scholarly journals Developmental expression of Pax1/9 genes in urochordate and hemichordate gills: insight into function and evolution of the pharyngeal epithelium

Development ◽  
1999 ◽  
Vol 126 (11) ◽  
pp. 2539-2550 ◽  
Author(s):  
M. Ogasawara ◽  
H. Wada ◽  
H. Peters ◽  
N. Satoh
Keyword(s):  
Transcription Factors ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Developmental Expression ◽  
Cdna Libraries ◽  
Cdna Clones ◽  
Halocynthia Roretzi ◽  
Molecular Phylogenetic ◽  
Ptychodera Flava ◽  
Pharyngeal Epithelium

The epithelium of the pharynx contributes to the formation of gills in hemichordates, urochordates, cephalochordates and primitive vertebrates, and is therefore a key structure for understanding developmental mechanisms underlying the establishment of chordate body plans. Pax1- and Pax9-related genes encode transcription factors which are expressed in the pharyngeal region of cephalochordates as well as in the vertebrate pharyngeal pouch epithelium that forms the thymus and parathyroid glands. To explore the molecular basis underlying the occurrence and modifications of the pharyngeal epithelium during evolution, we isolated cDNA clones for Pax1- and Pax9-related genes of urochordates (HrPax1/9 of Halocynthia roretzi and CiPax1/9 of Ciona intestinalis) and a hemichordate (PfPax1/9 of Ptychodera flava) from gill cDNA libraries. Each gene is present as a single copy per haploid genome. All of the cDNAs encode typical paired domains and octapeptides but not a homeodomain, as is also true of other Pax1- and Pax9-related genes. Molecular phylogenetic analysis based on comparison of the paired domain amino-acid sequences suggests that HrPax1/9, CiPax1/9 and PfPax1/9 belong to the Pax1/9 subfamily, and that they are descendants of a single precursor of Pax1/Pax9. Screening of HrPax1/9 cDNA clones yielded six different types of transcripts which were generated by alternative splicing. Northern blot, RT-PCR/Southern and in situ hybridization analyses revealed that HrPax1/9, CiPax1/9 and PfPax1/9 are not expressed during early embryogenesis but are expressed in the epithelia of differentiating gills, suggesting that these genes encode gill-specific transcription factors. The Pax1/9 genes therefore might provide the first developmental genetic corroboration of hypotheses of organ-level homology that unifies hemichordates, urochordates and cephalochordates.

scholarly journals Cloning and sequence analysis of cDNAs encoding the α1, α2 and α3 chains of mouse collagen VI

1993 ◽  
Vol 291 (3) ◽  
pp. 787-792 ◽  
Author(s):  
R Z Zhang ◽  
T C Pan ◽  
R Timpl ◽  
M L Chu
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Untranslated Regions ◽  
Cdna Libraries ◽  
Cdna Clones ◽  
Collagen Vi ◽  
Central Segment ◽  
Glycosylation Sites ◽  
Key Features ◽  
Triple Helical Domain

cDNA clones encoding the alpha 1, alpha 2 and alpha 3 chains of mouse collagen VI have been isolated by screening cDNA libraries with the corresponding human probes. The composite cDNAs for the alpha 1, alpha 2, and alpha 3 chains are 2.5, 1.6 and 2.9 kb in size respectively. The alpha 1 and alpha 2 cDNAs encode the C-terminal portions of the chains as well as the entire 3′-untranslated regions, while the alpha 3 cDNAs encode a central segment of 959 amino acids flanking the triple-helical domain. The deduced amino acid sequences share 86-88% identity with the human counterparts and 67-73% identity with the chicken equivalents. Alignment of the deduced amino acid sequences of mouse, human and chicken collagens reveal that the key features of the protein, including the cysteine residues, imperfections in the Gly-Xaa-Xaa regions, Arg-Gly-Asp sequences and potential N-glycosylation sites, are mostly conserved.

scholarly journals Wpkci, Encoding an Altered Form of PKCI, Is Conserved Widely on the Avian W Chromosome and Expressed in Early Female Embryos: Implication of Its Role in Female Sex Determination

