Vitellogenin motifs conserved in nematodes and vertebrates

Summary Caenorhabditis elegans vitellogenins are encoded by a family of six genes, one of which,vit-5, has been previously sequenced and shown to be surprisingly closely related to the vertebrate vitellogenin genes. Here we report an alignment of the amino acid sequences of vitellogenins from frog and chicken with those from threeC. elegans genes:vit-5 and two newly sequenced genes,vit-2 andvit-6. The four introns ofvit-6 are all in different places from the four introns ofvit-5, but three of these eight positions are identical or close to intron locations in the vertebrate vitellogenin genes. The encoded polypeptides have diverged from one another sufficiently to allow us to draw some conclusions about conserved positions. Many cysteine residues have been conserved, suggesting that vitellogenin structure has been maintained over a long evolutionary distance and is dependent upon disulfide bonds. In addition, a 20-residue segment shows conservation between the vertebrate and the nematode vitellogenins. This sequence may play a highly conserved role in vitellogenesis, such as specific recognition by oocytes. On the whole, however, selection may be acting more strongly on amino acid composition and codon usage than on amino acid sequence, as might be expected for abundant storage proteins: The amino acid compositions ofvit-2, vit-5, andvit-6 products are remarkably similar, despite the fact that the sequence of thevit-2 protein is only 22% and 50% identical to the sequences ofvit-6 andvit-5 proteins, respectively.     

Compositional compartmentalization and gene composition in the genome of vertebrates

Summary The compositional distribution of coding sequences from five vertebrates (Xenopus, chicken, mouse, rat, and human) is shifted toward higher GC values compared to that of the DNA molecules (in the 35–85-kb size range) isolated from the corresponding genomes. This shift is due to the lower GC levels of intergenic sequences compared to coding sequences. In the cold-blooded vertebrate, the two distributions are similar in that GC-poor genes and GC-poor DNA molecules are largely predominant. In contrast, in the warm-blooded vertebrates, GC-rich genes are largely predominant over GC-poor genes, whereas GC-poor DNA molecules are largely predominant over GC-rich DNA molecules. As a consequence, the genomes of warm-blooded vertebrates show a compositional gradient of gene concentration. The compositional distributions of coding sequences (as well as of DNA molecules) showed remarkable differences between chicken and mammals, and between mouse (or rat) and human. Differences were also detected in the compositional distribution of housekeeping and tissue-specific genes, the former being more abundant among GC-rich genes.     

Non-random base composition in codons of mitochondrial cytochrome b gene in vertebrates

Cytochrome b is the central catalytic subunit of the quinol:cytochrome c oxidoreductase of complex III of the mitochondrial oxidative phosphorylation system and is essential to the viability of most eukaryotic cells. Partial cytochrome b gene sequences of 14 species representing mammals, birds, reptiles and amphibians are presented here including some species typical for Poland. For the analysed species a comparative analysis of the natural variation in the gene was performed. This information has been used to discuss some aspects of gene sequence - protein function relationships. Review of relevant literature indicates that similar comparisons have been made only for basic mammalian species. Moreover, there is little information about the Polish-specific species. We observed that there is a strong non-random distribution of nucleotides in the cytochrome b sequence in all tested species with the highest differences at the third codon position. This is also the codon position of the strongest compositional bias. Some tested species, representing distant systematic groups, showed unique base composition differing from the others. The quail, frog, python and elk prefer C over A in the light DNA strand. Species belonging to the artiodactyls stand out from the remaining ones and contain fewer pyrimidines. The observed overall rate of amino acid identity is about 61%. The region covering Q(o) center as well as histidines 82 and 96 (heme ligands) are totally conserved in all tested species. Additionally, the applied method and the sequences can also be used for diagnostic species identification by veterinary and conservation agencies.     

