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PubMed2002

The human-specific Yp11.2/Xq21.3 homology block encodes a potentially functional testis-specific TGIF-like retroposon.

Yp11.2/Xq21.3 is a human-specific homology block that constitutes the largest shared region among the sex chromosomes, spanning some 3.5 Mb. Only two transcribed sequences have been mapped to this segment: the protocadherin genes PCDHX/Y, and the X-linked poly(A)-binding protein PABPC5 gene, whose Y-homolog has been lost during human evolution. This paper reports the genomic structure, expression, and evolutionary conservation of a third (X-Y homologous) transcribed sequence, TGIFLX/Y (TGIF-like X/Y), mapping to this region. TGIFLX/Y has a 2666-bp mRNA encoded by two exons separated by a 96-bp intron. TGIFLX/Y are homeodomain-containing genes related to the TALE superclass gene family. Comparative DNA analysis indicates that TGIFLX originated from retrotransposition of TGIF2, located on 20q11.2-12, onto the X Chromosome. RT-PCR analysis reveals that both X- and Y-linked genes are specifically expressed in adult testis. Cloning and sequencing of TGIFLX homologs in hominoids and Old World monkeys provides evidence for an open reading frame in the eight species studied. Interestingly, a single base pair deletion in the human TGIFLY (as compared with TGIFLX) creates a different reading frame where the C-terminal residues shared by TGIFLX and other TGIF proteins are missing. The conservation, similarity to protein-encoding transcription factors, and specific expression in testis points to a transcriptional role for TGIFLX/Y in this tissue.

Amino Acid Sequence↗
PubMed2004

Genomic organization and analysis of the hairless gene in four hypotrichotic rat strains.

More than 25 different hypotrichotic mutations have been described in laboratory rats, yet the molecular basis for these mutations has not been determined for most of these phenotypes. Their similarity to the hairless (hr) mutations described in mice suggests a possible role for the hairless gene in the formation of rat hypotrichotic phenotypes, though whether hr is responsible for these rat phenotypes has yet to be determined. Therefore, in order to understand the basis for the rat hypotrichotic phenotypes and their relationship to the hr gene, we determined the genomic organization of the hr gene and subsequently analyzed the coding sequence in four hypotrichotic rat strains. Analysis revealed that the first two exons of the mouse, monkey, and human hr gene were fused in the rat gene, while the rest of the gene showed strong evolutionary conservation. Despite their designation as "hairless," no mutations within the coding sequences were identified, indicating that the "hairless" phenotype in all four hypotrichotic rat strains are not allelic with hr.

Alleles↗
PubMed2006

Cloning of the bovine prion-like Shadoo (SPRN) gene by comparative analysis of the predicted genomic locus.

SPRN is a new prion-like gene coding for Sho, a protein with significant similarity to PrP. SPRN was initially described in zebrafish; however, the strong evolutionary conservation led to the hypothesis that SPRN might be the ancestral prion-like gene. We mapped SPRN in Bos taurus by comparative analysis of the locus and of the predicted flanking genes. BACs, spanning the whole SPRN genomic locus, were assigned to BTA26q23 by radiation hybrid mapping and fluorescent in situ hybridization (FISH). Sequencing of five genes flanking SPRN, namely, ECHS1, PAOX, MTG1, SPRN, and CYP2E1, high-resolution FISH on mechanically stretched chromosomes, and combed BAC DNA allowed us to establish their order and reciprocal orientation. The results confirmed that BTA26q23 corresponds to HSA10q24.3-26.3, which is the site where the human SPRN is located. The gene order in Bos taurus is the same as in man, cen-ECHS1-PAOX-MTG1-SPRN-CYP2E1-tel, but PAOX has a different orientation in the two species. SPRN has the typical two-exon PRNP arrangement, with the CDS fully contained within exon 2; furthermore, it codes for a 143-amino-acid protein with 74.8% identity and 84.7% similarity with the human PRNP. RT-PCR and Northern blot analysis showed that SPRN is expressed at high levels in brain and less in testis and lung.

Animals↗
PubMed1996

Molecular cloning of a mammalian ABC transporter homologous to Drosophila white gene.

Pigmentation of Drosophila eyes requires the concerted action of several genes, most of which have been cloned and characterized. Three of them, white, brown, and scarlet, have been directly implicated in the import of pigment precursors into the cells. These three genes encode similar proteins, belonging to the evolutionary conserved family of ATP Binding Cassette transporters. The identification of a novel mouse gene, ABC8, closely related to white is reported here, together with an analysis of its expression profile and its comparative mapping in mouse and human genome.