2000 ◽  
Vol 11 (10) ◽  
pp. 3645-3660 ◽  
Author(s):  
Tetsuya Hori ◽  
Shuichi Asakawa ◽  
Yuichiro Itoh ◽  
Nobuyoshi Shimizu ◽  
Shigeki Mizuno
Keyword(s):  
Fluorescent Protein ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Z Chromosome ◽  
Cdna Clones ◽  
W Chromosome ◽  
Interacting Protein ◽  
Altered Form ◽  
Α Helix ◽  
Green Fluorescent

Two W chromosome–linked cDNA clones, p5fm2 and p5fm3, were obtained from a subtracted (female minus male) cDNA library prepared from a mixture of undifferentiated gonads and mesonephroi of male or female 5-d (stages 26–28) chicken embryos. These two clones were demonstrated to be derived from the mRNA encoding an altered form of PKC inhibitor/interacting protein (PKCI), and its gene was namedWpkci. The Wpkci gene reiterated ∼40 times tandemly and located at the nonheterochromatic end of the chicken W chromosome. The W linkage and the moderate reiteration ofWpkci were conserved widely in Carinatae birds. The chicken PKCI gene, chPKCI, was shown to be a single-copy gene located near the centromere on the long arm of the Z chromosome. Deduced amino acid sequences of Wpkci and chPKCI showed ∼65% identity. In the deduced sequence of Wpkci, the HIT motif, which is essential for PKCI function, was absent, but the α-helix region, which was conserved among the PKCI family, and a unique Leu- and Arg-rich region, were present. Transcripts from bothWpkci and chPKCI genes were present at significantly higher levels in 3- to 6-d (stages 20–29) embryos. These transcripts were detected in several embryonic tissues, including undifferentiated left and right gonads. When the green fluorescent protein–fused form of Wpkci was expressed in male chicken embryonic fibroblast, it was located almost exclusively in the nucleus. A model is presented suggesting that Wpkci may be involved in triggering the differentiation of ovary by interfering with PKCI function or by exhibiting its unique function in the nuclei of early female embryos.

Sequence organization and developmental expression of an interspersed, repetitive element and associated single-copy DNA sequences in Dictyostelium discoideum

1985 ◽  
Vol 5 (8) ◽  
pp. 2123-2130
Author(s):  
A R Kimmel ◽  
R A Firtel
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Sequence Data ◽  
Single Copy ◽  
Developmental Expression ◽  
Cdna Clones ◽  
Base Pairs ◽  
Sequence Element ◽  
Copy Dna ◽  
Single Copy Dna

We have examined the genomic organization and developmental expression pattern of a short, transcribed, interspersed repeat element and its associated single-copy sequences. We have previously shown that 1% of the polyadenylated [poly(A)+] RNA from vegetative cells contains sequences that hybridize to this repeat. The complementary RNA is heterogeneous in size, and 90% of its mass hybridizes to single-copy DNA. In this study, we examined a series of genomic DNAs and cDNAs derived from poly(A)+ RNAs which are complementary to the repeat. Comparisons of sequence data from various genomic and cDNA clones indicated that (AAC)n X (GTT)n is the common sequence element. The tandem repeat occurred in approximately 100 short segments (approximately 35 to 150 base pairs) per haploid genome interspersed with single-copy DNA. Probes from regions adjacent to this element hybridized to unique restriction fragments on DNA blots and unique poly(A)+ RNA species on RNA blots. The (AAC)n X (GTT)n sequence was asymmetrically transcribed with only (AAC)n sequences represented in RNA. The repeat was localized within the transcribed regions of several genes and 70 base pairs 5' to the transcription initiation site of another gene. Individual (AAC)n-containing RNAs exhibited a developmental pattern of expression suggestive of the coordinate expression of many AAC gene family members.

cDNA cloning of transcription factor E4TF1 subunits with Ets and notch motifs

1993 ◽  
Vol 13 (3) ◽  
pp. 1385-1391
Author(s):  
H Watanabe ◽  
J Sawada ◽  
K Yano ◽  
K Yamaguchi ◽  
M Goto ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Amino Acid ◽  
Dna Binding ◽  
Amino Acid Sequence ◽  
Binding Activity ◽  
Amino Acid Sequences ◽  
Predicted Amino Acid Sequence ◽  
Cdna Clones ◽  
Dna Binding Activity