Diversity in isochore structure among cold-blooded vertebrates based on GC content of coding and non-coding sequences

To review the general consideration about the different compositional structure of warm and cold-blooded vertebrates genomes, we used of the increasing number of genetic sequences, including coding (exons) and non-coding (introns) regions, that have been deposited on the databases throughout last years. The nucleotide distributions of the third codon positions (GC3) have been analyzed in 1510 coding sequences (CDS) of fish, 1414 CDS of amphibians and 320 CDS of reptiles. Also, the relationship between GC content of 74, 56 and 25 CDS of fish, amphibians and reptiles, respectively and that of their corresponding introns (GCI) have been considerated. In accordance with recent data, sequence analysis showed the presence of very GC3-rich CDS in these poikilotherm vertebrates. However, very high diversity in compositional patterns among different orders of fish, amphibians and reptiles was found. Significant positive correlations between GC3 and GCI was also confirmed for the genes analyzed. Nevertheless, introns resulted to be poorer in GC than their corresponding CDS, this difference being larger than in human genome. Because the limited number of available sequences including exons and introns we must be cautious about the results derived from them. However, the indicious of higher GC richness of coding sequences than of their corresponding introns could aid to understand the discrepancy of sequence analysis with the ultracentrifugation studies in cold-blooded vertebrates that did not predict the existence of GC-rich isochores.     

The SCPP gene repertoire in bony vertebrates and graded differences in mineralized tissues

The vertebrate tooth is covered with enamel in most sarcopterygians or enameloid in chondrichthyans and actinopterygians. The evolutionary relationship among these two tissues, the hardest tissue in the body, and other mineralized tissues has long been controversial. We have recently reported that specific combinations of secretory calcium-binding phosphoprotein (SCPP) genes are involved in the mineralization of bone, dentin, enameloid, and enamel. Thus, the early repertoire of SCPP genes would elucidate the evolutionary relationship across these tissues. However, the diversity of SCPP genes in teleosts and tetrapods and the roles of these genes in distinct tissues have remained unclear, mainly because many SCPP genes are lineage-specific. In this study, I show that the repertoire of SCPP genes in the zebrafish, frog, and humans includes many lineage-specific genes and some widely conserved genes that originated in stem osteichthyans or earlier. Expression analysis demonstrates that some frog and zebrafish SCPP genes are used primarily in bone, but also in dentin, while the reverse is true of other genes, similar to some mammalian SCPP genes. Dentin and enameloid initially use shared genes in the matrix, but enameloid is subsequently hypermineralized. Notably, enameloid and enamel use an orthologous SCPP gene in the hypermineralization process. Thus, the hypermineralization machinery ancestral to both enameloid and enamel arose before the actinopterygian–sarcopterygian divergence. However, enamel employs specialized SCPPs as structuring proteins, not used in enameloid, reflecting the divergence of enamel from enameloid. These results show graded differences in mineralized dental tissues and reinforce the hypothesis that bone–dentin–enameloid–enamel constitutes an evolutionary continuum. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

拟南芥AtJ3基因的克隆和分析

克隆并分析了拟南芥（Ａｒａｂｉｄｏｐｓｉｓｔｈａｌｉａｎａ（Ｌ．）Ｈｅｙｎｈ．）ＡｔＪ３的ｃＤＮＡ核苷酸序列,并证明其翻译产物与Ｅ．ｃｏｌｉ的ＤｎａＪ蛋白高度同源。ＡｔＪ３蛋白分子中具有全部这类蛋白的典型特征包括Ｊ结构域（ｄｏｍａｉｎ）、Ｇ或ＧＦ结构域、富含半胱氨酸的锌指结构域,Ｃ末端的ＣＡＱＱ是一个蛋白法尼基化信号。用ＡｔＪ３的ｃＤＮＡ序列末端非翻译区作探针,从拟南芥基因组文库中分离获得ＡｔＪ３基因。基因序列分析表明该基因是由被５个内含子分隔的６个外显子组成。根据Ｓｏｕｔｈｅｒｎ杂交分析,ＡｔＪ３基因为单拷贝基因。Ｎｏｒｔｈｅｒｎ分析结果表明,ＡｔＪ３在子叶、叶、根、花及长角果中都表达。３５℃的热激能增加叶中ＡｔＪ３的ｍＲＮＡ表达     

