What determines the rate of sequence evolution?

High rates of amino-acid sequence evolution have sometimes been considered to be diagnostic for genes undergoing adaptive change. However, two recent studies have shown that rapid evolution of amino-acid sequence can also be congruent with neutrality.     

Nucleotide sequence evidence of the unicentric origin of the βC mutation in Africa

Summary The origin of the ^C mutation was studied by characterizing nucleotide sequence polymorphisms on ^C chromosomes of patients from various African countries. In the majority of cases, the ^C mutation was found in linkage disequilibrium with a single chromosomal structure as defined by classical RFLP haplotypes, intergenic nucleotide sequence polymorphisms immediately upstream of the -globin gene, and intragenic -globin gene polymorphisms (frameworks). In addition, three atypical variant chromosomes carrying the ^C mutation were observed, and are most probably explained either by a meiotic recombination (two cases) or by one nucleotide substitution occurring in an unstable array of tandemly repeated sequences (one case). These data demonstrate the unicentric origin of the ^C mutation in central West Africa, with subsequent mutational modification in a small number of instances. The data also supports gene flow of the ^C chromosome from subsaharan Africa to North Africa.     

Isolation and characterization of the mitochondrial ATP synthase fromChlamydomonas reinhardtii. cDNA sequence and deduced protein sequence of the α subunit

We have isolated the F₀F₁-ATP synthase complex from oligomycin-sensitive mitochondria of the green algaChlamydomonas reinhardtii. A pure and active ATP synthase was obtained by eans of sonication, extraction with dodecyl maltoside and ion exchange and gel permeation chromatography in the presence of glycerol, DTT, ATP and-21. The enzyme consists of 14 subunits as judged by SDS-PAGE. A cDNA clone encoding the ATP synthase subunit has been sequenced. The deduced protein sequence contains a presequence of 45 amino acids which is not present in the mature protein. The mature protein is 58–70% identical to corresponding mitochondrial proteins from other organisms. In contrast to the ATP synthase subunit fromC. reinhardtii (Franzen and Falk, Plant Mol Biol 19 (1992) 771–780), the protein does not have a C-terminal extension. However, the N-terminal domain of the mature protein is 15–18 residues longer than in ATP synthase subunits from other organisms. Southern blot analysis indicates that the protein is encoded by a single-copy gene.Abbreviations DM dodecyl--D-maltoside - OSCP oligomycin sensitivity conferring protein - PMSF phenyl-methylsulfonylfluoride - DTT dithiothreitol - EDTA ethylenediaminotetraacetic disodium salt     

5′ Flanking sequence of the hamster desmin gene

Molecular Biology Reports -     

Nucleotide sequence of the humanθ 1-globin gene

We have cloned and sequenced the human ₁-globin gene. The nucleotide sequence and organization of the human ₁ gene (exons, introns, promoter, and polyadenylation signals) are similar to those reported for the orangutan ₁-globin gene. If these genes are functional, the sequences of their ₁-globin chains would differ by only one amino acid residue (at position 137).This research was supported by USPHS Research Grants HLB-05168 and HLB-15158. This is contribution No. 1085 from the Department of Cell and Molecular Biology at the Medical College of Georgia in Augusta.     

Hucleotide sequence of the Bos indicus α‐lactalbumin 5’ flanking region: Comparison with the 605 taurus sequence

Abstract

The 5’ flanking region of the α‐lactalbumin gene from Bos indicus (Brahman) and Bos taurus (Holstein) have been sequenced. The sequences were compared to detect potential sequence variations. The 538 bp of 5’ flanking region contained nine sequence variations between the two breeds. Seven of the variations occur in the 5’ flanking region of the α‐lactalbumin gene and two occur in the region encoding the 5’ untranslated region of the mRNA. Seven of the variations are conservative purine to purine or pyrimidine to pyrimidine variations, while two are purine to pyrimidine variations.     

