Homologues In Other Vertebrates Research Articles

Identification and Characterization of the Stimulator of Interferon Genes (STING) in Chinese Giant Salamander Andrias davidianus

The stimulator of interferon genes (STING) is a central and multifaceted mediator in innate immunity, and plays vital roles in defending against pathogen infection. In this study, we identified and functionally characterized the STING homolog from the Chinese giant salamander Andrias davidianus (AdSTING) for the first time. The open reading frame of AdSTING encodes a 362 amino acid protein with a predicted molecular mass of 41.6 kDa, which shares 31.1–46.7% of its sequence identity with STING homologs in other vertebrates. Structural analysis revealed that AdSTING possesses four predicted transmembrane domains (TMs) at the N-terminal, and a C-terminal domain (CTD) featuring a dimerization domain (DD), a c-di-GMP-binding domain (CBD), and a short C-terminal tail (CTT). Tissue distribution analysis showed that AdSTING mRNA was ubiquitously expressed in all examined tissues, with abundant expression in muscles, intestine, and thymus. During Andrias davidianus ranavirus (ADRV) infection, significant up-regulation of AdSTING expression was observed in the thymus, spleen, and kidney. Upon different stimuli in vitro, the expression of AdSTING was significantly induced by ADRV infection or polyinosin-polycytidylic acid (poly I:C) stimulation, but no obvious changes were observed during lipopolysaccharide (LPS) stimulation. Subcellular localization analysis revealed that AdSTING mainly localized in the cytoplasm in the Chinese giant salamander thymus cell line (GSTC) and co-localized with the endoplasmic reticulum (ER). Luciferase reporter assays confirmed the ability of AdSTING to activate the interferon-stimulated response element (ISRE) and interferon (IFN) promoter. Furthermore, overexpression of AdSTING effectively decreased ADRV infection, as evidenced by the reduction of virus titers and viral gene expression. Collectively, our findings underscore the pivotal role of AdSTING in the antiviral innate immunity of the Chinese giant salamander, offering insights into the functional evolution of STING in amphibians.

CCR7, CD80/86 and CD83 in yellow catfish (Pelteobagrus fulvidraco): Molecular characteristics and expression patterns with bacterial infection

Dendritic cells (DCs) have a strong ability to stimulate naive T lymphocyte proliferation, so DCs play an important regulatory role in the initiation of the specific immune response. DCs cannot play the role of antigen presentation without the expression of surface molecules. The chemokine receptor CCR7 and the costimulatory molecules CD80/86 and CD83 are not only markers of DC maturation but also important functional molecules in the immune response of DC-T cells. In this study, partial cDNA sequences of CCR7, CD80/86 and CD83 were obtained by rapid amplification of cDNA ends (RACE) technology from yellow catfish. Bioinformatics analysis of deduced amino acid sequences of these three genes showed that CCR7, CD80/86 and CD83 genes in yellow catfish have similar functional domains to the homologs in other vertebrates, which indicated that the functions of these genes may be somewhat conserved during the evolution process. Afterward, the expression characteristics of these three genes in different tissues were detected by q-PCR. This result indicated that CCR7, CD80/86 and CD83 were expressed in all examined tissues, and the highest expression levels of CCR7 and CD80/86 and CD83 were detected in the trunk kidney, muscle and midgut, respectively. Meanwhile, the expression levels of CCR7 and CD80/86 were lowest in the gill, and the expression of CD83 was lowest in the stomach. Finally, healthy yellow catfish were infected with A.hydrophila (1.0 × 107 CFU/mL) or E.ictaluri (1.0 × 106 CFU/mL), q-PCR results indicated that both pathogenic bacteria can induce significant upregulation of CCR7, CD80/86 and CD83 in immune organs, and the expression levels of these genes in the intestine were higher than those in the skin and gill. Our results in this study provide a molecular basis for exploring the role of CCR7, CD80/86 and CD83 in the immune responses induced by bacteria, and can help us to understand the difference of immune responses induced by extracellular and intracellular bacteria.

