The chicken transforming growth factor-beta 3 gene: genomic structure, transcriptional analysis, and chromosomal location

Identification of a novel transforming growth factor-beta (TGF-beta6) gene in fish: regulation in skeletal muscle by nutritional state

Background

The transforming growth factor-β (TGF-β) family constitutes of dimeric proteins that regulate the growth, differentiation and metabolism of many cell types, including that of skeletal muscle in mammals. The potential role of TGF-βs in fish muscle growth is not known.

Results

Here we report the molecular characterization, developmental and tissue expression and regulation by nutritional state of a novel TGF-β gene from a marine fish, the gilthead sea bream Sparus aurata. S. aurata TGF-β6 is encoded by seven exons 361, 164, 133, 111, 181, 154, and 156 bp in length and is translated into a 420-amino acid peptide. The exons are separated by six introns: >643, 415, 93, 1250, 425 and >287 bp in length. Although the gene organization is most similar to mouse and chicken TGF-β2, the deduced amino acid sequence represents a novel TGF-β that is unique to fish that we have named TGF-β6. The molecule has conserved putative functional residues, including a cleavage motif (RXXR) and nine cysteine residues that are characteristic of TGF-β. Semi-quantitative analysis of TGF-β6 expression revealed differential expression in various tissues of adult fish with high levels in skin and muscle, very low levels in liver, and moderate levels in other tissues including brain, eye and pituitary. TGF-β6 is expressed in larvae on day of hatching and increases as development progresses. A fasting period of five days of juvenile fish resulted in increased levels of TGF-β6 expression in white skeletal muscle compared to that in fed fish, which was slightly attenuated by one injection of growth hormone.

Conclusion

Our findings provide valuable insights about genomic information and nutritional regulation of TGF-β6 which will aid the further investigation of the S. aurata TGF-β6 gene in association with muscle growth. The finding of a novel TGF-β6 molecule, unique to fish, will contribute to the understanding of the evolution of the TGF-β family of cytokines in vertebrates.

A genomic analysis of chicken cytokines and chemokines

As most mechanisms of adaptive immunity evolved during the divergence of vertebrates, the immune systems of extant vertebrates represent different successful variations on the themes initiated in their earliest common ancestors. The genes involved in elaborating these mechanisms have been subject to exceptional selective pressures in an arms race with highly adaptable pathogens, resulting in highly divergent sequences of orthologous genes and the gain and loss of members of gene families as different species find different solutions to the challenge of infection. Consequently, it has been difficult to transfer to the chicken detailed knowledge of the molecular mechanisms of the mammalian immune system and, thus, to enhance the already significant contribution of chickens toward understanding the evolution of immunity. The availability of the chicken genome sequence provides the opportunity to resolve outstanding questions concerning which molecular components of the immune system are shared between mammals and birds and which represent their unique evolutionary solutions. We have integrated genome data with existing knowledge to make a new comparative census of members of cytokine and chemokine gene families, distinguishing the core set of molecules likely to be common to all higher vertebrates from those particular to these 300 million-year-old lineages. Some differences can be explained by the different architectures of the mammalian and avian immune systems. Chickens lack lymph nodes and also the genes for the lymphotoxins and lymphotoxin receptors. The lack of functional eosinophils correlates with the absence of the eotaxin genes and our previously reported observation that interleukin- 5 (IL-5) is a pseudogene. To summarize, in the chicken genome, we can identify the genes for 23 ILs, 8 type I interferons (IFNs), IFN-gamma, 1 colony-stimulating factor (GM-CSF), 2 of the 3 known transforming growth factors (TGFs), 24 chemokines (1 XCL, 14 CCL, 8 CXCL, and 1 CX3CL), and 10 tumor necrosis factor superfamily (TNFSF) members. Receptor genes present in the genome suggest the likely presence of 2 other ILs, 1 other CSF, and 2 other TNFSF members.