What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence

The German Neurospora Genome Project has assembled sequences from ordered cosmid and BAC clones of linkage groups II and V of the genome of Neurospora crassa in 13 and 12 contigs, respectively. Including additional sequences located on other linkage groups a total of 12 Mb were subjected to a manual gene extraction and annotation process. The genome comprises a small number of repetitive elements, a low degree of segmental duplications and very few paralogous genes. The analysis of the 3218 identified open reading frames provides a first overview of the protein equipment of a filamentous fungus. Significantly, N.crassa possesses a large variety of metabolic enzymes including a substantial number of enzymes involved in the degradation of complex substrates as well as secondary metabolism. While several of these enzymes are specific for filamentous fungi many are shared exclusively with prokaryotes.     

A reevaluation of the amino acid sequence of human follitropin β-subunit

A collaborative study from two laboratories has been undertaken to re-evaluate the human follitropin β-subunit sequence (hFSHβ), since areas of uncertainty remain in the wake of two earlier reports. The first report was by Shome and Parlow (1974). The second, by Saxena and Rathnam (1976), proposed revisions for sequence not definitively placed in the first study, as well as some differences in other placements. We have re-examined the sequence of the hFSHβ with more recent methodology. This has led to revision of certain areas of the sequence and resolution of differences between the two earlier proposals. Specifically, an-Ile-Ser- is established at 21–22, Asp at 41, Arg at 44, Lys at 46, and Glu at 111. These were areas of disagreement in the earlier proposals. A definitive placement of the residues around tryptophan-27 has now been obtained by three laboratories. C-terminal heterogeneity was observed with subunits ending at residue 107, 109, or 111. N-terminal heterogeneity has been observed in all preparations examined to date. A significant population of molecules with a proteolytic nick between residues 38–39 is noted. This is very likely an artifact of the collection and processing. The preparations examined in the present studies showed no evidence of residues 112–118 proposed by Saxena and Rathnam.     

Nucleotide sequence of the gene presumably encoding the adsorption protein of filamentous phage φLf

A 1170-nucleotide fragment of φLf DNA was sequenced. This fragment contains an open reading frame, ORF367, encoding a protein of 367 amino acids (aa) (36710 Da). ORF367 is located downstream from the gene encoding the major coat protein (gVIIIp) and a Rho-independent termination signal. Sequence analysis revealed that the gene product has a Gly-rich domain (70 aa) at the center and a hydrophobic region (26 aa) at the C terminus. These structural features suggest that ORF367 may encode the adsorption protein of φLf.     

Evolution: What determines the rate of sequence evolution?

High rates of amino-acid sequence evolution have sometimes been considered to be diagnostic for genes undergoing adaptive change. However, two recent studies have shown that rapid evolution of amino-acid sequence can also be congruent with neutrality.     

The Escherichia coli genome sequence: the end of an era or the start of the FUN?

Our dream of determining the entire Escherichia coli K12 genome sequence has been realized. This calls for new approaches for the analysis of gene expression and function in biology's best-understood organism. Comparison of the E. coli genome sequence with others will provide important taxonomic insights and have implications for the study of bacterial virulence. Approximately 20% of E. coli genes have been designated FUN genes, because they have no known function or homologies to sequence databases. FUN genes promise to have an exciting impact on bacterial research. The post-genome era requires novel strategies that address gene regulation at the level of the entire cell. These strategies need to supersede the reductionist approach to genetic analysis. Only then will the genome sequence lead us to an understanding of how a bacterial cell really works.     

The nucleotide sequence of the β-glucosidase gene from Cellvibrio gilvus

A gene encoding β-glucosidase from Cellvibrio gilvus, a cellobiose-producing bacterium, was cloned into Escherichia coli and sequenced. The structural gene consisted of 2565 bp encoding 854 amino acid residues with a characteristic signal peptide. A typical promoter sequence and SD region were located upstream of the initiation ATG codon. A sequence (180 amino acids) having high homology with those of β-glucosidases from several microorganisms was found in the deduced amino acid sequence of C. gilvus β-glucosidase. This sequence contains the aspartic acid residue which was found to be an active site residue in Aspergillus wentii β-glucosidase A3. The β-glucosidase gene of C. gilvus contains a high amount (69.4%) of G+C. These bases are localized not in the 3rd position of the codon, as is usually observed in G+C-rich genes, but rather in the 1st position. This result in a peptide which contains an extremely high amount (48%) of four amino acids (Pro, Ala, Arg, Gly) coded by CCN, GCN, CGN, and GGN.     