Olfactory receptors in aquatic and terrestrial vertebrates

In species representing different levels of vertebrate evolution, olfactory receptor genes have been identified by molecular cloning techniques. Comparing the deduced amino-acid sequences revealed that the olfactory receptor gene family of Rana esculenta resembles that of Xenopus laevis, indicating that amphibians in general may comprise two classes of olfactory receptors. Whereas teleost fish, including the goldfish Carassius auratus, possess only class I receptors, the `living fossil' Latimeria chalumnae is endowed with both receptor classes; interestingly, most of the class II genes turned out to be pseudogenes. Exploring receptor genes in aquatic mammals led to the discovery of a large array of only class II receptor genes in the dolphin Stenella Coeruleoalba; however, all of these genes were found to be non-functional pseudogenes. These results support the notion that class I receptors may be specialized for detecting water-soluble odorants and class II receptors for recognizing volatile odorants. Comparing the structural features of both receptor classes from various species revealed that they differ mainly in their extracellular loop 3, which may contribute to ligand specificity. Comparing the number and diversity of olfactory receptor genes in different species provides insight into the origin and the evolution of this unique gene family. Accepted: 29 July 1998     

Legumin-like and vicilin-like seed storage proteins: Evidence for a common single-domain ancestral gene

Legumin-like 11S and vicilin-like 7S globulins are the main storage proteins of most angiosperms and gymnosperms. The subunits of the hexameric legumin are synthesized as a precursor comprising a N-terminal acidic - and a C-terminal basic -chain. The trimeric vicilin molecule consists of subunits composed of two symmetrical N- and C-terminal structural domains.In a multiple alignment we have compared the N-terminal and C-terminal domains of 11 legumns and seven vicilins of several dicot, monocot, and gymnosperm species. The comparisons using all six possible pairwise combinations reveal that the N-terminal and C-terminal domains of both protein families are similar to each other. These results together with data on the distribution of variable and conserved regions, on the positions of susceptible sites for proteolytic attack, as well as on the published 7S protein tertiary structure suggest that both protein families share a common single-domain ancestor molecule and lead to the hypothesis that a triplication event has occurred during the evolution of a putative legumin/vicilin ancestor gene.Moreover, the comparison of the intron/exon pattern reveals that at least three out of five intron positions are precisely conserved between the genes of both protein families, further supporting the idea of a common evolutionary origin of recent legumin and vicilin encoding genes. Correspondence to: H. Bäumlein     

Amelogenin gene similarity in vertebrates: DNA sequences encoding amelogenin seem to be conserved during evolution

Summary Mouse amelogenin cDNA was used in hybridization assays with genomic DNA, cut with the restriction enzyme Eco RI, from the edentulous chicken (Gallus domesticus), the monophyodont mouse (as control), diphyodont man, and the polyphyodont fishes Atlantic salmon (Salmo salar) and seawolf (Anarrhichas lupus). The hybridization assay was performed under stringent conditions with non-radioactive probes. Hybridization was obtained with mouse (6.4-kb band), man (9-kb and 13-kb bands), and seawolf (18-kb band) genomic DNA. This demonstrates DNA sequence similarities between these species, and supports the theory that DNA sequences encoding enamel proteins appear to be highly conserved during the evolution of vertebrates. Lack of hybridization in salmon and chicken may be due to sequence divergencies or structural differences in an amelogenin gene analog, or it may be that no amelogenin gene is present in these animals.     

Genomic structure and expression of parathyroid hormone-related protein gene (PTHrP) in a teleost, Fugu rubripes

In this study we describe the isolation and characterisation of the parathyroid hormone-related protein (PTHrP) gene from the teleost Fugu rubripes. The gene has a relatively simple structure, compared with tetrapod PTHrP genes, composed of three exons and two introns, encompassing 2.25 kb of genomic DNA. The gene encodes a protein of 163 amino acids, with a putative signal peptide of 37 amino acids and a mature peptide of 126 amino acids. The overall homology with known tetrapod PTHrP proteins is low (36%), with a novel sequence inserted between positions 38 and 65, the absence of the conserved pentapeptide (TRSAW) and shortened C-terminal domain. The N-terminus shows greater conservation (62%), suggesting that it may have a hypercalcaemic function similar to that of tetrapod PTHrP. In situ localisation and RT–PCR have demonstrated the presence of PTHrP in a wide range of tissues with varying levels of expression. Sequence scanning of overlapping cosmids has identified three additional genes, TMPO, LDHB and KCNA1, which map to human chromosome 12, with the latter two mapping to 12p12-11.2. PTHrP in human also maps to this chromosome 12 sub-region, thus demonstrating conservation of synteny between human and Fugu.     

