Distant Evolutionary Relationship Research Articles

RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins.

An RNA recognition motif (RRM) of approximately 80 amino acids constitutes the core of RNA-binding domains found in a large family of proteins involved in RNA processing. The U1 RNA-binding domain of the A protein component of the human U1 small nuclear ribonucleoprotein (RNP), which encompasses the RRM sequence, was analyzed by using NMR spectroscopy. The domain of the A protein is a highly stable monomer in solution consisting of four antiparallel beta-strands and two alpha-helices. The highly conserved RNP1 and RNP2 consensus sequences, containing residues previously suggested to be involved in nucleic acid binding, are juxtaposed in adjacent beta-strands. Conserved aromatic side chains that are critical for RNA binding are clustered on the surface of the molecule adjacent to a variable loop that influences recognition of specific RNA sequences. The secondary structure and topology of the RRM are similar to those of ribosomal proteins L12 and L30, suggesting a distant evolutionary relationship between these two types of RNA-associated proteins.

Highly conserved structure of proliferating cell nuclear antigen (DNA polymerase δ auxiliary protein) gene in plants

In a previous paper [Suzuka, I., Daidoji, H., Matsuoka, M., Kadowaki, K., Takasaki, Y., Nakane, P. K. & Moriuchi, T. (1989) Proc. Natl Acad. Sci. USA 86, 3189-3193], we demonstrated the presence of a rice genomic-DNA fragment which hybridized with a rat proliferating-cell nuclear antigen (PCNA) cDNA probe, and proposed that plants possess the homolog of the PCNA gene which plays an essential role in DNA replication in mammals. Here we show that the sequence of the rice PCNA gene supports this proposal. The rice gene consists of four exons. The 5'-flanking region contains a variety of sequences similar to several consensus sequences believed to be important for the regulation of gene expression in eukaryotes. Determination of the transcription-start site and the structure of the 3'-flanking region of the gene indicated that the coded mRNA is 1073 bases. The rice PCNA genomic and cDNA clones are composed of 789 nucleotides; they encode a putative protein of 263 amino acids having a molecular mass of 29275 Da. Comparison of the coding regions of rice PCNA and rat PCNA revealed about 64% similarity at the nucleotide level and about 62% similarity at the amino acid level. Furthermore, comparison of the predicted amino acid sequence of the soybean PCNA with the rice PCNA sequence indicated a high degree of similarity (88%). The structural similarity between PCNA from plants and animals, despite the distant evolutionary relationship, indicates a strong selection pressure for conservation of this structure and suggests the presence of conserved DNA-replication mechanisms throughout the eukaryotes.

Homologous DNA sequences on the virulence plasmids of pathogenic Yersinia and Salmonella dublin Lane

Yersinia and Salmonella harbour plasmids that encode traits important for virulence, enabling both pathogenic genera to survive and grow in cells of the reticulo-endothelial organs during systemic infections. We have detected DNA homology between the Salmonella dublin virulence plasmid pSDL2 and the plasmids of the pathogenic Yersinia species pestis, pseudotuberculosis, and enterocolitica. Three regions of pSDL2 were found to share homology with the virulence plasmid pIB1 of Yersinia pseudotuberculosis. Two separate hybridizing segments mapped within the previously characterized 6.4 kb vir region of pSDL2 in the SalI B fragment. The third homologous region involved the replicon of pIB1, which hybridized to the SalI C2 fragment of pSDL2. The virulence plasmid pCD1 from Y. pestis showed similar homology with the three regions of pSDL2. Homologies to the vir and SalI C2 regions of pSDL2 were also found on plasmids from Yersinia enterocolitica serotypes 0:9, 0:3 and 0:5, 27. The discovery of separate homologous regions on the virulence plasmids of Salmonella and Yersinia suggests a distant evolutionary relationship.