ATP-Binding Cassette Transporters↗
PubMed1999

The physiological role of presenilins in cellular differentiation: lessons from model organisms.

Mutations in the human presenilin genes cause the most frequent and aggressive forms of Alzheimer's Disease. They results in an increase of the 42 amino acid variant of amyloid beta peptide that rapidly aggregates into neurotoxic plaques. In addition, lack of presenilin activity prevents the proteolytic cleavage of the Notch receptor of intercellular signaling. The biological role of presenilins is evolutionary conserved in animals. This review summarizes recent results obtained from animal models to understand presenilin activity and malfunction.

Alzheimer Disease↗
PubMed2006

The cenH3 histone variant defines centromeres in Giardia intestinalis.

Histone H3 variants play critical roles in the functional specialization of chromatin by epigenetically marking centromeric chromatin and transcriptionally active or silent genes. Specifically, the cenH3 histone variant acts as the primary epigenetic determinant of the site of kinetochore assembly at centromeres. Although the function of histone variants is well studied in plants, animals, and fungi, there is little knowledge of the evolutionary conservation of histone variants and their function in most protists. We find that Giardia intestinalis--a diplomonad parasite with two equivalent nuclei--has two phylogenetically distinct histone H3 variants with N-terminal extensions and nonconserved promoters. To determine their role in chromatin dynamics, conventional H3 and the two H3 variants were GFP-tagged, and their subcellular location was monitored during interphase and mitosis. We demonstrate that one cenH3-like variant has a conserved function in epigenetically marking centromeres. The other H3 variant (H3B) has a punctate distribution on chromosomes, but does not colocalize with active transcriptional regions as indicated by H3K4 methylation. We suggest that H3B could instead mark noncentromeric heterochromatin. Giardia is a member of the Diplomonads and represents an ancient divergence from metazoans and fungi. We confirm the ancient role of histone H3 variants in modulating chromatin architecture, and suggest that monocentric chromosomes represent an ancestral chromosome morphology.

Amino Acid Sequence↗
PubMed2025

Phosphorylation as a regulatory mechanism of HP1 protein multifunctionality.

The Heterochromatin Protein 1 (HP1) family proteins are key regulators of chromatin structure and genome function, acting as "reader" proteins that recognize and bind to histone H3 lysine 9 methylation (H3K9me). Beyond their canonical role in heterochromatin formation and transcriptional repression, HP1 proteins exhibit functional versatility, participating in transcriptional activation, RNA processing, DNA repair, and chromosome segregation. This multifunctionality is mediated partially by post-translational modifications (PTMs), with phosphorylation emerging as a central regulatory mechanism. This review explores the diverse effects of HP1 phosphorylation on protein function and chromatin interactions, focusing on Drosophila melanogaster HP1a and its orthologs, mammalian HP1α and S. pombe Swi6. Phosphorylation in the N-terminal tail enhances HP1's affinity for H3K9me, promoting transcriptional silencing. Mitotic phosphorylation of serine residues in the hinge region, regulated by kinases such as AURKB and NDR1/2, leads to chromatin release and relocalization to the kinetochore, enabling proper chromosome segregation. Additionally, phosphorylation modulates HP1 phase separation dynamics, influencing nuclear compartmentalization and chromatin condensation. These findings highlight phosphorylation as a versatile molecular switch that enables HP1 proteins to transition between structural and regulatory roles, contributing to their evolutionary conserved multifunctionality in genome regulation and cell division. Further investigation into HP1 phosphorylation across species and contexts is essential to fully understand its contributions to chromatin biology.

Phosphorylation↗
PubMed1999

A T-type calcium channel from mouse brain.

A member of the low-voltage-activated calcium channel family was identified in mouse brain by taking advantage of amino acid sequences that have been evolutionary conserved. The identified sequence is similar to that of the recently cloned rat alpha1G T-type calcium channel, but there are differences in two insertions in the intracellular connecting loops. Northern blot analysis indicates that its expression is strong in the brain. In situ hybridization revealed that, in mouse brain, the alpha1G mRNA is found in the cerebellum, hippocampus, thalamus and olfactory bulb. In contrast to L-type calcium channel currents, IBa and ICa through the alpha1G channel expressed in HEK293 cells did not differ in terms of current density, voltage dependence of current activation, inactivation and deactivation, and speed of recovery from voltage-dependent inactivation. The kinetics of ICa inactivation were significantly slower than those of IBa. The expressed alpha1G channel has a relatively high sensitivity to mibefradil, but is only slightly affected by Ni2+.

Amino Acid Sequence↗
PubMed2006

Polarised expression of FoxB and FoxQ2 genes during development of the hydrozoan Clytia hemisphaerica.