Genetic susceptibility to keloid disease: mutation screening of the TGFβ3 gene

Keloid disease (KD) is a fibroproliferative dermal tumour of unknown aetiology. The increased familial clustering in KD, its increased prevalence in certain races and its presence in identical twins suggest a strong genetic predisposition to keloid formation. Transforming growth factor beta isoforms (TGFbeta) play a central role in wound healing and fibrosis and have been implicated in KD pathogenesis. Recent data has suggested that TGFbeta(3) has an important role in scar formation. There is little known about the genetic variation present within the TGFbeta(3) gene, which contains seven exons and six introns spanning 43,000 base pairs of the human genome. Exons one to seven and the promoter region (1000 bp upstream from exon 1 in the 5'-flanking regions) were screened in 95 Caucasian KD cases and 95 Caucasian controls for the presence of novel mutations using a high throughput DHPLC mutation detection technology. There were no mutations identified in any of the exonic regions, however, multiple nondisease associated mutations were found in the promoter region of the TGFbeta(3) gene. These data demonstrate that there is no association between the exonic and promoter regions of TGFbeta(3) gene and keloid scarring in our cohort of Caucasian patients.

Genomic, cDNA, and embryonic expression analysis of zebrafish transforming growth factor beta 3 (tgfbeta3)

TGFbeta3, a member of the transforming growth factor beta family, regulates a spectrum of biological processes and is involved in mammalian pulmonary and craniofacial development. Homologs of human TGFbeta3 have been identified in several vertebrate species. We sequenced a cDNA clone of zebrafish tgfbeta3, consisting of a 271-bp 5' untranslated region, a 1,233-bp open reading frame that encodes a predicted 410 amino acid peptide, and a 527-bp 3' untranslated region. Using 5' rapid amplification of cDNA ends, the transcription start site of this gene was determined to lie an additional 29 nucleotides upstream. The gene is composed of seven exons and maps to a segment of linkage group 17 that is syntenic to the human TGFbeta3 locus on chromosome 14q24. One stimulating protein 1 (Sp1) and two (TATA binding protein) (TBP) transcription factor binding sites were identified in the putative promoter segment upstream of the transcription start site. Comparative alignment analysis revealed a high degree of tgfbeta3 nucleotide and amino acid identity between zebrafish and other species, including complete conservation of the cysteine knot structure that facilitates protein-protein interaction. Also, 9 of 10 amino acid residues critical for ligand/receptor binding in human TGFbeta3 are conserved in zebrafish, suggesting a high degree of functional conservation even in lower vertebrates. Zebrafish tgfbeta3 transcripts were first detected in the notochord (10 somite to high-pec stage), followed by expression in the developing pharyngeal arch and neurocranial cartilage (18 somite to protruding mouth stage), lens and heart (21 somite to protruding mouth stage), and pectoral fins (prim-25 to protruding mouth stage). The strong expression in the pectoral fins, not reported in the orthologous mammalian forelimb, suggests a modified or novel function of tgfbeta3 during early fish development.

Temporal and spatial expression of TGF-beta2 in chicken somites during early embryonic development

A multifunctional growth and differentiation factor TGF-beta is expressed at various developmental stages, and its principle role may be involvement in organogenesis. The present study was performed to evaluate the temporal and spatial expression of TGF-beta2 mRNA in developing somites of chicken embryos during their early developmental periods. TGF-betas were expressed in various tissues of the whole embryo obtained at stage 26 (5 days of incubation) as revealed by whole-mount in situ hybridization. TGF-beta2 mRNA was predominantly expressed in somites as well as the head, branchial arch, wing buds, and leg buds. TGF-beta2 mRNA first appeared in the rostral somites on E4, and its expression sites expanded to the middle range of somites at stage 26. At stages 29-31 (6-7 days), expression in the rostral somites disappeared, and it appeared in the caudal somites. TGF-beta2 expression was also analyzed in sections of the embryo by in situ hybridization. The expression sites of TGF-beta2 were clearly observed in the myotomal somite tips as well as the neural tube. RT-PCR analysis showed that TGF-beta2 expression was very low in the blastocyte stage embryo and thereafter increased linearly in the whole trunk until stage 26. These data indicate that TGF-beta2 may be a regulatory factor participating in the somitogenesis of chicken embryos.

