Cloning and characterization of a cDNA for the B beta chain of rat fibrinogen: evolutionary conservation of translated and 3'-untranslated sequences

Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear beta-fibrinogen intron 7 to carnivores

The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear beta-fibrinogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; approximately 3750 bp) and combined mt and nuclear data (nine genes; approximately 6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manul within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear beta-fibrinogen intron 7.

Conservation of the 3'-untranslated region of the Rab1a gene in amniote vertebrates: exceptional structure in marsupials and possible role for posttranscriptional regulation

The YPT1/RAB1 protein, a key regulator of the intracellular vesicle transport in eukaryotes, is highly conserved in function and amino acid sequence. Here we report that the most highly conserved nucleotide sequence of the Rab1a gene of amniote vertebrates corresponds to the 3'-untranslated region (3'-UTR) of the mRNA. Sequences of 27 species ranging from mammals to sauropsida are >91% identical in this region. Secondary structure prediction procedures applied to the 3'-UTR sequences between positions 750 and 984 and 1428 (mouse cDNA: Y00094), respectively, of the RAB1a mRNAs revealed families of alternative structures around nucleotide position 800 as recurrent features. The two hairpin loops are also predicted for marsupials, despite of their exceptional extension of the A-rich sequence in between. Yet, sequence conservation is much higher than required to conserve secondary structure. Implications for posttranscriptional regulation and protein binding are discussed.

Differential hepatic lobar gene expression in offspring exposed to altered maternal dietary protein intake

Increased plasma fibrinogen concentrations are a recognized risk factor for coronary heart disease, and increased fibrinogen levels in adults are associated with parameters of reduced early growth. We studied fibrinogen gene expression in adult offspring of dams fed either a 20% (control) or an 8% protein diet [maternal low-protein (MLP) rats] during pregnancy and lactation and determined whether any effects were consistent between left and right liver lobes, since the fetal liver has a unique blood supply that produces differential stimuli to the left and right lobes. In MLP offspring, there was a reduction in all three fibrinogen mRNA copy numbers in the left liver lobe [left vs. right lobes for alpha-, beta-, and gamma-fibrinogen (x10(6) copies/ng total RNA): 8.04 vs. 23.16, P<0.001; 4.74 vs. 13.07, P<0.001; and 4.61 vs. 16.38, P = 0.007, respectively], with a parallel reduction in fibrinogen concentration in the left liver lobe (8.53+/-0.33 vs. 10.41 +/-0.65 arbitrary units, P = 0.014, left and right lobes, respectively). No such effect was observed in offspring of control dams. To investigate the underlying mechanism, glucocorticoid receptor function and mRNA levels were studied, since expression of fibrinogen genes is regulated by glucocorticoid hormones. The binding affinity of the high-affinity glucocorticoid receptor was reduced only in the left liver lobe of the MLP offspring (P = 0.02, left. vs. right), with a parallel reduction in this lobe in glucocorticoid receptor mRNA level (P = 0.006, left vs. right). In conclusion, maternal dietary protein restriction reduces fibrinogen gene expression, fibrinogen protein, and mRNA level and binding affinity of glucocorticoid receptors only in the left liver lobe of the adult offspring.

A novel highly reproducible quantitative competitve RT PCR system

Small changes in plasma fibrinogen concentration are often clinically important. To detect changes in fibrinogen mRNA level, we have designed a novel quantitative competitive reverse transcriptase (RT) PCR system, based on our recent understanding that an important factor causing imprecision with RT PCR is a change in the initial ratio of target to standard RNA templates during reverse transcription. The system comprises: (1) titration of a fixed amount of standard RNA with four different amounts of total RNA in each tube during cDNA synthesis; (2) amplification of each of the four cDNAs with four consecutive PCR cycles; and (3) quality control reactions in which synthesised quality control RNA (rather than total RNA) is added to the standard RNA under the same RT PCR conditions as the assay reaction. To obtain reproducible data, we suggest three criteria for analysis of RT PCR results. Employing these criteria, reproducibility of RT PCR was markedly improved with an inter-assay CV of 6.5% (n=5). Using this system, we are able to detect reduction in mRNA levels of all fibrinogen genes caused by dietary protein restriction in rats after weaning (alpha 39%, p= 0. 028; beta 55%, p = 0.017; gamma 35 %, p= 0.038), with a parallel reduction of plasma fibrinogen concentration (mean (+/-SD), 157(+/-19) versus 130(+/-14) mg/dl, p=0.006).

