Antonio Garcia-España

Appearance of new tetraspanin genes during vertebrate evolution

A detailed phylogenetic analysis of tetraspanins from 10 fully sequenced metazoan genomes and several fungal and protist genomes gives insight into their evolutionary origins and organization. Our analysis suggests that the superfamily can be divided into four large families. These four families-the CD family, CD63 family, uroplakin family, and RDS family-are further classified as consisting of several ortholog groups. The clustering of several ortholog groups together, such as the CD9/Tsp2/CD81 cluster, suggests functional relatedness of those ortholog groups. The fact that our studies are based on whole genome analysis enabled us to estimate not only the phylogenetic relationships among the tetraspanins, but also the first appearance in the tree of life of certain tetraspanin ortholog groups. Taken together, our data suggest that the tetraspanins are derived from a single (or a few) ancestral gene(s) through sequence divergence, rather than convergence, and that the majority of tetraspanins found in the human genome are vertebrate (21 instances), tetrapod (4 instances), or mammalian (6 instances) inventions.

Medaka Oct4 is expressed during early embryo development, and in primordial germ cells and adult gonads

Oct4 is a crucial transcription factor for controlling pluripotency in embryonic stem cells and the epiblast of mouse embryos. We have characterized the expression pattern of medaka (Oryzias latipes) Ol‐Oct4 during embryonic development and in the adult gonads. Genomic analysis showed that Ol‐Oct4 is the ortholog of zebrafish spg/pou2. However, their expression patterns are not the same, suggesting that Oct4 may play different roles in zebrafish and medaka. Using specific antibodies for the Ol‐Oct4 protein, we showed that Ol‐Oct4 is also expressed in primordial germ cells, in the spermatogonia (male germ stem cells), and during different stages of oocyte development. These results suggest that Ol‐Oct4 plays a post‐embryonic role in the maturing gonads and gametes. The Ol‐Oct4 mRNA and protein expression patterns are similar to those of mammalian Oct4 and introduce medaka fish as a valid model for the functional and evolutionary study of pluripotency genes in vivo. Developmental Dynamics 239:672–679, 2010.

Nanog Regulates Proliferation During Early Fish Development

Nanog is involved in controlling pluripotency and differentiation of stem cells in vitro. However, its function in vivo has been studied only in mouse embryos and various reports suggest that Nanog may not be required for the regulation of differentiation. To better understand endogenous Nanog function, more animal models should be introduced to complement the murine model. Here, we have identified the homolog of the mammalian Nanog gene in teleost fish and describe the endogenous expression of Ol‐Nanog mRNA and protein during medaka (Oryzias latipes) embryonic development and in the adult gonads. Using medaka fish as a vertebrate model to study Nanog function, we demonstrate that Ol‐Nanog is necessary for S‐phase transition and proliferation in the developing embryo. Moreover, inhibition or overexpression of Ol‐Nanog does not affect gene expression of various pluripotency and differentiation markers, suggesting that this transcription factor may not play a direct role in embryonic germ layer differentiation. STEM CELLS 2009;27:2081–2091

Activity-Dependent Phosphorylation of Tyrosine Hydroxylase in Dopaminergic Neurons of the Rat Retina

We studied in vivo activity-dependent phosphorylation of tyrosine hydroxylase (TH) in dopaminergic (DA) neurons of the rat retina. TH phosphorylation (TH-P) was evaluated by immunocytochemistry, using antibodies specific for each of three regulated phosphorylation sites. TH synthesis rate was measured by dihydroxyphenylalanine (DOPA) accumulation in the presence of NSD-1015, an inhibitor of aromatic amino acid decarboxylase. TH-P was increased markedly by light or after intraocular injection of GABAA and glycine inhibitors. All three phosphospecific antibodies responded similarly to test drugs or light. A 30 min exposure to light increased DOPA accumulation by threefold over that seen after 30 min in darkness. Immunostaining to an anti-panNa channel antibody was found in all parts of the DA neuron. TTX blocked TH-P induced by light or GABA/glycine inhibitors but only in varicosities of the DA axon plexus, not in perikarya or dendrites. Veratridine increased TH-P in all parts of the DA neuron. The distribution of the monoamine vesicular transporter 2 was shown by immunocytochemistry to reside in varicosities of the DA plexus but not in dendrites, indicating that the varicosities are sites of dopamine release. Collectively, these data indicate that, in the retina, dopamine synthesis in varicosities is affected by the spiking activity of retinal neurons, possibly including that of the DA neurons themselves.