E4TF1 was originally identified as one of the transcription factors responsible for adenovirus E4 gene transcription. It is composed of two subunits, a DNA binding protein with a molecular mass of 60 kDa and a 53-kDa transcription-activating protein. Heterodimerization of these two subunits is essential for the protein to function as a transcription factor. In this study, we identified a new E4TF1 subunit, designated E4TF1-47, which has no DNA binding activity but can associate with E4TF1-60. We then cloned the cDNAs for each of the E4TF1 subunits. E4TF1 was purified, and the partial amino acid sequence of each subunit was determined. The predicted amino acid sequence of each cDNA clone revealed that E4TF1-60 had an ETS domain, which is a DNA binding domain common to ets-related transcription factors. E4TF1-53 had four tandemly repeated notch-ankyrin motifs. The putative cDNA of E4TF1-47 coded almost the same amino acid sequences as E4TF1-53. Three hundred and thirty-two amino acids of the N termini of E4TF1-47 and -53 were identical except for one amino acid insertion in E4TF1-53, and they differ from each other at the C terminus. These three recombinant cDNA clones were expressed in Escherichia coli, and the proteins behaved in the same manner as purified proteins in a gel retardation assay. Nucleotide and predicted amino acid sequences were highly homologous to GABP-alpha and -beta, which is further supported by the observation that GABP-specific antibody can recognize human E4TF1.

scholarly journals Sequence organization and developmental expression of an interspersed, repetitive element and associated single-copy DNA sequences in Dictyostelium discoideum.

1985 ◽  
Vol 5 (8) ◽  
pp. 2123-2130 ◽  
Author(s):  
A R Kimmel ◽  
R A Firtel
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Sequence Data ◽  
Single Copy ◽  
Developmental Expression ◽  
Cdna Clones ◽  
Base Pairs ◽  
Sequence Element ◽  
Copy Dna ◽  
Single Copy Dna

We have examined the genomic organization and developmental expression pattern of a short, transcribed, interspersed repeat element and its associated single-copy sequences. We have previously shown that 1% of the polyadenylated [poly(A)+] RNA from vegetative cells contains sequences that hybridize to this repeat. The complementary RNA is heterogeneous in size, and 90% of its mass hybridizes to single-copy DNA. In this study, we examined a series of genomic DNAs and cDNAs derived from poly(A)+ RNAs which are complementary to the repeat. Comparisons of sequence data from various genomic and cDNA clones indicated that (AAC)n X (GTT)n is the common sequence element. The tandem repeat occurred in approximately 100 short segments (approximately 35 to 150 base pairs) per haploid genome interspersed with single-copy DNA. Probes from regions adjacent to this element hybridized to unique restriction fragments on DNA blots and unique poly(A)+ RNA species on RNA blots. The (AAC)n X (GTT)n sequence was asymmetrically transcribed with only (AAC)n sequences represented in RNA. The repeat was localized within the transcribed regions of several genes and 70 base pairs 5' to the transcription initiation site of another gene. Individual (AAC)n-containing RNAs exhibited a developmental pattern of expression suggestive of the coordinate expression of many AAC gene family members.

scholarly journals cDNA cloning of transcription factor E4TF1 subunits with Ets and notch motifs.

1993 ◽  
Vol 13 (3) ◽  
pp. 1385-1391 ◽  
Author(s):  
H Watanabe ◽  
J Sawada ◽  
K Yano ◽  
K Yamaguchi ◽  
M Goto ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Amino Acid ◽  
Dna Binding ◽  
Amino Acid Sequence ◽  
Binding Activity ◽  
Amino Acid Sequences ◽  
Predicted Amino Acid Sequence ◽  
Cdna Clones ◽  
Dna Binding Activity