We have characterised the expression of four genes coding for Forkhead box-containing ('Fox') transcription factors identified from the hydrozoan (Leptomedusa) Clytia hemisphaerica. Phylogenetic analyses including all available non-bilaterian Fox sequences placed these genes in subfamilies B, Q2 (two genes) and O, and indicated that at least 17 Fox subfamilies were present in the common cnidarian/bilaterian ancestor, with multiple subsequent losses in cnidarian lineages. Chordate FoxB and FoxQ2A subfamily genes show polarised expression in early embryos. Correspondingly, Clytia CheFoxB expression was localised around the gastrulation site (future oral pole) at blastula and gastrula stages, with CheFoxQ2a expressed in a complementary aboral domain, maintained through larval development. Distinct later expression domains were observed for CheFoxB in the larval endoderm region, and in the statocyst, gonad and tentacle bulb of the medusa. A second Clytia FoxQ2 gene, CheFoxQ2b, not expressed in the embryo, larva or polyp, was detected uniquely in the gonads of the medusa. In contrast, CheFoxO, whose sequence indicates regulation by the PI3-Kinase/PKB signalling pathway consistent with known roles in bilaterian developmental regulation, was detected throughout the Clytia life cycle. CheFoxO expression was enhanced in regions associated with growth control including larval poles, gonad and the margin of the medusa bell. These results support the idea that an early embryonic patterning system involving FoxB and FoxQ2 family genes has been evolutionary conserved and indicate that Fox family genes have also acquired distinct roles during other phases of the hydrozoan life cycle.

Amino Acid Sequence↗
PubMed2006

Cloning and developmental expression of the Xenopus homeobox gene Xvsx1.

In contrast to the high degree of evolutionary conservation of the Vsx2/Chx10 gene family, vertebrate orthologues of Vsx1 display more divergent sequences and spatio-temporal expression patterns. Here, we report the cloning and expression pattern of Xenopus laevis Vsx1. Differently from the mouse and zebrafish orthologues, Xvsx1 transcription is activated at early neurula both in the evaginating eye vesicles and in the presumptive spinal cord. Compared to other retinal homeobox genes, such as Xrx1, Xsix3 and Xpax6, Xvsx1 is activated at a later stage; in addition, its anterior expression appears to be more specifically restricted to the retina. At tail bud stage, Xvsx1 expression in retinal progenitors persists, and its neural tube expression, which in the spinal cord corresponds to interneurons, progressively expands anteriorly reaching the midbrain-hindbrain boundary. During retinal neurogenesis, Xvsx1 expression is maintained in retinal progenitors and in a peripheral region of the ciliary marginal zone, while in the central retina, it becomes restricted to differentiated bipolar cells.

Amino Acid Sequence↗
PubMed2000

Amphicoup-TF, a nuclear orphan receptor of the lancelet Branchiostoma floridae, is implicated in retinoic acid signalling pathways.

In vertebrates, the orphan nuclear receptors of the COUP-TF group function as negative transcriptional regulators that inhibit the hormonal induction of target genes mediated by classical members of the nuclear hormone superfamily, such as the retinoic acid receptors (RARs) or the thyroid hormone receptors (TRs). To investigate the evolutionary conservation of the roles of COUP-TF receptors as negative regulators in the retinoid and thyroid hormone pathways, we have characterized AmphiCOUP-TF, the homologue of COUP-TFI and COUP-TFII, in the chordate amphioxus (Branchiostoma floridae), the closest living invertebrate relative of the vertebrates. Electrophoretic mobility shift assays (EMSA) showed that AmphiCOUP-TF binds to a wide variety of response elements, as do its vertebrate homologues. Furthermore, AmphiCOUP-TF is a transcriptional repressor that strongly inhibits retinoic acid-mediated transactivation. In situ hybridizations revealed expression of AmphiCOUP-TF in the nerve cord of late larvae, in a region corresponding to hindbrain and probably anterior spinal cord. Although the amphioxus nerve cord appears unsegmented at the gross anatomical level, this pattern reflects segmentation at the cellular level with stripes of expressing cells occurring adjacent to the ends and the centers of each myotomal segment, which may include visceral motor neurons and somatic motor neurons respectively, among other cells. A comparison of the expression pattern of AmphiCOUP-TF with those of its vertebrate homologues, suggests that the roles of COUP-TF in patterning of the nerve cord evolved prior to the split between the amphioxus and vertebrate lineages. Furthermore, in vitro data also suggest that Amphi-COUP-TF acts as a negative regulator of signalling by other nuclear receptors such as RAR, TR or ER.