Differential Expression of Cell Cycle Regulators in Phenotypic Variants of Transgenically Induced Bladder Tumors: Implications for Tumor Behavior

Proteins controlling cell growth, differentiation, apoptosis, and oncogenic stress are often deregulated in tumor cells. However, whether such deregulations affect tumor behavior remains poorly understood in many tumor types. We recently showed that the urothelium-specific expression of activated H-ras and SV40 T antigen in transgenic mice produced two distinctive types of tumors strongly resembling the human superficial papillary tumors and carcinoma in situ of the bladder, respectively. Here we assessed the expression of a key set of cell cycle regulators in these mouse tumors and in a new transgenic line expressing a cyclin D1 oncogene in the urothelium. We found that urothelia of the wild-type and cyclin D1 transgenic mice exhibited a profile of cell cycle regulators found in quiescent (G(0)) cells, indicating that urothelium overexpressing the cyclin D1 (an 8-fold increase) is reminiscent of normal urothelium and remains slow-cycling. Low-grade superficial papillary tumors induced by activated H-ras had no detectable Rb family proteins (Rb, p107, and p130) and late cell cycle cyclins and kinases (cyclin A, E, and CDK1), but had increased level of p16, p53, and MDM2. These data suggest that the inactivation of the Rb pathway plays an important role in H-ras-induced superficial papillary tumors and that oncogenic H-ras can induce a compensatory activation of alternative tumor suppressor pathways. In contrast, carcinoma in situ of the bladder induced by SV40 T antigen had increased expression of cell cycle regulators mainly active in post-G(1) phases. The fact that phenotypically different bladder tumors exhibit different patterns of cell cycle regulators may explain why these tumors have different propensity to progress to invasive tumors. Our results indicate that the transgenic mouse models can be used not only for studying tumorigenesis but also for evaluating therapeutic strategies that target specific cell cycle regulators.

Diurnal and Circadian Variation of Protein Kinase C Immunoreactivity in the Rat Retina

We studied the dependence of the expression of protein kinase C immunoreactivity (PKC‐IR) in the rat retina on the light:dark (LD) cycle and on circadian rhythmicity in complete darkness (DD). Two anti‐PKC alpha antibodies were employed: One, which we call PKCαβ recognized the hinge region; the other, here termed PKCα, recognized the regulatory region of the molecule. Western blots showed that both anti‐PKC antibodies stained an identical single band at approximately 80 kD. The retinal neurons showing PKC‐IR were rod bipolar cells and a variety of amacrine neurons. After 3 weeks on an LD cycle, PKCαβ‐IR in both rod bipolar and certain amacrine cells manifested a clear rhythm with a peak at zeitgeber time (ZT) of 06–10 hours and a minimum at ZT 18. No rhythm in total PKC‐IR was observed when using the PKCα antibody, but, at ZT 06–10 hours, rod bipolar axon terminals showed increased immunostaining. After 48 hours in DD, with either antibody, rod bipolar cells showed increased PKC‐IR. The PKCα antibody alone revealed that, after 48 hours, AII amacrine neurons, which lacked PKC‐IR in an LD cycle, manifested marked PKC‐IR, which became stronger after 72 hours. Light administered early in the dark period greatly increased PKCαβ‐IR in rod bipolar and some amacrine neurons. Our data indicate that light and darkness exert a strong regulatory influence on PKC synthesis, activation, and transport in retinal neurons. J. Comp. Neurol. 439:140–150, 2001.

Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins.