E4TF1 was originally identified as one of the transcription factors responsible for adenovirus E4 gene transcription. It is composed of two subunits, a DNA binding protein with a molecular mass of 60 kDa and a 53-kDa transcription-activating protein. Heterodimerization of these two subunits is essential for the protein to function as a transcription factor. In this study, we identified a new E4TF1 subunit, designated E4TF1-47, which has no DNA binding activity but can associate with E4TF1-60. We then cloned the cDNAs for each of the E4TF1 subunits. E4TF1 was purified, and the partial amino acid sequence of each subunit was determined. The predicted amino acid sequence of each cDNA clone revealed that E4TF1-60 had an ETS domain, which is a DNA binding domain common to ets-related transcription factors. E4TF1-53 had four tandemly repeated notch-ankyrin motifs. The putative cDNA of E4TF1-47 coded almost the same amino acid sequences as E4TF1-53. Three hundred and thirty-two amino acids of the N termini of E4TF1-47 and -53 were identical except for one amino acid insertion in E4TF1-53, and they differ from each other at the C terminus. These three recombinant cDNA clones were expressed in Escherichia coli, and the proteins behaved in the same manner as purified proteins in a gel retardation assay. Nucleotide and predicted amino acid sequences were highly homologous to GABP-alpha and -beta, which is further supported by the observation that GABP-specific antibody can recognize human E4TF1.

scholarly journals SpMyb functions as an intramodular repressor to regulate spatial expression of CyIIIa in sea urchin embryos

Development ◽  
1997 ◽  
Vol 124 (23) ◽  
pp. 4717-4727 ◽  
Author(s):  
J.A. Coffman ◽  
C.V. Kirchhamer ◽  
M.G. Harrington ◽  
E.H. Davidson
Keyword(s):  
Transcription Factors ◽  
Sea Urchin ◽  
Regulatory Region ◽  
Ectopic Expression ◽  
Amino Acid Sequences ◽  
Target Site ◽  
Cdna Clones ◽  
Sequence Information ◽  
Oral Ectoderm ◽  
Myb Domain

The CyIIIa actin gene of Strongylocentrotus purpuratus is transcribed exclusively in the embryonic aboral ectoderm, under the control of 2.3 kb cis-regulatory domain that contains a proximal module that controls expression in early embryogenesis, and a middle module that controls expression in later embryogenesis. Previous studies demonstrated that the SpRunt-1 target site within the middle module is required for the sharp increase in CyIIIa transcription which accompanies differentiation of the aboral ectoderm, and that a negative regulatory region near the SpRunt-1 target site is required to prevent ectopic transcription in the oral ectoderm and skeletogenic mesenchyme. This negative regulatory region contains a consensus binding site for the myb family of transcription factors. In vitro DNA-binding experiments reveal that a protein in blastula-stage nuclei interacts specifically with the myb target site. Gene transfer experiments utilizing CyIIIa reporter constructs containing oligonucleotide substitutions indicate that this site is both necessary and sufficient to prevent ectopic expression of CyIIIa. Synthetic oligonucleotides containing the myb target site were used to purify a protein from sea urchin embryo nuclear extracts by affinity chromatography. This protein is immunoprecipitated by antibodies specific to the evolutionarily conserved myb domain, and amino acid sequences obtained from the purified protein were found to be identical to sequences within the myb domain. Sequence information was used to obtain cDNA clones of SpMyb, the S. purpuratus member of the myb family of transcription factors. Through interactions within the middle module, SpMyb functions to repress activation of CyIIIa in the oral ectoderm and skeletogenic mesenchyme.

scholarly journals Diversity of the cadherin family: evidence for eight new cadherins in nervous tissue.

1991 ◽  
Vol 2 (4) ◽  
pp. 261-270 ◽  
Author(s):  
S Suzuki ◽  
K Sano ◽  
H Tanihara
Keyword(s):  
Amino Acid ◽  
Northern Blot Analysis ◽  
Amino Acid Sequences ◽  
Cdna Libraries ◽  
Cdna Clones ◽  
Chain Reaction ◽  
Significant Similarity ◽  
New Members ◽  
The Central Nervous System ◽  
Polymerase Chain

To examine the diversity of the cadherin family, we isolated cDNAs from brain and retina cDNA preparations with the aid of polymerase chain reaction. The products obtained included cDNAs for two of three known cadherins as well as eight distinct cDNAs, of which deduced amino acid sequences show significant similarity with the known cadherin sequences. Larger cDNA clones were isolated from human cDNA libraries for six of the eight new molecules. The deduced amino acid sequences show that the overall structure of these molecules is very similar to that of the known cadherins, indicating that these molecules are new members of the cadherin family. We have tentatively designated these cadherins as cadherin-4 through -11. The new molecules, with the exception of cadherin-4, exhibit features that distinguish them as a group from previously cloned cadherins; they may belong to a new subfamily of cadherins. Northern blot analysis showed that most of these cadherins are expressed mainly in brain, although some are expressed in other tissues as well. These findings show that the cadherin family of adhesion molecules is much larger than previously thought, and suggest that the new cadherins may play an important role in cell-cell interactions within the central nervous system.