Comparison of the structures of globins and phycocyanins: Evidence for evolutionary relationship

Globins and phycocyanins are two classes of proteins with different function, different ligands, and no substantial sequence similarity, yet the conformations of their polypeptide chains show very similar folding patterns. Does this arise from a genuine, albeit very distant, evolutionary relationship, or does it represent a common solution of a structural problem? We address this question by a very detailed comparison of the structures of the two protein families. An analysis of the helices and their interactions shows many features common to globins and phycocyanins, including some exceptional features of the globins such as a 3-10 C helix and the unusual "crossed-ridge" packing pattern at the B/E helix interfaces. We conclude that the evidence supports the hypothesis of distant evolutionary relationship between globins and phycocyanins.

Complete nucleotide sequence of the M RNA segment of Uukuniemi virus encoding the membrane glycoproteins G1 and G2

We have determined the complete nucleotide sequence of the virion M RNA segment of Uukuniemi virus ( Uukuvirus genus, Bunyaviridae) from cloned cDNA. The RNA that encodes the two membrane glycoproteins G1 and G2 is 3231 residues long (mol wt 1.1 × 10 6). The 5′ and 3′ ends of the RNA are partially complementary to each other for some 30 bp, enabling the formation of a stable panhandle structure (ΔG = −40 kcal/mol) and the circularization of the molecule. The extreme 5′ and 3′ terminal nucleotides are identical for 10 to 13 residues to those of the M RNA of Punta Toro and Rift Valley fever viruses, two members of the Phlebovirus genus. A single open reading frame comprising 1008 amino acid residues (mol wt 113,588) was found in the mRNA-sense strand between nucleotides 18 and 3042. This probably corresponds to the previously identified 110,000-Da precursor (pl 10) of G1 and G2. By comparing the partial aminoterminal sequences of purified G1 and G2 with the deduced protein sequence we confirmed that the gene order is NH 2-G1-G2-COOH. Both mature G1 and G2 are preceded by a stretch of 17 predominantly hydrophobic amino acids likely to represent the signal sequences. At their COON-terminal ends, G1 and G2 have a hydrophobic stretch of amino acids, 19 and 27 residues, respectively, that probably anchors the proteins to the lipid bilayer. The sequence indicates that mature G2 is 495 amino acids long (mol wt 54,869), whereas the exact size of G1 is unclear, since the location of the COON-terminus of G1 is not known. An upper value of 479 amino acids (mol wt 55,181) can, however, be suggested. Both G1 and G2 contain four potential glycosylation sites for Asn-linked glycans and both are unusually rich in cysteines, 6.1% in G1 and 5.4% in G2. Comparison of the amino acid sequence of the M RNA product of Uukuniemi virus with that of Punta Toro and Rift Valley fever viruses showed in both cases a weak homology that was more pronounced for the proteins located at the COON-terminal end of the precursor. This suggests a distant evolutionary relationship between the Phlebo- and Uukuvirus genera.

Molecular analysis of the human class I alcohol dehydrogenase gene family and nucleotide sequence of the gene encoding the beta subunit.

Human alcohol dehydrogenase (ADH) exists as a heterogeneous group of isozymes capable of oxidizing a wide variety of aliphatic and aromatic alcohols. The five distinct human ADH subunits, each encoded by a separate gene, are differentially expressed during development and are subject to tissue-specific regulation. To analyze the organization and regulation of human ADH genes we first isolated a cDNA clone (pADH12) encoding the 3' portion of the beta ADH gene. In the current study pADH12 was used to screen a human genomic library, and several overlapping and nonoverlapping clones were selected. Hybridization and partial nucleotide sequence analyses of the clones indicated that three full-length human ADH genes encoding the alpha, beta, and gamma subunits were isolated. Human genomic DNA hybridization results indicate that the alpha, beta, and gamma ADH genes form a closely related gene family and suggest that the other known human ADH genes (i.e. those encoding the pi and chi subunits) share a more distant evolutionary relationship. Nucleotide sequence analysis of the beta ADH gene reveals that the coding region is interrupted by eight introns and spans approximately 15 kilobases. A presumptive transcription initiation site for the beta ADH gene was located by S1 nuclease mapping at a position 70 base pairs upstream of the start codon. The 5' flanking region possesses a TATA box promoter element as well as two tandem DNA sequences which display homology to previously examined glucocorticoid-responsive elements.