Background Although large scale informatics studies on introns can be useful in making broad inferences concerning patterns of intron gain and loss, more specific questions about intron evolution at a finer scale can be addressed using a gene family where structure and function are well known. Genome wide surveys of tetraspanins from a broad array of organisms with fully sequenced genomes are an excellent means to understand specifics of intron evolution. Our approach incorporated several new fully sequenced genomes that cover the major lineages of the animal kingdom as well as plants, protists and fungi. The analysis of exon/intron gene structure in such an evolutionary broad set of genomes allowed us to identify ancestral intron structure in tetraspanins throughout the eukaryotic tree of life. Methodology/Principal Findings We performed a phylogenomic analysis of the intron/exon structure of the tetraspanin protein family. In addition, to the already characterized tetraspanin introns numbered 1 through 6 found in animals, three additional ancient, phase 0 introns we call 4a, 4b and 4c were found. These three novel introns in combination with the ancestral introns 1 to 6, define three basic tetraspanin gene structures which have been conserved throughout the animal kingdom. Our phylogenomic approach also allows the estimation of the time at which the introns of the 33 human tetraspanin paralogs appeared, which in many cases coincides with the concomitant acquisition of new introns. On the other hand, we observed that new introns (introns other than 1–6, 4a, b and c) were not randomly inserted into the tetraspanin gene structure. The region of tetraspanin genes corresponding to the small extracellular loop (SEL) accounts for only 10.5% of the total sequence length but had 46% of the new animal intron insertions. Conclusions/Significance Our results indicate that tests of intron evolution are strengthened by the phylogenomic approach with specific gene families like tetraspanins. These tests add to our understanding of genomic innovation coupled to major evolutionary divergence events, functional constraints and the timing of the appearance of evolutionary novelty.

Evolution of cysteine patterns in the large extracellular loop of tetraspanins from animals, fungi, plants and single-celled eukaryotes.

By analyzing the evolution of cysteine patterns in the large extracellular loop (LEL) of tetraspanins across all eukaryotes, we report the following: (1) the origin of the cysteine-cysteine-glycine (CCG) motif in the common ancestor of unikonts (Animalia, fungi and amoebozoa); (2) tracing cysteine motifs on an eukaryotic phylogeny which includes protists, animals and plants match organismal evolution; (3) using this evolutionary approach we have determined some of the cysteines in these proteins that are involved in specific bonds in the LEL. Our study provides a framework to better understand tetraspanin formation, diversification and the evolutionary history of these important proteins.

Mn(II) complexes of scorpiand-like ligands. A model for the MnSOD active centre with high in vitro and in vivo activity.

Manganese complexes of polyamines consisting of an aza-pyridinophane macrocyclic core functionalised with side chains containing quinoline or pyridine units have been characterised by a variety of solution techniques and single crystal x-ray diffraction. Some of these compounds have proved to display interesting antioxidant capabilities in vitro and in vivo in prokaryotic (bacteria) and eukaryotic (yeast and fish embryo) organisms. In particular, the Mn complex of the ligand containing a 4-quinoline group in its side arm which, as it happens in the MnSOD enzymes, has a water molecule coordinated to the metal ion that shows the lowest toxicity and highest functional efficiency both in vitro and in vivo.

The unr Gene: Evolutionary Considerations and Nucleic Acid-Binding Properties of Its Long Isoform Product

The unr transcription unit is located just upstream of the N-ras gene in the genome of mammals, in which unr, like N-ras, is ubiquitously expressed. To determine at what point in evolution the unr/N-ras linkage was created, analysis of nucleic acids by Southern and Northern blotting was performed, allowing us to track the presence of the unr gene to the start of vertebrate evolution and the unr/N-ras linkage to the time at which the reptilian and bird lines diverged. We have investigated, with specific anti-unr antibodies, a potential relation between unr protein levels and cellular processes in which N-ras is implicated. A positive correlation in the proliferation of 3T3 cells, but not differentiation of PC12 cells induced by nerve growth factor (NGF), was found. To study the nucleic acid-binding properties of unr, a protein with multiple repeats of a nucleic acid-binding motif, we expressed the long splicing isoform in a eukaryotic cell line and purified it in native form. The results obtained-a high affinity of unr for single-stranded DNA and RNA and lower affinity for double-stranded DNA without regard to nucleic acid sequence, and its intracellular localization in both the nuclear and non-nuclear compartments, together with its ubiquious expression in mammalian tissues-provide molecular information about the function of one of the closest gene tandems in mammalian cells (unr-N-ras).