Identification and characterization of a functional, alternatively spliced Toll-like receptor 7 (TLR7) and genomic disruption of TLR8 in chickens

Based upon the recognition of antiviral compounds and single stranded viral RNA the Toll-like receptors TLR7 and TLR8 are suggested to play a significant role in initiating antiviral immune responses. Here we report the molecular characterization of the chicken TLR7/8 loci which revealed an intact TLR7 gene and fragments of a TLR8-like gene with a 6-kilobase insertion containing chicken repeat 1 (CR1) retroviral-like insertion elements. The chicken TLR7 gene encodes a 1047-amino-acid protein with 62% identity to human TLR7 and a conserved pattern of predicted leucine-rich repeats. Highest levels of chicken TLR7 mRNA were detected in immune-related tissues and cells, especially the spleen, caecal, tonsil and splenic B cells. Alternative spliced forms of TLR7 mRNA were identified in chicken, mouse and human and expressed in similar tissues and cell types to the major form of chicken TLR7. The chicken TLR7+ HD11 cell line and fresh splenocytes produced elevated levels of interleukin-1beta (IL-1beta) mRNA after exposure to the agonists R848 and loxoribine. Interestingly, none of the TLR7 agonists stimulated increased type I interferon (IFN) mRNA whereas poly(I:C) (a TLR3 agonist) up-regulated both chicken IFN-alpha and chicken IFN-beta mRNA. In contrast, TLR7 agonists, particularly R848 and poly(U) stimulated up-regulation of chicken IL-1beta, and chicken IL-8 mRNAs more effectively than poly(I:C). Stimulation of chicken TLR7 with R848 was chloroquine sensitive, suggesting signalling within an endosomal compartment, as for mammalian TLR7. The deletion of TLR8 in galliforms, accompanied with the differential response after exposure to TLR7 agonists, offers insight into the evolution of vertebrate TLR function.

Differential expression sites of TGF-β isoforms in chicken limb buds during morphogenesis

TGF-β gene is expressed at various developmental stages and its principle role may be an involvement in organogenesis. The present study was performed to investigate the temporal expression of these TGF-β isoforms in the developing limb of White Leghorn Chicken, Gallus gallus (L., 1758). TGF-β isoforms were expressed in the developing limb as revealed by whole-mount in situ hybridization, but each showed a different pattern of expression. TGF-β2 was the dominant isoform compared with the other two isoforms. TGF-β2 first appeared along the proximodistal axis of the limb at stage 24 and condensed at the tip at stage 26. At stages 29–31, expression appeared in digits and then was extended to the interdigital spaces. A weak signal for TGF-β3 was first shown in the developing limb at stage 26, but there was no interdigital expression, unlike for TGF-β2. TGF-β4 was expressed in the developing limb at stage 26 and only in the interdigital spaces at stage 29. Reverse transcription – polymerase chain reaction analysis also showed that the transcript levels of TGF-β isoforms, especially TGF-β2, drastically increased at stage 29. These results suggest that TGF-β isoforms, with their patterns of expression, are specific regulatory factors that participate in limb development and digit morphogenesis.

Function of TGF-beta2 in the growth of chicken primordial germ cells and germinal ridge stroma cells during embryonic development

The development of chicken embryonic gonads is locally regulated by the systematic action of growth factors. Recently, we used suppressive subtraction cloning to identify transforming growth factor beta2 (TGF-beta2) as a growth factor gene preferentially expressed in chicken embryonic ovaries and testes during the early periods of development (Hattori et al. 2002a. Prominent expression of transforming growth factor beta2 gene in the chicken embryonic gonad as revealed by suppressive subtraction cloning. Gen Comp Endocrinol 125:311-316). In the present study, the function of TGF-beta2 in chicken embryonic gonads was investigated using a serum-free culture system in the presence of several growth factors, which may behave as mitogenic or survival factors of primordial germ cells (PGCs). Chicken germinal ridges containing PGCs and germinal ridge stroma cells (GRSCs) were collected from six-day embryos. Addition of TGF-beta2 caused a dose-dependent inhibition of the number of co-cultured PGCs and GRSCs in the presence of these growth factors. However, there was no obvious difference between embryonic ovaries and testes in the effects of TGF-beta2. Immunocytochemical analysis using anti-SSEA-1 antibody revealed that TGF-beta2 induced fragmentation of PGCs. Expression of the TGF-beta2 gene was estimated in the co-cultured PGCs and GRSCs by semi-quantitative RT-PCR. The mRNA level of TGF-beta2 was significantly suppressed in the presence of the growth factors. These results suggest that TGF-beta2 is a gonadal regulator preferentially expressed at the early stages of chicken embryonic development and reduces the growth of PGCs and GRSCs by suppressing proliferation. However, expression of TGF-beta2 may be controlled by mitogenic or survival factors of PGCs.

