chain and skeletal alpha-actin expression were increased at all post-MI time points. In contrast, neither changes in the expression of the calcium-handling proteins (SERCA and phospholamban) were not observed, nor was there a change in TGFbeta1 or TGFbeta3. These results demonstrate that in rats with post-MI heart failure, there was an immediate induction of the fetal/embryonic transcriptional gene program which preceded myocyte hypertrophy and appeared to persist longer than in pressure-overload models. In further contrast to pressure-overload, expression of sarcoplasmic reticulum Ca2+-ATPase and phospholamban, was not altered despite a comparable degree of cellular hypertrophy and more severe hemodynamic decompensation. These findings suggest that there may be important differences in the regulatory mechanisms underlying these two forms of myocardial hypertrophy and heart failure.

Actins↗
PubMed2002

Multiple regulatory changes contribute to the evolution of the Caenorhabditis lin-48 ovo gene.

Recent work points to the importance of changes in gene expression patterns in species-specific differences. Here, we investigate the evolution of the nematode lin-48 ovo gene. lin-48 is expressed in several cells in both Caenorhabditis elegans and Caenorhabditis briggsae, but acts in the excretory duct cell only in C. elegans. We find the differences result both from alterations in the cis-regulatory sequences and in proteins that mediate lin-48 expression. One factor that contributes to the species differences is the bZip protein CES-2. Our results indicate the accumulation of several regulatory changes affecting one gene can contribute to evolutionary change.

Animals↗
PubMed2001

A novel MADS-box gene subfamily with a sister-group relationship to class B floral homeotic genes.

Class B floral homeotic genes specify the identity of petals and stamens during the development of angiosperm flowers. Recently, putative orthologs of these genes have been identified in different gymnosperms. Together, these genes constitute a clade, termed B genes. Here we report that diverse seed plants also contain members of a hitherto unknown sister clade of the B genes, termed B(sister) (B(s)) genes. We have isolated members of the B(s) clade from the gymnosperm Gnetum gnemon, the monocotyledonous angiosperm Zea mays and the eudicots Arabidopsis thaliana and Antirrhinum majus. In addition, MADS-box genes from the basal angiosperm Asarum europaeum and the eudicot Petunia hybrida were identified as B(s) genes. Comprehensive expression studies revealed that B(s) genes are mainly transcribed in female reproductive organs (ovules and carpel walls). This is in clear contrast to the B genes, which are predominantly expressed in male reproductive organs (and in angiosperm petals). Our data suggest that the B(s) genes played an important role during the evolution of the reproductive structures in seed plants. The establishment of distinct B and B(s) gene lineages after duplication of an ancestral gene may have accompanied the evolution of male microsporophylls and female megasporophylls 400-300 million years ago. During flower evolution, expression of B(s) genes diversified, but the focus of expression remained in female reproductive organs. Our findings imply that a clade of highly conserved close relatives of class B floral homeotic genes has been completely overlooked until recently and awaits further evaluation of its developmental and evolutionary importance. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00438-001-0615-8.

Amino Acid Sequence↗
PubMed2004

Profiling of aortic smooth muscle cell gene expression in response to chronic inhibition of nitric oxide synthase in rats.

BACKGROUND: Chronic inhibition of nitric oxide (NO) synthesis by N(omega)-nitro-L-arginine methyl ester (L-NAME) induces hypertension associated with remodeling of the arterial wall. In this study, we aimed at identifying genes and pathways involved in this process in aortic smooth muscle cells from Fischer 344 rats, which exhibit an accelerated hypertension after administration of L-NAME. METHODS AND RESULTS: We studied the transcriptional profile of aortic media after 15 days (moderate hypertension) and 30 days (accelerated hypertension) of L-NAME administration (50 mg x kg(-1) x d(-1)) by using rat Affymetrix Genechips, and we present a large-scale validation of the DNA chip results by real-time reverse transcription-polymerase chain reaction (RT-PCR). We observed, in aortic media, a progressive increase in the number of modulated genes during L-NAME administration, with 53 genes significantly modulated after 15 days and 147 genes after 30 days. These expression changes were confirmed at 87% by RT-PCR. We found 28 known genes regulated at both 15 and 30 days (96% confirmation by RT-PCR). The functional classification of the regulated genes highlights 3 major biological pathways modulated in aortic media during L-NAME administration: genes regulating cell proliferation, genes involved in the extracellular matrix remodeling, and genes of the NO/cGMP signaling pathway. CONCLUSIONS: As a consequence of the genomic approach, we observed a large increase in modulation of gene expression along the evolution of the model and the progressive implication of compensatory mechanisms, making expression profile analysis more complex.

Animals↗
PubMed2006

Identification of differentially expressed genes in virulent and nonvirulent Entamoeba species: potential implications for amebic pathogenesis.