Cloning, characterization, and expression of glucose transporter 2 in the freeze-tolerant wood frog, Rana sylvatica

BackgroundThe essential role of glucose transporter 2 (GLUT2) in glucose homeostasis has been extensively studied in mammals; however, little is known about this important protein in lower vertebrates. The freeze-tolerant wood frog (Rana sylvatica), which copiously mobilizes glucose in response to freezing, represents an excellent system for the study of glucose transport in amphibians. MethodsGLUT2 was sequenced from northern and southern phenotypes of R. sylvatica, as well as the freeze-intolerant Rana pipiens. These proteins were expressed and functionally characterized in Xenopus oocytes. Abundance of GLUT2 in tissues was analyzed using immunoblotting techniques. ResultsGLUT2s cloned from these anurans encoded proteins with high sequence homologies to known vertebrate GLUT2s and had similar transport properties, although, notably, transport of the glucose analog 3-O-methyl-d-glucose (3-OMG) was strongly inhibited by 150mM urea. Proteins from all study subjects had similar affinity constants (~12mM) and other kinetic properties; however, GLUT2 abundance in liver was 3.5-fold greater in northern R. sylvatica than in the southern conspecific and R. pipiens. ConclusionOur results indicate that amphibian GLUT2s are structurally and functionally similar to their homologs in other vertebrates, attesting to the conserved nature of this transport protein. The greater abundance of this protein in the northern phenotype of R. sylvatica suggests that these transporters contribute importantly to freezing survival. General significanceThis study provides the first functional characterization of any GLUT isoform from an anuran amphibian and novel insights into the role of these proteins in glucose homeostasis and cryoprotectant mobilization in freeze-tolerant vertebrates.

MOV10 RNA Helicase Is a Potent Inhibitor of Retrotransposition in Cells

MOV10 protein, a putative RNA helicase and component of the RNA–induced silencing complex (RISC), inhibits retrovirus replication. We show that MOV10 also severely restricts human LINE1 (L1), Alu, and SVA retrotransposons. MOV10 associates with the L1 ribonucleoprotein particle, along with other RNA helicases including DDX5, DHX9, DDX17, DDX21, and DDX39A. However, unlike MOV10, these other helicases do not strongly inhibit retrotransposition, an activity dependent upon intact helicase domains. MOV10 association with retrotransposons is further supported by its colocalization with L1 ORF1 protein in stress granules, by cytoplasmic structures associated with RNA silencing, and by the ability of MOV10 to reduce endogenous and ectopic L1 expression. The majority of the human genome is repetitive DNA, most of which is the detritus of millions of years of accumulated retrotransposition. Retrotransposons remain active mutagens, and their insertion can disrupt gene function. Therefore, the host has evolved defense mechanisms to protect against retrotransposition, an arsenal we are only beginning to understand. With homologs in other vertebrates, insects, and plants, MOV10 may represent an ancient and innate form of immunity against both infective viruses and endogenous retroelements.

Dynamic expression of the LAP family of genes during early development of Xenopus tropicalis

The leucine-rich repeats and PDZ (LAP) family of genes are crucial for the maintenance of cell polarity as well as for epithelial homeostasis and tumor suppression in both vertebrates and invertebrates. Four members of this gene family are known: densin, erbin, scribble and lano. Here, we identified the four members of the LAP gene family in Xenopus tropicalis and studied their expression patterns during embryonic development. The Xenopus LAP proteins show a conserved domain structure that is similar to their homologs in other vertebrates. In Xenopus embryos, these genes were detected in animal cap cells at the early gastrula stage. At later stages of development, they were widely expressed in epithelial tissues that are highly polar in nature, including the neural epithelia, optic and otic vesicles, and in the pronephros. These data suggest that the roles of the Xenopus LAP genes in the control of cell polarity and morphogenesis are conserved during early development. Erbin and lano show similar expression patterns in the developing head, suggesting potential functional interactions between the two molecules in vivo.