The utility of DNA sequences of an intron from the beta-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves: Picidae)

Estimating phylogenies from DNA sequence data has become the major methodology of molecular phylogenetics. To date, molecular phylogenetics of the vertebrates has been very dependent on mtDNA, but studies involving mtDNA are limited because the several genes comprising the mt-genome are inherited as a single linkage group. The only apparent solution to this problem is to sequence additional genes, each representing a distinct linkage group, so that the resultant gene trees provide independent estimates of the species tree. There exists the need to find novel gene sequences which contain enough phylogenetic information to resolve relationships between closely related species. A possible source is the nuclear-encoded introns, because they evolve more rapidly than exons. We designed primers to amplify and sequence the 7 intron from the beta-fibrinogen gene for a recently evolved group, the woodpeckers. We sequenced the entire intron for 10 specimens representing five species. Nucleotide substitutions are randomly distributed along the length of the intron, suggesting selective neutrality. A preliminary analysis indicates that the phylogenetic signal in the intron is as strong as that in the mitochondrial encoded cytochrome b (cyt b) gene. The topology of the beta-fibrinogen tree is identical to that of the cyt b tree. This analysis demonstrates the ability of the 7 intron of beta-fibrinogen to provide well resolved, independent gene trees for recently evolved groups and establishes it as a source of sequences to be used in other phylogenetic studies.

cDNA and amino-acid sequences and organization of the gene encoding the B beta subunit of fibrinogen from Xenopus laevis

Fibrinogen, the major blood-clotting protein, is made up of three chains, A alpha, B beta and gamma, which are synthesized and secreted by the liver. In this communication, we describe the complete cDNA sequence, deduced amino acid (aa) sequence and organization of the gene encoding the B beta subunit of fibrinogen from Xenopus laevis (Xl). The cDNA representing the predominant form of the B beta mRNA comprises 2390 nucleotides (nt), with an open reading frame of 1467 nt coding for a 488-aa protein. The percent identity between Xl B beta and that of other animals ranges from 50% for lamprey to 66% for human. The Xl B beta gene consists of nine exons, one more than found in the human gene. The exon/intron boundaries in the frog and human B beta genes are in exactly conserved positions, except for junctions in the highly variable fibrinopeptide-encoding regions. Three of the exon/intron boundaries in the Xl B beta gene are also analogous to ones in A alpha and gamma genes of other species, supporting the notion of a close evolutionary relationship between the genes for all three subunits. This analysis of B beta from an amphibian provides the first complete description of the arrangement of exons and introns in any fibrinogen subunit gene from a non mammal and gives insight into the most highly conserved aspects of fibrinogen protein structure and gene organization.

Sequence of a human transcript expressed in T-lymphocytes and encoding a fibrinogen-like protein

A murine cDNA sequence (termed pT49), encoding a protein related to the fibrinogen (Fib) beta and gamma chains, has been previously reported [Koyama et al., Proc. Natl. Acad. Sci. USA 84 (1987) 1609-1613]. We used a murine pT49 probe to screen a human small intestine cDNA library, and obtained a set of overlapping cDNA clones encoding a Fib-like protein that is 80% identical with the product of the murine pT49 gene. The deduced amino acid (aa) sequence contains a predicted signal peptide and five consensus motifs for N-linked glycosylation. The presence of conserved Cys residues involved in the assembly of the mature Fib complex and of two alpha-helical regions permissive for coiled-coil formation, suggests that this Fib-like protein may be secreted as a multichain complex. Two mRNA species of approx. 4.5 and approx. 1.5 kb were detected by Northern blot hybridization of a human pT49-homolog cDNA probe with RNA obtained from resting peripheral blood T-lymphocytes. By RT-PCR analysis of purified peripheral blood T-lymphocyte subsets, we found expression of the pT49-homolog transcript in both CD3+/CD4+ and CD3+/CD8+ T-lymphocytes. The coding region of the human pT49-homolog cDNA was fused at its 3' end with a tag-coding sequence and was expressed in CHO cells. The corresponding gene product was immunoprecipitated with an anti-tag antibody from the cell lysate and from the culture supernatant of metabolically labeled transfectants and was identified as approx. 62 and approx. 64-70-kDa proteins, respectively.

The beta chain of chicken fibrinogen contains an atypical thrombin cleavage site

A cDNA corresponding to almost the entire coding region of the mRNA for the beta chain of chicken fibrinogen was sequenced. At the protein level, significant homology to the beta subunits of other vertebrate fibrinogens was found, with the highest degree of amino acid identity localized in the C-terminal region. In general, features conserved in the fibrinogens from other species also characterize the chicken sequence, including the cysteine motifs bordering an alpha-helical permissive region of fixed length and a single glycosylation site in the C-terminal region. However, the site of thrombin-catalyzed cleavage, which in other species consists of an Arg-Gly peptide bond, is instead an Arg-Ala bond in the chicken beta chain. The Ala was confirmed directly from a sequencing analysis of the purified beta chain of chicken fibrin. This finding may explain the observed slow clotting time of chicken fibrinogen relative to that of other species.