Characterization and molecular cloning of a human parvovirus genome.

The genome of the small human virus serologically associated with erythrocyte aplasia and erythema infectiosum (fifth disease) is shown to be a linear, nonpermuted, single-stranded DNA molecule with self-priming hairpin termini, properties which are characteristic of the genomes of the family Parvoviridae. This human parvovirus chromosome was molecularly cloned into bacterial plasmid vectors and the cloned DNA was used to explore its relatedness to other mammalian parvovirus serotypes by DNA:DNA hybridization. It is not related to the human adeno-associated viruses but does show a distant evolutionary relationship to genomes of the helper-independent parvoviruses of rodents. This strongly suggests that it is an autonomous parvovirus, and as such is the first example of a member of this group of common animal pathogens to cause disease in man.

Structure of the influenza C glycoprotein gene as determined from cloned DNA

The complete nucleotide sequence of RNA segment 4 of influenza C/JHB/1/66 virus has been determined, utilizing cloned cDNA derived from the viral RNA segment. The gene is 2073 nucleotides in length, and can code for a polypeptide of 655 amino acids, which corresponds to the viral glycoprotein. The predicted polypeptide has a molecular weight of 72063, not including oligosaccharides linked to eight predicted glycosylation sites. The influenza C glycoprotein shares structural features with hemagglutinin (HA) glycoproteins of influenza A and B viruses, including three stretches of hydrophobic amino acids believed to function as a signal sequence, a fusion function, and a membrane anchor. However, a substantial part of the protein lacks direct sequence homology to these HA glycoproteins. The results suggest a more distant evolutionary relationship between influenza C virus and influenza A and B viruses, compared to that between influenza A and B themselves.

Structural homology of the major internal proteins of endogenous type C viruses of two distantly related species of old world monkeys: Macaca arctoides and Colobus polykomos

The major internal protein (p30) of MAC-1, an endogenous type C virus of Macaca arctoides and the p30 of CPC-1, an endogenous type C virus of Colobus polykomos were purified and subjected to primary structure analysis. Despite the distant evolutionary relationship (≈20 Myr) between these two species of Old World monkeys, the amino acid compositions of the viral p30s were very similar and their COOH-terminal sequences (5 residues) were found to be identical. Moreover, the NH 2-terminal sequences (up to 36 residues) differed only in three positions. Both the NH 2- and COOH-terminal sequences showed extensive homology to respective sequences of p30s of known type C viruses from other mammalian species. Statistical analysis of the sequence relatedness revealed that MAC-1 and CPC-1 p30s are not more closely related to the p30s of another family of endogenous primate viruses isolated from baboons ( Papio genus) than they are to p30s of those viruses isolated from lower mammals. On the basis of these p30 sequence relationships MAC-1 and CPC-1 together with MMC-1, an endogenous virus of Macaca mulatta, can be classified into a new (fourth) subgroup. Avian reticuloendotheliosis virus and its relatives, transforming viruses of birds are more related to this primate virus subgroup than to any of the three other subgroups of mammalian type C viruses.

Alignment statistic for identifying related protein sequences.

Closely related proteins show an obvious kinship by having numerous matching amino acids in their aligned sequences. Kinship between anciently separated proteins requires a statistical evaluation to rule out fortuitous similarities. A simple statistic is developed which assumes equal probability for all codon pairs, and a table of critical values for amino acid sequence alignments of lengthnments of length 200 or less is presented. Applying this statistic to V and C regions of immunoglobulin chains, aligned on the basis of shared features of three-dimensional structure, provides evidence that the V and C sequences descended from a common ancestor. Similarly the distant evolutionary relationship of dehydrogenases, flavdoxin, and subtilisin, suggested by structural alignments, is verified. On the other hand, the statistic does not verify a common evolutionary origin for the heme binding pocket in globins and cytochrome bs. Empirical evidence from the distribution of MMD values of amino acid pairs in comparisons of misaligned polypeptide chains and from Monte Carlo trials of sequences aligned with arbitrary gaps supports the validity of the statistic.