Computational Identification of Putative miRNAs fromFelis Catus

microRNAs represent a class of noncoding small RNAs of approximately 20–23 nt length, which are evolutionarily conserved and play a vital role in various biological processes by either degrading or repressing mRNA translation. The Felis catus (cat) genome sequence has been published, and just revealed the number of miRNAs in the genome–-without mention of any further details on these miRNAs. This paper discusses an in silico comparative approach using all known sequences of vertebrate pre-miRNA as query sequence, and report 405 putative miRNAs from cat genome. We determine the identity values of pre-miRNAs and mature miRNAs besides statistical sequence characteristics. Interestingly, among 405 miRNAs–-90, 53 and 50 showed 100% identity to cattle, human and dog, respectively. Further, we have validated 6 miRNAs, whose identity are <85% with the query sequence and validated them using MiPred algorithm. We also identify 25 miRNA clusters in cat based on their homologs in other vertebrates. Most importantly, based on identities among pre-miRNA, mature miRNA, miRNA families and clusters, we observe that miRNAs from cat are more identical to cattle, than humans. Our results, therefore may add a new dimension to the studies related to the evolution of cat.

Characterization of a nervous system-specific promoter for growth-associated protein 43 gene in Medaka ( Oryzias latipes)

Genes expressed by neurons are controlled by specific, interacting cis-regulatory elements and trans-acting factors within their promoters. In the present study, we asked whether the transcriptional machinery regulating neuron-specific gene expression was conserved in evolution. We identified a GAP-43 homolog in Medaka ( Oryzias latipes), and analyzed its expression during various stages of development. Compared with the amino acid sequences of GAP-43 homologs in other vertebrates, the amino-terminus of GAP-43 was highly conserved evolutionarily, but the carboxy-terminus exhibited significant variability. Expression of GAP-43 predominantly occurred in cells of the central and peripheral nervous systems as determined by in situ hybridization and by RT-PCR. Expression of GAP-43 increased throughout development and significant levels continued to be expressed into adulthood. We also showed that a proximal ∼ 2.0 kbp fragment in the 5′-flanking region had promoter activity as determined by in vivo reporter assays. Furthermore, based upon computational analysis of transcription factor binding sites and an in vivo reporter analysis using sequentially deleted promoters, we demonstrated that cis-regulatory elements for neuronal expression were widely distributed in this region. In mammals, a TATA-box, E-box and neuronal repressive elements have been thought to contribute to neuronal expression. However, these features were not found in the orthologous region of the Medaka GAP-43 promoter. Our results suggest that the arrangement of cis-regulatory elements of the GAP-43 ortholog in Medaka is different from that in mammals, yet maintains neuron-specific regulation.

Morphology, Intrinsic Membrane Properties, and Rotation-Evoked Responses of Trochlear Motoneurons in the Turtle

Intrinsic properties and rotation-evoked responses of trochlear motoneurons were investigated in the turtle using an in vitro preparation consisting of the brain stem with attached temporal bones that retain functional semicircular canals. Motoneurons were divided into two classes based on intrinsic properties. The first class exhibited higher impedance (123.0 +/- 11.0 MOmega), wider spikes (0.99 +/- 0.05 ms), a single spike afterhyperpolarization (AHP), little or no spike frequency adaptation (SFA), and anomalous rectification, characterized by an initial "sag" in membrane potential in response to hyperpolarizing current injection. The second class exhibited lower impedance (21.8 +/- 2.5 MOmega), narrower spikes (0.74 +/- 0.03 ms), a double AHP, substantial SFA, and little or no rectification. Vestibular responses were evoked by horizontal sinusoidal rotation (1/12-1/3 Hz; peak velocity: 30-100 degrees /s). Spiking in higher-impedance cells was recruited earlier in the response and exhibited a more limited dynamic range relative to that of lower impedance cells. Spiking evoked by injecting depolarizing current during rotation was blocked during contraversive motion and was consistent with a shunting inhibition. No morphological features were identified in neurobiotin-filled cells that correlated with the two physiological classes. Recovered motoneurons were multipolar but exhibited a less-complex dendritic morphology than ocular motoneurons of similarly sized mammals. The two physiologically defined cell classes have homologues in other vertebrates, suggesting that intrinsic membrane properties play an important role in oculomotor processing.