Association of transforming growth factor beta genes with quantitative trait loci for antibody response kinetics in hens

Antibody responses (primary and secondary phases) were measured in an F2 population. The resource population was derived from grandsires of two highly inbred major histocompatibility complex (MHC)-congenic Fayoumi chicken lines (named M5.1 and M15.2) mated with highly inbred Leghorn G-B1 hens. Secondary phase parameters of maximum titres (Ymax) and time required to achieve Ymax (Tmax) were estimated from post-secondary titres by using a non-linear regression model. Associations of single nucleotide polymorphisms (SNP) in transforming growth factor beta2 (TGFB2), 3, and 4 genes with antibody response parameters were evaluated. Multiple immune response parameters were significantly associated with the TGFB2 gene primarily in the lineage of the M5.1 grandsire, suggesting that TGFB2 or linked genes affect antibody response in hens. Significant main effects of the three genes were mostly found in the lineage of the M5.1 grandsire. Significant two-way interactions on antibody response were primarily detected between TGFB3 and TGFB4 genes, and in the lineage of the M15.2 grandsire. Effects preferentially detectable in only one of the MHC-congenic lineages suggest that there was interaction between the MHC and TGFB genes. The characterized TGFB SNPs might be applied in marker-assisted selection to improve antibody production.

Prominent expression of transforming growth factor beta2 gene in the chicken embryonic gonad as revealed by suppressive subtraction cloning

cDNA cloning from chicken embryonic gonad subtracted from tissues of the brain, heart, liver, gizzard, mesonephros, and muscle was performed to identify growth factor genes with expression unique to embryonic ovary and testis. We obtained several cDNA clones encoding known and many unknown genes. We found for the first time that the transforming growth factor beta2 (TGF-beta2) is preferentially expressed in the chicken embryonic ovary and testis. cDNA subtraction cloning with respect to the selective expression of TGF-beta2 in the ovary and testis was further analyzed by reverse transcription-polymerase chain reaction analyses of other embryonic tissues. The ontogeny of TGF-beta2 was evaluated in chicken embryonic ovary and testis. In both testis and ovary, the levels of TGF-beta2 transcripts were high during the early period of embryonic development (E7), gradually decreased until the late embryonic days (E14--E17), and then slightly increased at the last embryonic day (E21). There was no difference in the TGF-beta2 transcripts per RNA between the left and the right ovaries. TGF-beta2 may have a critical role in the regulation of the development of chicken ovarian and testicular germ cells during the embryonic period.

Isolation and characterization of As60A, a transforming growth factor-beta gene, from the malaria vector Anopheles stephensi

We have isolated the first mosquito member of the TGF-beta superfamily, As60A. As60A is a single copy gene, approximately 5 kb in length and encodes eight exons. Here we report the isolation and characterization of two of four transcripts produced from this gene. The transcripts As60A(1)and As60A(2)encode related 5'UTR/exon 1 sequences. As60A is most similar to the 60A genes from Drosophila and is thus a member of the Dpp/BMP subfamily of the TGF-beta superfamily. The splice junction of intron 2 is conserved among As60A, BMP2, BMP4, Tc-Dpp, Bm-tgh-1, TGF-beta1 and Dpp. Intron 2 also contains three putative binding sites for a Dorsal/Gambif1 transcription factor. The large number of introns and the conservation of intron 2 indicate that As60A is relatively ancient compared to the other arthropod TGF-beta genes. We also propose that As60A plays a role in the mosquito immune response to Plasmodium infection.

The expression and structure of TGF-beta2 transcripts in rat muscles

The transforming growth factor-beta2 (TGF-beta2) transcripts expressed in various tissues of rat were characterised by RT-PCR and the nucleotide sequence of the cDNAs determined. A transcript with an 84-nucleotide insert in the latency-associated peptide region, the long form, was found. The long form of TGF-beta2 was detected in the aorta, primary bronchus, uterus, heart, skeletal muscle, sciatic nerve and spinal cord but not in the intestine. The 3' untranslated region of TGF-beta2 contained several putative AU-rich elements and multiple polyadenylation sites, indicating post-transcriptional regulation of TGF-beta2 synthesis. The levels of TGF-beta2 transcripts were estimated using semi-quantitative RT-PCR. They were down-regulated during muscle development and up-regulated after denervation. The long form constituted approximately 6% of the total TGF-beta2 messages in skeletal muscle.