Entamoeba histolytica is a protozoan parasite that causes colitis and liver abscesses. Several Entamoeba species and strains with differing levels of virulence have been identified. E. histolytica HM-1:IMSS is a virulent strain, E. histolytica Rahman is a nonvirulent strain, and Entamoeba dispar is a nonvirulent species. We used an E. histolytica DNA microarray consisting of 2,110 genes to assess the transcriptional differences between these species/strains with the goal of identifying genes whose expression correlated with a virulence phenotype. We found 415 genes expressed at lower levels in E. dispar and 32 genes with lower expression in E. histolytica Rahman than in E. histolytica HM-1:IMSS. Overall, 29 genes had decreased expression in both the nonvirulent species/strains than the virulent E. histolytica HM-1:IMSS. Interestingly, a number of genes with potential roles in stress response and virulence had decreased expression in either one or both nonvirulent Entamoeba species/strains. These included genes encoding Fe hydrogenase (9.m00419), peroxiredoxin (176.m00112), type A flavoprotein (6.m00467), lysozyme (6.m00454), sphingomyelinase C (29.m00231), and a hypothetical protein with homology to both a Plasmodium sporozoite threonine-asparagine-rich protein (STARP) and a streptococcal hemagglutinin (238.m00054). The function of these genes in Entamoeba and their specific roles in parasite virulence need to be determined. We also found that a number of the non-long-terminal-repeat retrotransposons (EhLINEs and EhSINEs), which have been shown to modulate gene expression and genomic evolution, had lower expression in the nonvirulent species/strains than in E. histolytica HM-1:IMSS. Our results, identifying expression profiles and patterns indicative of a virulence phenotype, may be useful in characterizing the transcriptional framework of virulence.

Animals↗
PubMed1999

On the homology of structures and Hox genes: the vertebral column.

Research on expression patterns of Hox genes has revealed a surprisingly high conservation among vertebrates. In agreement with this conservation, a correlation has been found between the anterior limits of expression areas of certain Hox genes and the borders between morphological regions of the vertebral axis. These similarities are striking and important, but also counterintuitive, unless there are strong selection pressures to protect this conservatism. It is important to identify the selective forces that maintain these conservative networks. These selective forces can be due to pleiotropy or to internal selection. Discussed are the selective factors that are involved in the evolutionary constraint on the number of cervical vertebral numbers in mammals. Factors involved are due to internal selection and involve susceptibility to cancer, stillbirths and neuronal problems. It is intriguing how similar genetic networks can lead to fundamentally different animals. Clearly the same genes are used for different purposes. It is therefore important to try to find these differences. The search, for homology between organisms, and the enthusiasm about similarities that come with it, at times impedes the discovery of such differences. I have searched the literature for differences within vertebrates in the functioning and expression patterns of Hox genes during the development of the vertebral axis. The ensuing implications for homology of structures and genes are discussed. The vertebral column is a promising model system for the evaluation of the relationship between homologous Hox genes and homologous structures because of the large conservation of Hox gene expression patterns along the anterior axis. However, extensive remodelling of the vertebrate column indicates that important changes in the genetic basis must have taken place. A survey of the literature indicates that the correlation between Hox gene expression areas and vertebral regions is not such that one can predict the borders between vertebral regions on the basis of Hox gene expression patterns. The involvement of Hox genes in the development of identity of vertebrae is complex and the problems regarding the value of gene expression patterns for the determination of anatomical homology are discussed.

Animals↗
PubMed2002

Prediction of temporal gene expression. Metabolic opimization by re-distribution of enzyme activities.

A computational approach is used to analyse temporal gene expression in the context of metabolic regulation. It is based on the assumption that cells developed optimal adaptation strategies to changing environmental conditions. Time-dependent enzyme profiles are calculated which optimize the function of a metabolic pathway under the constraint of limited total enzyme amount. For linear model pathways it is shown that wave-like enzyme profiles are optimal for a rapid substrate turnover. For the central metabolism of yeast cells enzyme profiles are calculated which ensure long-term homeostasis of key metabolites under conditions of a diauxic shift. These enzyme profiles are in close correlation with observed gene expression data. Our results demonstrate that optimality principles help to rationalize observed gene expression profiles.

Databases as Topic↗
PubMed2004

Differential pattern of expression and sugar regulation of Arabidopsis thaliana ADP-glucose pyrophosphorylase-encoding genes.