Reassignment of the murine 3′TRDD1 recombination signal sequence

T cell receptor genes are assembled in developing T lymphocytes from discrete V, D, and J genes by a site-specific somatic rearrangement mechanism. A flanking recombination signal, composed of a conserved heptamer and a semiconserved nonamer separated by 12 or 23 variable nucleotides, targets the activity of the rearrangement machinery to the adjoining V, D, and J genes. Following the rearrangement of V, D, or J genes, their respective recombination signals are ligated together. Although these signal joints are allegedly invariant, created by the head-to-head abuttal of the heptamers, some do exhibit junctional diversity. Recombination signals were initially identified by comparison and alignment of germ-line sequences with the sequence of rearranged genes. However, their overall low level of sequence conservation makes their characterization solely from sequence data difficult. Recently, computational analysis unraveled correlations between nucleotides at several positions scattered within the spacer and recombination activity, so that it is now possible to identify putative recombination signals and determine and predict their recombination efficiency. In this paper, we analyzed the variability introduced in signal joints generated after rearrangement of the TRDD1 and TRDD2 genes in murine thymocytes. The recurrent presence of identical nucleotides inserted in these signal joints led us to reconsider the location and sequence of the TRDD1 recombination signal. By combining molecular characterization and computational analysis, we show that the functional TRDD1 recombination signal is shifted inside the putative coding sequence of the TRDD1 gene and, consequently, that this gene is shorter than indicated in the databases.     

Role of the carboxy-terminal sequence on the biological activity of human immune interferon (IFN-γ)

The biological activity of human immune interferon depends on its carboxy-terminal structure. New genes coding for mature immune interferon molecules lacking 4, 5, 6, 8, 9, 10 and 11 amino acid residues were constructed, expressed in Escherichia coli and purified to homogeneity. Deletions with 14 and 18 carboxy-terminal amino acids were obtained by limited proteolysis of full-length immune interferon with mouse submaxillary gland ‘Arg-C’ protease and human plasmin, respectively. If a limited number of carboxy-terminal residues are removed, the antiviral and antiproliferative activities and the potential to activate macrophages is drastically enhanced. Maximal enhancement is found with the deletion of 9 or 10 residues. However, removal of 14 or more carboxy-terminal residues results in a sharp decrease of activity. We suggest that human immune interferon is synthesized as a preprotein and that its activity is modulated by proteolytic digestion.     

The isolation and amino acid sequence of the β- and γ-subunits of the lectin from the seeds of Dioclea Grandiflora

Although the two smaller β- and γ- subunits of the lectin from Dioclea grandiflora were clearly resolved by sodium dodecyl sulphate (SDS) gel electrophoresis, the concensus of other techniques including ultracentrifugation, isoelectric focusing in 8 M urea, size-exclusion chromatography in dissociating solvents and amino acid and sequence analysis indicated that they were similar in molecular size and that they had arisen either by a single enzymic cleavage at Asn¹¹⁸-Ser¹¹⁹ in the middle of the 237 residue-long mature α-subunit or by multiple cleavages occurring during post-translational processing of intermediates. The existence of minor forms of the β- and γ- subunits resulting from a cleavage at Asn¹²⁴-Ser¹²⁵ of the α-subunit was also recognized. The results indicated that the apparent difference in molecular size of the β- and γ-subunits deduced from SDS-gel electrophoresis could be explained by the anomalous behaviour of both subunits in this separation technique. The structural features of the D. grandiflora lectin are compared with those of concanavalin A obtained from seeds of the botanically related Canavalia ensiformis.     

Reinvestigation of the N-terminal amino acid sequence of β-lipotropin from human pituitary glands

The N-terminal sequence of the first 60 amino acid residues of human β-LPH was reinvestigated by automated Edman degradation on the intact peptide. The result shows some differences with the recently proposed data. We have established the amino acid sequence of residues 9–26 to be Glu-Gly-Asp-Gly-Pro-Asp-Gly-Pro-Ala-Asp-Asp-Gly-Ala-Gly-Ala-Gln-Ala-Asp. From residues 1–8 and 27–60 the sequence is exactly identical with that of recently reported data.