Animals↗
PubMed2002

Expression of Kin, a nuclear protein binding to curved DNA, in the brain of the frog (Rana esculenta), turtle (Trachemys scripta), quail (Coturnix coturnix) and mouse (Mus musculus).

The distribution of Kin protein, the vertebrate homologue of the bacterial recA nuclear protein involved in illegitimate recombinant DNA repair and gene regulation, was analysed in the brain of the mouse, quail, turtle and frog by immunocytochemical methods. The protein was expressed in all brains, but not in a uniform manner. Immunoreactivity was absent from major fibre tracts. In the cerebral nuclei, immunolabelling in the various species showed an important variation. A comparative analysis, based on the homologies between different brain structures in these species, showed that this variation was not due to interspecific variation but that of an ancestral pattern of distribution of Kin protein. It is also shown that whatever the species examined, Kin protein is consistently more highly expressed in those regions of the brain with a conservative evolutionary history (e.g. the olfactory and limbic systems, the hypothalamus, the monoaminergic system, the cerebellum, and the nuclei of sensory and motor cranial nerves). The protein is markedly less heavily expressed in the dorsal striatum and the sensory nuclei of the thalamus.

Animals↗
PubMed2006

Expression pattern of BMPs during chick limb development.

In vertebrates, BMPs (bone morphogenic proteins) play critical roles in establishing the basic embryonic body plan and are involved in the development of a large variety of organs and tissues. Here, we analyzed the expression pattern of various BMPs (2, 4, 5 and 7) by whole mount in situ hybridization during chick limb development. In limb, expression of BMPs suggests evolutionary conserved mechanisms of BMP-dependent differentiation between lower and higher vertebrates. During the early developmental stages, BMP-2 and BMP-7 are expressed in the posterior distal mesenchyme leaving a less prominent expression anteriorly. BMP-4 is initially expressed in the anterior mesenchyme and spreads later to the whole mesenchyme leaving a stronger expression at the anterior side. From HH-stage 25, expression of BMP-4 is observed in the anterior-posterior margins of the limb bud. The BMPs 2, 4 and 7 are expressed strongly in the AER, whereas BMP-5 is expressed as a weak signal in the distal mesoderm during the early stages of limb development. Later from HH-stage 25 onwards, BMP-5 is expressed in the dorsal and ventral muscular mass of the developing limb. As digits become identifiable, expression of BMPs are observed in the interdigital mesenchyme and can also be detected along the contours of the developing phalanges and at the distal tips of the digits. All these BMPs are found to be expressed in the developing feather buds from day 8 onwards.

Animals↗
PubMed2005

Characterization of Na, K-ATPase genes in Atlantic salmon (Salmo salar) and comparative genomic organization with rainbow trout (Oncorhynchus mykiss).

A combination of molecular and in silico approaches was employed to assemble a survey of Na, K-ATPase genes contained in the ancestrally tetraploid genome of the Atlantic salmon (Salmo salar). Molecular characterization of genomic clones coding for the alpha subunit revealed two single genes (alpha1a and alpha2) and two pairs of presumably homeologous genes (alpha1b/i-ii and alpha1c/i-ii). Each of the six genes showed high sequence similarity to isoforms previously isolated from rainbow trout and extensive structural differences relative to putative orthologs in the human genome. In silico analysis of expressed sequence tag (EST) collections indicated that at least five alpha (alpha1a, alpha1b, alpha1c, alpha2, and alpha3) and four beta (beta1a, beta1b, beta2, and beta3b) subunit isoforms are expressed in Atlantic salmon. Meiotic linkage analysis further showed that Na, K-ATPase genes are dispersed throughout the salmon genome, with the exception of two multigene clusters on linkage groups AS-22 and AS-28. Duplicate gene copies for the isoform alpha1b were assigned to linkage groups with multiple homeologous anchors (AS-22 and AS-23), while beta2 duplicates suggested a new homeologous affinity between AS-05 and AS-28. In addition, the comparison of linkage arrangements with rainbow trout also showed that the genomic organization of Na, K-ATPase genes is consistent with the evolutionary conservation of syntenic chromosome regions between these species.

Amino Acid Sequence↗
PubMed2005

Analysis of missense variants in the PKHD1-gene in patients with autosomal recessive polycystic kidney disease (ARPKD).