Genomic structure and expression of parathyroid hormone-related protein gene (PTHrP) in a teleost, Fugu rubripes

In this study we describe the isolation and characterisation of the parathyroid hormone-related protein (PTHrP) gene from the teleost Fugu rubripes. The gene has a relatively simple structure, compared with tetrapod PTHrP genes, composed of three exons and two introns, encompassing 2.25 kb of genomic DNA. The gene encodes a protein of 163 amino acids, with a putative signal peptide of 37 amino acids and a mature peptide of 126 amino acids. The overall homology with known tetrapod PTHrP proteins is low (36%), with a novel sequence inserted between positions 38 and 65, the absence of the conserved pentapeptide (TRSAW) and shortened C-terminal domain. The N-terminus shows greater conservation (62%), suggesting that it may have a hypercalcaemic function similar to that of tetrapod PTHrP. In situ localisation and RT–PCR have demonstrated the presence of PTHrP in a wide range of tissues with varying levels of expression. Sequence scanning of overlapping cosmids has identified three additional genes, TMPO, LDHB and KCNA1, which map to human chromosome 12, with the latter two mapping to 12p12-11.2. PTHrP in human also maps to this chromosome 12 sub-region, thus demonstrating conservation of synteny between human and Fugu.     

Terrestrial vertebrates have two keratin gene clusters; striking differences in teleost fish

Keratins I and II form the largest subgroups of mammalian intermediate filament (IF) proteins and account as obligatory heteropolymers for the keratin filaments of epithelia. All human type I genes except for the K18 gene are clustered on chromosome 17q21, while all type II genes form a cluster on chromosome 12q13, that ends with the type I gene K18. Highly related keratin gene clusters are found in rat and mouse. Since fish seem to lack a keratin II cluster we screened the recently established draft genomes of a bird (chicken) and an amphibian (Xenopus). The results show that keratin I and II gene clusters are a feature of all terrestrial vertebrates. Because hair with its multiple hair keratins and inner root sheath keratins is a mammalian acquisition, the keratin gene clusters of chicken and Xenopus tropicalis have only about half the number of genes found in mammals. Within the type I clusters all genes have the same orientation. In type II clusters there is a rare gene of opposite orientation. Finally we show that the genes for keratins 8 and 18, which are the first expression pair in embryology, are not only adjacent in mammals, but also in Xenopus and three different fish. Thus neighboring K8 and K18 genes seem a feature shared by all vertebrates. In contrast to the two well defined keratin gene clusters of terrestrial vertebrates, three teleost fish show an excess of type I over type II genes, the lack of a keratin type II gene cluster and a striking dispersal of type I genes, that are probably the result of the teleost-specific whole genome duplication followed by a massive gene loss. This raises the question whether keratin gene clusters extend beyond the ancestral bony vertebrate to cartilage fish and lamprey. We also analyzed the complement of non-keratin IF genes of the chicken. Surprisingly, an additional nuclear lamin gene, previously overlooked by cDNA cloning, is documented on chromosome 10. The two splice variants closely resemble the lamin LIII a + b of amphibia and fish. This lamin gene is lost on the mammalian lineage.     

Creatine kinase,energy-rich phosphates and energy metabolism in heart muscle of different vertebrates

Maximal activities of creatine kinase, pyruvate kinase and cytochrome oxidase and total concentrations of creatine and phosphorylated adenylates were measured in cardiac muscle of hagfish, eight teleost species, frog, turtle, pigeon and rat. The ratio of creatine kinase to cytochrome oxidase with cytochrome oxidase as a rough estimate of aerobic capacity and cellular “energy turnover”, was increased in myocardia of hagfish, turtle and crucian carp. These myocardia are likely to be frequently exposed to oxygen deficiency. In agreement with this, they possess a high relative glycolytic capacity as indicated by a high pyruvate kinase/cytochrome oxidase ratio. The creatine kinase/cytochrome oxidase ratio for the other myocardia varied within a factor of 2, except the value for cod myocardium which was below the others. Total creatine varied among species and was high in active species such as herring, pigeon and rat but also high in crucian carp. The variation in total concentration of phosphorylated adenylates was considerably less than the variation in total creatine. The high creatine kinase/ cytochrome oxidase ratio in myocardia likely to be challenged by hypoxia may represent an enhanced efficiency for both “spatial” and “temporal” buffering of phosphorylated adenylates to attenuate the impact of a depressed energy liberation. As to the differences in total creatine, this factor influences not only the cellular energy distribution but possibly also contractility via an effect on the free phosphate level.     