Isolation of Frog and Chicken cDNAs Encoding Heparin Cofactor II

1998 ◽  
Vol 80 (11) ◽  
pp. 784-790 ◽  
Author(s):  
Niall Colwell ◽  
Douglas Tollefsen
Keyword(s):  
Mouse Liver ◽  
Dermatan Sulfate ◽  
Cdna Probe ◽  
Amino Acid Sequences ◽  
Cdna Libraries ◽  
Cdna Clones ◽  
Reactive Site ◽  
Heparin Cofactor Ii ◽  
Acidic Domain ◽  
Physiologic Role

SummaryHeparin cofactor II (HCII) is a serpin that inhibits thrombin rapidly in the presence of heparin or dermatan sulfate. HCII activity has been detected in human, rabbit, and mouse plasma, and cDNA clones for HCII have been isolated previously from human, rabbit, rat, and mouse liver libraries, suggesting a conserved physiologic role for HCII among mammals. In this report, we show that both frog and chicken plasma contain a dermatan sulfate-dependent inhibitor that forms a 118-kDa complex with human 125I-thrombin. Screening of frog and chicken liver cDNA libraries in bacteriophage λ with a human HCII cDNA probe yielded nearly full-length clones with inserts of 1.8 and 1.7 kb, respectively. The amino acid sequences deduced from the frog and chicken HCII cDNAs are ~60% identical to one another and to each of the mammalian sequences. In particular, the N-terminal acidic domain, the glycosaminoglycan-binding site, and the reactive site sequences are highly conserved. Our results indicate that HCII is widely distributed among vertebrates and may have a common function in birds, amphibians, and mammals.

scholarly journals Molecular cloning and developmental expression patterns of the MyoD and MEF2 families of muscle transcription factors in the carp.

1998 ◽  
Vol 201 (20) ◽  
pp. 2801-2813 ◽  
Author(s):  
A Kobiyama ◽  
Y Nihei ◽  
Y Hirayama ◽  
K Kikuchi ◽  
H Suetake ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Northern Blot Analysis ◽  
Juvenile Fish ◽  
Expression Patterns ◽  
Developmental Expression ◽  
Muscle Fibres ◽  
Cdna Clones ◽  
The Common ◽  
Polymerase Chain ◽  
Enhancer Factor

cDNA clones encoding the myogenic regulatory factors (MRFs) myogenin, MyoD and myf-5 were isolated by reverse-transcription polymerase chain reaction from larvae and embryos of the common carp (Cyprinus carpio L.). Myocyte-specific enhancer factor 2 (MEF2) cDNAs were identified from a cDNA library from adult carp. Northern blot analysis showed that MyoD, myf-5 and MEF2C transcripts were present in three-somite embryos, whereas myogenin and MEF2A transcripts were not detected until the 15-somite stage. Intense signals of myogenin and MyoD transcripts were observed even in 1-month-old juveniles. Levels of MyoD, myogenin and MEF2A transcripts declined between 1 and 7 months after hatching, and myf-5 gave only a weak signal in the oldest fish. In contrast, levels of MEF2C transcripts were considerably higher in 7-month-old juveniles than in 1-month-old larvae. mRNAs encoding carp myosin heavy chain and -actin were first detected at approximately the time of the first heartbeat, and levels were maximal in juveniles 1 month post-hatching. The relatively high levels of MRF mRNA in juvenile fish probably reflect the recruitment of new muscle fibres from the satellite cell population. It was concluded that the relative importance of the different members of the MyoD and MEF2 families of transcription factors for muscle differentiation changes during ontogeny in the carp.

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