Molecular Identification and Expression Analysis of Tumor Necrosis Factor Receptor-associated Factor 2 in Grass Carp <italic>Ctenopharyngodon idella</italic>

Tumor necrosis factor receptor-associated factor 2 (TRAF2) is a crucial component of almost the entire tumor necrosis factor receptor superfamily signaling pathway. In the present study, a TRAF2 gene has been cloned from grass carp (Ctenopharyngodon idella) by reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends. The full-length cDNA is 3162 bp, including a 60 bp 5' untranslated region (UTR), a 1611 bp open reading frame, and a 1491 bp 3' UTR. The polyadenylation signal (AATAAA) and the mRNA instability motifs (ATTTTA, ATTTA) were followed by a poly(A) tail in the 3' UTR. No signal peptide or transmembrane region has been found in the putative amino acids of grass carp TRAF2 (gcTRAF2). Phylogenetic tree analysis clearly showed that gcTRAF2 is nearest to the TRAF2 gene of goldfish. The identity of gcTRAF2 with its homologs in other vertebrates ranges from 56% to 97%. It is characterized by one RING-type signature at the N-terminus, one zinc finger in the middle part, and one conserved TRAF domain consisting of a C-proximal (TRAF-C) subdomain and a N-proximal (TRAF-N) subdomain. The identity of TRAF-C among all TRAF2 homologs in vertebrates varies from 78% to 97%, whereas the identity of TRAF-N ranges from 56% to 100%. The recombinant gcTRAF2 has been expressed in Escherichia coli using pET-32a expression vector. The rabbit anti-gcTRAF2 polyclonal antibody was obtained. The expression of gcTRAF2 in different organs was examined by real-time quantitative polymerase chain reaction and Western blot analysis. It was widely distributed in heart, head kidney, thymus, brain, gill, liver, spleen, and trunk kidney. This is the first report of a TRAF2 homolog molecule in fish.

Organisation of the Hb 1 genes of the Antarctic skate Bathyraja eatonii: New insights into the evolution of globin genes

An extensive investigation of the organisation of globin genes has greatly contributed to the understanding of universal mechanisms of gene evolution and expression. Cartilaginous fish are the first organisms that have evolved the tetrameric form of hemoglobin (Hb). So far, there has been absolute lack of data about globin genes in chondrichthyans. Bathyraja is the dominant rajid south of 60°S. In the framework of the investigations on globin genes of Antarctic red-blooded and Hb-less fish we obtained the cloning of the α- and β-globin cDNAs of the main Hb (Hb 1) of the skate Bathyraja eatonii. Then, a genomic fragment of 6.2 kb was isolated where the Hb 1 α and β genes are linked in a tail-to-head (3′ to 5′) orientation. The β-globin gene promoter region and the chromosomal organisation of the Hb 1 genes of B. eatonii have been compared to their homologues in other vertebrates. The finding of a tail-to-head linkage of the Hb 1 α- and β-globin genes in B. eatonii is the first characterisation of the organisation of globin genes in chondrichthyes; such finding offers a novel contribution to the understanding of the evolution of this class of genes. Moreover, the characterisation of chondrichthyan genes is very important for gaining insight into the ancestral state of vertebrate genomes.

Comparative analysis of structure, expression and PSD95-binding capacity of Lrfn, a novel family of neuronal transmembrane proteins

Leucine-rich repeat and fibronectin III domain-containing ( Lrfn) has five members in mouse and human ( Lrfn1, Lrfn2, Lrfn3, Lrfn4, Lrfn5), and homologues in other vertebrates . Lrfn proteins share leucine-rich repeat (LRR)–immunoglobulin-like (Ig)–fibronectin type III (Fn)–transmembrane domain structure, which is also found in LRR–Ig–Fn superfamily proteins. Mouse Lrfn genes were expressed at adult stage predominantly in the brain. In the course of development, expression of Lrfn1, Lrfn3, and Lrfn4 started from immature neural cells, whereas that of Lrfn2 and Lrfn5 was limited to mature ones. Lrfn1–5 commonly encode glycoproteins spanning the plasma membrane, with their N-terminus located on the extracellular side. C-termini of Lrfn1, Lrfn2 and Lrfn4 were bound by PDZ domains of postsynaptic protein PSD95, re-distributing PSD95 to cell periphery where the Lrfn proteins were detected. These results suggest that Lrfn proteins are neuronal components with a role in the developing or mature vertebrate nervous system.