Integration of the genetic and physical maps of the chicken macrochromosomes

A large amount of genetic mapping information has been obtained in the chicken from the East Lansing, Compton and Wageningen reference populations. Physical mapping information has however, been more limited. We have mapped 14 new clones, both genetically and physically, and all 14 have been assigned to macrochromosomes. The orientation of linkage groups E01C01C11W01 (Chr 1), E06C02W02 (Chr 2), E02C03W03 (Chr 3), E05C04W04 (Chr 4), E07E34C05W05 (Chr 5), E11C10W06 (Chr 6), E45C07W07 (Chr 7) and E43C12W11 (Chr 8) has been established. Here we present integrated maps of the eight macrochromosomes and the Z chromosome of the chicken and correlate genetic with physical distances for chromosomes 1-3 and the Z sex chromosome.

Genomic organisation of rainbow trout, Oncorhynchus mykiss TGF-beta

The genomic organisation of Oncorhnchus mykiss TGF-beta has been determined through the generation of contiguous clones by PCR. The O. mykiss TGF-beta gene is approximately 3.4 Kb in length and consists of 7 coding exons with no introns in the 5'-UTR. Whilst this is the same number of exons found in TGF-beta genes of amphibians, birds and mammals, in the O. mykiss gene intron 2 of other vertebrates is absent and an additional intron is present at the 3' end of the molecule, splitting exon 7 of the other known TGF-beta genes into two exons (trout exons 6 and 7). Comparison of exon sizes in the coding region support the suggestion that the Xenopus TGF-beta5 and trout TGF-beta sequences are the forerunners of TGF-beta1. Conservation of exons coding for the mature TGF-beta peptide is relatively high (63-73% identity) but other exons show lower identities (37-58%). Comparison of the TGF-beta intron sequences reveals that in general the O. mykiss introns are considerably shorter than the avian homologs. The impact of the teleost TGF-beta gene organisation on theories of the gene evolution of this cytokine family are discussed.

MIRs are present in coding regions of human genes

By using a weighted function and the method of enlarged similarity a search has been performed to identify mammalian interspersed repeats (MIRs) in DNA sequences from the EMBL data bank. The existence of MIRs is shown in coding regions of human genes and also in chicken and duck genomes. It is possible to conclude from the results obtained that MIRs were established in the coding regions of some genes and may have taken part in gene evolution. Furthermore, MIRs may have been amplified in vertebrate genomes before the origin of mammals.

Axolotl (Ambystoma mexicanum) lymphocytes produce and are growth-inhibited by transforming growth factor-beta

Recombinant (r)TGF-beta 5, an isoform of TGF-beta thus far identified only in the frog, Xenopus' laevis, inhibited phytohemagglutinin (PHA)-induced mitogenesis of salamander (axolotl) splenocytes and thymocytes, and T cell growth factor-induced proliferation of splenic lymphoblasts. This inhibition could be reversed by incubating (r)TGF-beta 5 with an anti-TGF-beta 5 antibody, but not with an antibody directed against TGF-beta 2, another Xenopus-produced TGF-beta isoform. Acid-treated supernatants from cultures of PHA-stimulated axolotl splenocytes (PHA-SNs) inhibited proliferation of mink lung fibroblasts (MLF), cells whose growth is sensitive to all known isoforms of TGF-beta. This inhibition was reversed by incubating the supernatants with the anti-pan-specific TGF-beta antibody which neutralizes TGF-beta 1, TGF-beta 2, TGF-beta 3 and TGF-beta 5. This inhibition was unaffected by antibodies that specifically neutralize either TGF-beta 1, TGF-beta 2, TGF-beta 3 or TGF-beta 5. Acid-treated axolotl PHA-SNs also inhibited proliferation of PHA-stimulated freshly harvested axolotl spleen cells. Once again, this inhibition could be reversed by treating supernatants with an anti-pan-specific TGF-beta antibody but not with anti-TGF-beta 2 or anti-TGF-beta 5 antibodies. All these data are consistent with the hypothesis that axolotl lymphocytes secrete a previously unknown TGF-beta isoform.