Autosomal recessive polycystic kidney disease (ARPKD) is a severe form of polycystic kidney disease characterized by enlarged kidneys and congenital hepatic fibrosis. Given the poor prognosis for the majority of children with the severe perinatal ARPKD phenotype, there is a regular request for prenatal testing. ARPKD is caused by mutations in the polycystic kidney and hepatic disease 1 (PKHD1) gene, which consists of 86 exons that are variably assembled into a number of alternatively spliced transcripts. The longest transcript, comprising 67 exons, encodes the protein fibrocystin/polyductin. We have set up mutation analysis by direct sequencing of these 67 exons. In 39 mainly Dutch families we identified: 11 nonsense mutations, 15 deletions/insertions, 5 splice site mutations, and 39 missense mutations. To classify missense variants we combined evolutionary conservation, using the human, chimpanzee, dog, mouse, chicken and frog Pkhd1 sequences, with the Grantham score for chemical differences. Thirty-three missense mutations were considered pathogenic and seven were classified as rare, probably pathogenic variants. In addition to sequence analysis, multiplex ligation-dependent probe amplification (MLPA) was used to identify multiple exon deletions. However, no large deletions in the PKHD1 gene were identified. In 31 index patients two mutations were found, in 6 patients one mutation was found, leading to a mutation detection rate of 87%. The analysis of amino acid conservation as well as applying the Grantham score for chemical differences allowed us to determine the pathogeneity for nearly all new missense mutations and thus proved to be useful tools to classify missense variants.

Amino Acid Sequence↗
PubMed2000

Characterization of the human complex I NDUFB7 and 17.2-kDa cDNAs and mutational analysis of 19 genes of the HP fraction in complex I-deficient-patients.

Deficiency of NADH:ubiquinone oxidoreductase, the first enzyme complex of the mitochondrial respiratory chain, is one of the most frequent causes of human mitochondrial encephalomyopathies. A relatively small percentage of human complex I deficiency is associated with mitochondrial DNA mutations. cDNA characterization and mutational analysis of the structural complex I genes in 19 complex I-deficient patients, in whom common mtDNA mutations have been excluded, has so far revealed five patients with alterations in evolutionary conserved nuclear-encoded proteins. In order to complete our knowledge about the expected 36 structural nuclear complex I genes, we characterized the NDUFB7 and the 17.2-kDa cDNA sequences of the hydrophobic (HP) fraction of the complex. Subsequently, we screened all subunits of this fraction for the presence of mutations in those 14 patients of our initial patient cohort in whom the underlying genetic cause had not been elucidated. Strikingly, no pathogenic mutations were found in the HP subunits that would explain the complex I deficiency in our patients. Other strategies are needed to unravel proteins involved in the pathogenesis of the complicated cellular network of transcription until correct assemblage of complex I.

Amino Acid Sequence↗
PubMed1998

A common point mutation in the tyrosine hydroxylase gene in autosomal recessive L-DOPA-responsive dystonia in the Dutch population.

This report concerns one new mutation in the tyrosine hydroxylase (TH) gene in three patients originating from three unrelated Dutch families with autosomal recessive L-DOPA-responsive dystonia (DRD). In this study, all exons of the TH gene were amplified by the polymerase chain reaction and subjected to analyses by single-strand conformation polymorphism. An aberrant migration pattern was observed for exon 6 of the TH gene in all patients. Direct sequencing of the coding region of exon 6 revealed the presence of one novel missense mutation. An a698g transition resulted in the substitution of the evolutionary conserved arginine 233 by a histidine (R233H). All patients were homozygous for the mutation. This new mutation in the TH gene was confirmed by restriction enzyme analysis with the restriction enzyme HhaI. Thus, a high proportion of defective TH alleles may be R233H in The Netherlands.

Chromosomes, Human, Pair 11↗
PubMed2000

Age-dependent memory loss, synaptic pathology and altered brain plasticity in the Drosophila mutant cardinal accumulating 3-hydroxykynurenine.

A search for Drosophila mutants with phenotypes similar to human diseases might help to unravel evolutionary conserved genes implicated in polygenic human disorders. Among these are neurodegenerative diseases, characterized by a late onset disturbance of memory, synaptic and glial pathology, structural brain impairments and altered content of the intermediates of the kynurenine pathway, the modulators of glutamate excito- and oxidative toxicity. This pathway is conserved in insects, in rodents, and in humans. We tested the Drosophila mutants cardinal (3-hydroxykynurenine excess) and cinnabar (kynurenic acid excess) for age-dependent changes in memory, synaptic pathology, structural brain plasticity and glial immunoreactivity. The mutant cardinal demonstrated a decline in learning and memory from the 12th to the 29th day of life in a paradigm of conditioned courtship suppression. Memory decline was accompanied by a sharp decrease in immunoreactivity to the synaptic cysteine string protein, and alterations in volumetric parameters of the mushroom bodies, the brain structures implicated in memory.

Age Factors↗