Xenopus U8 snoRNA Binding Protein Is a Conserved Nuclear Decapping Enzyme

U8 snoRNP is required for accumulation of mature 5.8S and 28S rRNA in vertebrates. We are identifying proteins that bind U8 RNA with high specificity to understand how U8 functions in ribosome biogenesis. Here, we characterize a Xenopus 29 kDa protein (X29), which we previously showed binds U8 RNA with high affinity. X29 and putative homologs in other vertebrates contain a NUDIX domain found in MutT and other nucleotide diphosphatases. Recombinant X29 protein has diphosphatase activity that removes m 7G and m 227G caps from U8 and other RNAs in vitro; the putative 29 kDa human homolog also displays this decapping activity. X29 is primarily nucleolar in Xenopus tissue culture cells. We propose that X29 is a member of a conserved family of nuclear decapping proteins that function in regulating the level of U8 snoRNA and other nuclear RNAs with methylated caps.

Cutting Edge: The Chicken TCR ζ-Chain Restores the Function of a Mouse T Cell Hybridoma

Abstract The TCR/CD3 complex has been intensively studied in mammals, but it has been difficult to isolate homologues in other vertebrates. Here, we characterize the chicken ζ-chain, the first nonmammalian homologue identified. The comparison of mammalian and chicken ζ proteins revealed high identity of the transmembrane and the C-terminal cytoplasmic domains. Transfection of a mouse ζ-deficient cell line, with the chicken ζ gene, restored surface expression of the murine TCR/CD3 complex. The chicken ζ-chain was stably associated with the mouse TCR/CD3 components and fully restored its signaling capacity upon stimulation with Ab, superantigen, and peptide Ag. This is the first report of a nonmammalian TCR component that is capable of fully restoring a mammalian TCR in every aspect analyzed, thus demonstrating the enormous selective pressure to maintain the ζ-chain as a structural and signaling component over a period of 300 million years.

Neuronal and Neuroendocrine Expression oflim3,a LIM Class Homeobox Gene, Is Altered in Mutant Zebrafish with Axial Signaling Defects

LIM class homeobox genes code for a family of transcriptional regulators that encode important determinants of cell lineage and cell type specificity. Thelim3gene from the zebrafish,Danio rerio,is highly conserved in sequence and expression pattern compared to its homologs in other vertebrates. In this paper we report immunocytochemical analysis of Lim3 protein expression in the pituitary, pineal, hindbrain, and spinal cord of the embryo, revealing an asymmetrical, lateral and late program of pituitary development in zebrafish, distinct from the pattern in other vertebrates. We studied Lim3 expression inno tail, floating head,andcyclopsmutant embryos, all of which have midline defects, with special reference to spinal cord differentiation where Lim3 marks mostly motoneurons.cyclopsembryos showed essentially normal Lim3 expression in the hindbrain and spinal cord despite the absence of the floor plate, whileno tailmutant embryos, which lack a differentiated notochord, displayed an excess of Lim3-expressing cells in a generally normal pattern. In contrast, Lim3-positive cells largely disappeared from the posterior spinal cord infloating headmutants, except in patches that correlated with remnants of apparent floor plate cells. These results support the view that either notochord or floor plate signaling can specify Lim3-positive motoneurons in the spinal cord.

Xenopus Pax-6 and retinal development

We have cloned a homolog of Pax-6 in Xenopus laevis. Its deduced amino acid sequence has a 95% overall identity with Pax-6 homologs in other vertebrates. It is expressed early in development in cells fated to form the eye and parts of the forebrain, hindbrain, and spinal cord. It has two phases of expression in the eye. In the early phase, from stage 12.5 to stage 33/34, Xenopus Pax-6 is expressed throughout the developing retina. In the late phase, after stage 33/34, it is excluded from mature cells in the outer half of the retina and from cells in the ciliary marginal zone, remaining only in amacrine and ganglion cells. Misexpression of Pax-6 early in development results in axial defects, but no specific eye phenotype is observed. Targeted misexpression in the retina at later stages does not result in any significant bias toward formation of amacrine or ganglion cells or away from photoreceptors. Ectopic expression of the proneural gene NeuroD alters the pattern of Pax-6, substantially reducing its expression in the eye field and later reducing or eliminating the eye itself. Our results show that Pax-6 expression appears to be necessary, but not sufficient, for eye formation in Xenopus.