Repeated structure and possible gene duplications in high potential iron protein and rubredoxin

Summary The three-dimensional structures of bacterial high potential iron protein (HIPIP) and rubredoxin have been searched for repeats to test whether these molecules evolved by independent tandem gene duplications. HIPIP has no structural repeats in spite of the observed repeated pattern in the amino acid sequence fromRhodopseudomonas gelatinosa. Rubredoxin fromClostridium pasteurianum has repeated hairpin loops of ten alpha-carbon atoms on both sides of the active centre iron-sulphur complex, which can be superposed within a root mean square deviation of 0.84 Å by rotating about a local pseudo-dyad axis. The structural repeat matches a weak repeat in the amino acid sequence. It is concluded that the sequence repeats in HIPIP are probably a coincidence but that rubredoxin may have evolved by gene duplication from a dimer of two primitive hairpin loops.     

Behavioral influences on gene structure and other new ideas concerning sex change in fishes

Synopsis The interpretation of experiments, designed to reveal whether sex change is induced behaviorally, can influence the type of physiological mechanism we propose to underlie sex change. Mechanisms involving stimulation differ from mechanisms of disinhibition and each is inferred from different ways of conceptualizing behavioral experiments. Both types of mechanism are likely to involve CNS, hypothalamus, pituitary, and gonad. Recent work, however, also implicates H-Y antigen and Bkm satellite DNA in the sex-change process. These studies raise the exciting possibility that the changes in behavioral relationships between the sexes that induce sex change also produce changes in certain aspects of DNA. The nature of the proximate causes of sex change plays a surprisingly important role in influencing evolutionary models of sex change. Such models can be evaluated by first examining their applicability to real populations and, if they are applicable, then testing their validity by comparing their predictions with observed data. The size advantage model, in spite of its proven ability to stimulate and direct research, does not fare well in either of these stages of evaluation. The basic weakness of the model is its failure to incorporate individual adaptability into the life history of sex-changing fishes.     

Relationships among msx gene structure and function in zebrafish and other vertebrates

The zebrafish genome contains at least five msx homeobox genes, msxA, msxB, msxC, msxD, and the newly isolated msxE. Although these genes share structural features common to all Msx genes, phylogenetic analyses of protein sequences indicate that the msx genes from zebrafish are not orthologous to the Msx1 and Msx2 genes of mammals, birds, and amphibians. The zebrafish msxB and msxC are more closely related to each other and to the mouse Msx3. Similarly, although the combinatorial expression of the zebrafish msx genes in the embryonic dorsal neuroectoderm, visceral arches, fins, and sensory organs suggests functional similarities with the Msx genes of other vertebrates, differences in the expression patterns preclude precise assignment of orthological relationships. Distinct duplication events may have given rise to the msx genes of modern fish and other vertebrate lineages whereas many aspects of msx gene functions during embryonic development have been preserved.      

转基因小鼠中外源基因部分内含子序列的缺失及其对转录的影响

利用PCR扩增及PCR测序在显微注射法产生的转基因小鼠中发现,整合在小鼠染色体上的肌球蛋白轻链2启动子(myosinlightchain2promoter,MLC2)-糜酶(chymase)外源融合基因存在两种形式,一种为全长的融合基因,另一种在糜酶结构基因的第一内含子中缺失了213bp的序列。RT-PCR结果表明,缺失了部分内含子序列的外源融合基因不能在转基因小鼠心脏中表达.而全长的外源融合基因则能较高水平地表达,竞争性PCR定量实验表明在200ng心脏总RNA反转录产物中约含5.05(±1.38)×106个糜酶cDNA分子。上述结果表明,糜酶结构基因的第一内含子可能对MLC2-糜酶基因的表达具有调控作用。