ADP-glucose pyrophoshorylase (ADP-Glc PPase) catalyzes the first and limiting step in starch biosynthesis. In plants, the enzyme is composed of two types of subunits (small and large) and is allosterically regulated by 3-phosphoglycerate and phosphate. The pattern of expression and sugar regulation of the six Arabidopsis thaliana ADP-Glc PPase-encoding genes (two small subunits, ApS1 and ApS2; and four large subunits, ApL1-ApL4) has been studied. Based on mRNA expression, ApS1 is the main small subunit or catalytic isoform responsible for ADP-Glc PPase activity in all tissues of the plant. Large subunits play a regulatory role, and the data presented define a clear functional distinction among them. ApL1 is the main large subunit in source tissues, whereas ApL3 and, to a lesser extent, ApL4 are the main isoforms present in sink tissues. Thus, in source tissues, ADP-Glc PPase would be finely regulated by the 3-phosphoglycerate/phosphate ratio, whereas in sink tissues, the enzyme would be dependent on the availability of substrates for starch synthesis. Sugar regulation of ADP-Glc PPase genes is restricted to ApL3 and ApL4 in leaves. Sugar induction of ApL3 and ApL4 transcription in leaves allows the establishment of heterotetramers less sensitive to the allosteric effectors, resembling the situation in sink tissues. The results presented on the expression pattern and sugar regulation allow us to propose a gene evolution model for the Arabidopsis ADP-Glc PPase gene family.

Adenosine Diphosphate↗
PubMed2025

A Functionally Conserved yet Dynamically Evolving Toolkit Underpinning Molluscan Biomineralization: Insights From Shell and Radula.

The molluscan shell and radula constitute pivotal molluscan innovations, each characterized by distinct functions and diverse forms, regulated by the highly specific biomineralization regulatory networks. Despite their paramount importance, the conserved components and adaptive evolutionary processes governing these regulatory networks remain unresolved. To address this knowledge gap, we advocate for the integration of data from less-explored lineages, such as Scaphopoda, as an essential step. This study presents the inaugural comprehensive transcriptome analysis of Pictodentalium vernedei, a representative species of Scaphopoda distinguished by a unique and evolutionarily conserved shell morphology and radula structure. Furthermore, comparative transcriptome/genome analyses are employed to unravel the conservatism and evolutionary innovation of the involved biomineralization regulatory elements. Our findings underscore the central role of secretomes in governing biomineralization processes, and we identified a fundamental set of 26 domains within molluscan secretomes, forming an essential functional protein domain repertoire necessary for the transformation of inorganic ions into biomineralized structures. This core biomineralization toolkit has undergone independent expansion and lineage-specific recruitment, giving rise to novel, modular domain architectures. This may be essential for the functional specialization and morphological diversification of shell and radula structures. These evolutionary processes are driven by the independent co-option of ancient genes and the emergence of novel de novo genes. This comprehensive investigation not only contributes insights into the evolution of molluscan biomineralization structures but also establishes avenues for further scholarly exploration.

Animals↗
PubMed2001

Shigella flexneri LuxS quorum-sensing system modulates virB expression but is not essential for virulence.

Quorum-sensing systems regulate the expression of virulence factors in a wide variety of plant and animal pathogens, including members of the Enterobacteriaceae. Studies of Shigella virulence gene expression have demonstrated that maximal expression of genes encoding the type III secretion system and its substrates and maximal activity of this virulence organelle occur at high cell density. In these studies, we demonstrate that the expression of ipa, mxi, and spa invasion operons is maximal in stationary-phase bacteria and that conditioned media derived from stationary-phase cultures enhance the expression of these loci. In contrast, expression of virB, a transcription factor essential for the expression of invasion loci, peaks in late log phase; accordingly, virB expression is enhanced by a signal(s) present in conditioned media derived from late-log-phase cultures. Autoinducer 2 (AI-2), a quorum signaling molecule active in late log phase, was synthesized by Shigella species and enteroinvasive Escherichia coli and shown to be responsible for the observed peak of virB expression. However, AI-2 does not influence invasion operon expression and is not required for Shigella virulence, as mutants deficient in AI-2 synthesis are fully virulent. The implications of these findings with regard to both virB and invasion operon expression and the evolution of circuitries governing virulence gene expression are discussed.

Animals↗
PubMed2002

Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene.

Processed genes are created by retroposition from messenger RNA of expressed genes. The estimated amount of processed copies of genes in the human genome is 10,000-14,000. Some of these might be pseudogenes with the expected pattern for nonfunctional sequences, but some others might be an important source of new genes. We have studied the evolution of a Phosphoglycerate mutase processed gene (PGAM3) described in humans and believed to be a pseudogene. We sequenced PGAM3 in chimpanzee and macaque and obtained polymorphism data for human coding region. We found evidence that PGAM3 likely produces a functional protein, as an example of addressing functionality for human processed pseudogenes. First, the open reading frame was intact despite many deletions that occurred in the 3' untranslated region. Second, it appears that the gene is expressed. Finally, interspecies and intraspecies variation for PGAM3 was not consistent with the neutral model proposed for pseudogenes, suggesting that a new functional primate gene has originated. Amino acid divergence was significantly higher than synonymous divergence in PGAM3 lineage, supporting positive selection acting in this gene. This role of selection was further supported by the excess of rare alleles in a population genetic analysis. PGAM3 is located in a region of very low recombination; therefore, it is conceivable that the rapid fixation events in this newly arising gene may have contributed to a selective sweep of variation in the region.