Early developmental expression and experimental axis determination by the chicken Vg1 gene

Background Genes of the transforming growth factor β (TGFβ) superfamily have been implicated in the earliest steps of developmental patterning in vertebrates. In Xenopus, the Vg1 gene is a candidate for the initiator of axis formation: its RNA and protein are broadly but appropriately localized at the start of development, and processed Vg1 protein is a powerful inducer of organized axial tissue in blastular animal caps in vitro and when locally produced in vivo after injection of Vg1 mRNA into blastomeres. Site-specific proteolytic processing occurs ubiquitously for most TGFβ members, producing the active peptide ligand, but is tightly restricted, by unknown mechanisms, for endogenous Vg protein in Xenopus and zebrafish embryos. This restriction may be involved in the spatial localization of activity required for an organizing role.Results We have characterized an amniote (chick) orthologue of Vg1, cVg1, and examined its developmental expression. The early expression of cVg1 includes a phase broadly related to the known time and site of axis (primitive streak) initiation; the initial transcription of cVg1 is centred in the posterior marginal zone (PMZ), a region of the blastoderm known to contain the axial organizing activity at this stage. We also observed later neural and paraxial mesodermal expression of cVg1, which has not been described previously for Vg homologues in other vertebrates. We have grafted transfected COS cells, producing processed cVg1 protein, to peripheral positions around the chick early blastoderm. Such grafts initiate formation of morphologically complete primitive streaks, simulating the properties of grafts from the PMZ.Conclusions In vertebrate development, Vg genes may be required for an evolutionarily conserved early step in positioning or induction of the axis.

Three Wnt genes expressed in a wide variety of tissues during development of the zebrafish, Danio rerio : developmental and evolutionary perspectives

Proteins encoded by the Wnt family of genes act as signals and have been shown to play important roles in a wide variety of developmental processes. Here we describe the cloning of three Wnt family members from the zebrafish, Danio rerio, which encode proteins with homology to murine Wnt-2, -4 and -5A/B. The expression patterns of the latter two zebrafish genes, designated ZfWnt4 and ZfWnt5 show considerable similarity with their homologues in other vertebrates; ZfWnt2, however, is expressed in the developing viscera in a pattern distinct from its closest murine homologue. In the light of the similarities and differences in the patterns of expression of these genes relative to their homologues in other vertebrates, we speculate on their possible functions.

Expression of Hoxb-1 during gastrulation and segmentation stages of carp (Cyprinus carpio).

This report describes the cDNA sequence and embryonic RNA expression pattern of carp Hoxb-1. Carp Hoxb-1 is a labial-like, homeobox-containing gene of the 3' end of the Hox gene cluster. The expression pattern in carp is compared to that of homologs in other vertebrates. As holds for other Hox genes, carp Hoxb-1 is expressed with highest intensity at a sharp anterior boundary, and expression fades out towards posterior. At later stages, gaps were found in the domain. The gene is expressed from late gastrulation onwards, first mainly in the hypoblast but later in all germ layers. Its most prominent expression area is rhombomere 4 (r4) of the hindbrain. Transcripts were also found in the neural tube, mesoderm (lateral, head and presomite), epidermis and neural crest. At 30 hours post fertilization, Hoxb-1 was still expressed in r4, in the anterior trunk neural tube and in the branchial arches posterior to r4. Hox genes are thought to be involved in the specification of positional values along the embryonic anterior-posterior axis, and Hoxb-1 expression in r4 is supposed to be important for specifying the unique identity of this hindbrain segment. The conserved expression in r4 suggests that this is also true for carp Hoxb-1.