Amino Acid Sequence↗
PubMed2003

Translational selection and yeast proteome evolution.

The primary structures of peptides may be adapted for efficient synthesis as well as proper function. Here, the Saccharomyces cerevisiae genome sequence, DNA microarray expression data, tRNA gene numbers, and functional categorizations of proteins are employed to determine whether the amino acid composition of peptides reflects natural selection to optimize the speed and accuracy of translation. Strong relationships between synonymous codon usage bias and estimates of transcript abundance suggest that DNA array data serve as adequate predictors of translation rates. Amino acid usage also shows striking relationships with expression levels. Stronger correlations between tRNA concentrations and amino acid abundances among highly expressed proteins than among less abundant proteins support adaptation of both tRNA abundances and amino acid usage to enhance the speed and accuracy of protein synthesis. Natural selection for efficient synthesis appears to also favor shorter proteins as a function of their expression levels. Comparisons restricted to proteins within functional classes are employed to control for differences in amino acid composition and protein size that reflect differences in the functional requirements of proteins expressed at different levels.

Adaptation, Physiological↗
PubMed1997

H3.3A variant histone mRNA containing an alpha-globin insertion: modulated expression during mouse gametogenesis correlates with meiotic onset.

Replacement-variant H3.3 histones have been isolated and sequenced in different eukaryotes, but no functional H3.3A gene has been characterized in the mouse so far. We have cloned an H3.3A cDNA from a mouse fetal ovary library, differentially screened with testis versus somatic cDNA probes. We showed this gene contains a region homologous to the reverse and complementary alpha-globin gene. We believe such a structure could have been generated by retroposition during the evolution of both globin and histone gene families. The sequence coding for H3.3A is 76.6% homologous to the mouse H3.3B gene at the nucleotide level and differs in only one amino acid at the protein level. The high degree of homology between these genes and the H3.3 variant histones from other eukaryotes reveals the conservation of these replication-independent class of histones throughout evolution. Analysis of gene expression reveals a developmental regulation concurrent with meiotic progression, with the highest level of transcript detection coincident with meiotic onset during both oogenesis and spermatogenesis.

Amino Acid Sequence↗
PubMed2003

Induced gene expression in human brain after the split from chimpanzee.

Despite only approximately 1% difference in genomic DNA sequence, humans and chimpanzees differ considerably in mental and linguistic capabilities, and in susceptibility to some diseases. A recent comparison of gene expression in human and great apes cast some light on the genetic basis of these differences, but more rigorous study is required. Our statistical reanalysis of these microarray data shows that there have indeed been dramatic alterations in the expression of genes in the human brain since the split from chimpanzees, mainly caused by a set of genes with increased (rather than decreased) expression in the human brain.

Animals↗
PubMed2003

Neurone-specific expression and regulation of the pufferfish isotocin and vasotocin genes in transgenic mice.

We used comparative genetics to investigate the location, structure and evolution of the oxytocin and vasopressin gene regulatory regions. The pufferfish, Fugu rubripes, is an attractive vertebrate model for comparison because of its maximal evolutionary distance from mammals and short intergenic regions. To determine whether regulatory DNA is conserved between oxytocin and vasopressin, and their Fugu homologs, isotocin and vasotocin, we generated transgenic mice bearing overlapping Fugu cosmids that contained the isotocin and/or vasotocin genes as well as short isotocin (5 kb) and vasotocin (9 kb) constructs. Our study shows that the Fugu isotocin and vasotocin genes express specifically in the mouse oxytocinergic and vasopressinergic neurones, respectively, and that the cis-regulatory elements which mediate neurone-specific expression are located within the short transgene constructs tested. Thus, the neurone-specific expression of the oxytocin and vasopressin gene families, and the mechanisms mediating the cell-specificity, evolved before the divergence of the fish and mammalian lineages. Salt-loading of transgenic mice induced an increase in abundance of isotocin, but not vasotocin mRNA in the cognate neurones. It appears that either the vasotocin gene does not respond to osmotic perturbations or the vasotocin transgene construct tested lacks osmotic response elements. Comparisons of homologous flanking sequences of the Fugu and mouse genes identified several short matching sequences, which are candidate regulatory elements.

Animals↗