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PubMed1994

Parallel beta/alpha-barrels of alpha-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase versus the barrel of beta-amylase: evolutionary distance is a reflection of unrelated sequences.

The structures of functionally related beta/alpha-barrel starch hydrolases, alpha-amylase, beta-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase, are discussed, their mutual sequence similarities being emphasized. Since these enzymes (except for beta-amylase) along with the predicted set of more than ten beta/alpha-barrels from the alpha-amylase enzyme superfamily fulfil the criteria characteristic of the products of divergent evolution, their unrooted distance tree is presented.

Amino Acid Sequence↗
PubMed1984

Structural and genetic relationships between cytosolic and mitochondrial isoenzymes.

The most common type of genetic relationship between cytosolic and mitochondrial isoenzymes will probably be found to be divergent evolution from a common ancestral form. This is firmly established for the aspartate aminotransferases and less directly so in other cases. The two isoenzymes of aspartate aminotransferase have evolved at roughly equal rates at the level of total amino acid sequence but certain limited surface regions of the mitochondrial form have been much more highly conserved than corresponding regions in the cytosolic protein; these regions probably play a role in topogenesis of the mitochondrial isoenzyme. It is of interest that nearly all mitochondrial proteins are initially synthesised as precursors of molecular weight greater than the mature forms. In the case of aspartate aminotransferase, and possibly of other such isoenzymes, the N-terminus of the mature protein is nearly coincident with that of the cytosolic isoenzyme. Hence during evolution either the gene for the mitochondrial isoenzyme has gained an extra coding region for this N-terminal extension or, less likely, the structural gene for the cytosolic form has suffered a sizeable terminal deletion. Cytosolic and mitochondrial superoxide dismutases have not shared a common ancestral form as shown by the fact that their primary structures are completely unrelated. On the other hand, the mitochondrial and prokaryotic enzymes are clearly related. There is now, however, evidence to suggest that some prokaryotes possess a copper/zinc enzyme related to the eukaryotic cytosolic form. Hence the possibility arises that primitive prokaryotes possessed both proteins. The copper/zinc superoxide dismutase has been retained in the cytosol of eukaryotic cells and a few bacterial species.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1988

Yeast gene SRP1 (serine-rich protein). Intragenic repeat structure and identification of a family of SRP1-related DNA sequences.

We have isolated and sequenced a yeast gene encoding a protein (Mr 24,875) very rich in serine (SRP) and alanine residues that accounted for 25% and 20% of the total amino acids, respectively. The SRP1 gene is highly expressed in culture conditions leading to glucose repression (Marguet & Lauquin, 1986), the amount of SRP1 mRNA representing about 1 to 2% of total poly(A)+ RNA. A repetitive structure of eight direct tandem repeats 36-base long, also reflected in the amino acid sequence, was found in the second half of the open reading frame. The consensus amino acid sequence of the repeat was Ser-Ser-Ser-Ala-Ala-Pro-Ser-Ser-Ser-Glu-Ala-Lys. Replacing the genomic copy of the cloned gene with a disrupted SRP1 gene indicated that the SRP1 gene was not essential for viability in yeast, but several SRP1-homologous sequences were found within the yeast genome, raising the possibility that the disrupted SRP1 gene is rescued by one of the other SRP-homologous sequences. Complete separation of yeast chromosomes by contour-clamped homogeneous field electrophoresis indicated that, apart from chromosome V, which carries the SRP1 gene, 12 chromosomes have SRP-related sequences with various degrees of homology. These sequences were located on chromosomes XV, VII and XI under stringent conditions of hybridization (tm -20 degrees C), and observed on chromosomes I, II, III, IV, VI, VIII, X, XI and XII, only under low-stringency conditions (tm -40 degrees C). Northern blot analysis of both the wild type and SRP1-disrupted strains indicated that along with SRP1 at least one more member of the SRP family was transcribed to a 0.7 kb (1 kb = 10(3) bases) polyadenylated RNA species clearly distinct from the SRP1-specific mRNA (1 kb long). Analyses of the SRP1 repeat domain suggested a model for the divergent evolution of the repeats in the SRP1 sequence.

Amino Acid Sequence↗
PubMed1986

Point mutations in the U3 region of the long terminal repeat of Moloney murine leukemia virus determine disease specificity of the myeloproliferative sarcoma virus.

The myeloproliferative sarcoma virus (MPSV) is made up entirely of sequences derived from the Moloney murine leukemia virus (Mo-MuLV) and the cellular mos oncogene. As other members of the Moloney murine sarcoma virus (Mo-MuSV) family, MPSV transforms fibroblasts in vitro and causes sarcomas in vivo. In addition, however, MPSV also causes an acute myeloproliferative disease in adult mice. The mos oncogene is essential for its transforming capacity, but sequences specific to the long terminal repeat (LTR) U3 region of MPSV account for its expanded target specificity as compared to Mo-MuSV (C. Stocking, R. Kollek, U. Bergholz, and W. Ostertag, Proc. Natl. Acad. Sci. USA 82, 5746-5750 (1985)). The U3 region of the LTR of MPSV is, however, closely related to that of the Mo-MuLV, and it appeared likely that the difference between MPSV and Mo-MuSV was caused by a divergent evolution of Mo-MuSV LTRs. In this paper, we show that this is not the case. The few nucleotide differences in the LTR between Mo-MuLV and MPSV are crucial for the expanded host range of MPSV. Moreover, Mo-MuLV-related gag sequences retained in MPSV are not essential for the distinctive biological properties of MPSV.

Animals↗
PubMed1988

The 5'-terminal sequence of VSV(NJ) (Ogden): is the interaction of the NS protein with the NS binding site responsible for heterotypic interference activity?

The 5'-terminal sequence of VSV(NJ) (Ogden) and VSV(NJ) (Hazelhurst) was compared in an attempt to understand why the defective interfering particle, DI-LT, heterotypically interferes with VSV(NJ) (Ogden) but not with VSV(NJ) (Hazelhurst). The 5'-terminal sequence of VSV(NJ) (Ogden) genomic RNA was determined by direct RNA sequencing and by DNA sequencing of cDNA clones of the 3'-terminal sequence of VSV(NJ) (Ogden) DI particle genome. Primer extension analysis of the 5'-terminus of VSV(NJ) (Ogden) standard genomic RNA confirmed these data. Within the last 47 nucleotides, equivalent to the negative-strand leader RNA, the only nucleotide changes between VSV(NJ) (Ogden) and VSV(NJ) (Hazelhurst) occur between nucleotides 19 and 26, representing part of the putative NS binding region described by Isaac and Keene (J. Virol. 43, 241-249 (1982] for VSV(IND) DI particles. The spacer (S) region, located between the polyadenylation signal of the L gene and the 47th nucleotide of the leader RNA, contains more differences. The polyadenylation signal of the L gene is fully conserved, but the remainder of the L gene region (177 nucleotides) has highly diverged between VSV(NJ) (Ogden) and VSV(NJ) (Hazelhurst). The changes in the NS binding region of the negative-strand leader RNA provide further evidence for the divergent evolution of VSV(NJ) (Ogden) and VSV(NJ) (Hazelhurst). The NS binding region has been implicated as a crucial site for the initiation of RNA transcription and replication. The interaction of the NS protein with this site may determine the ability of DI particles to interfere heterotypically.

Base Sequence↗
PubMed1989

The B allele of the NS gene of avian influenza viruses, but not the A allele, attenuates a human influenza A virus for squirrel monkeys.

The nonstructural (NS) genes of avian influenza A viruses have been divided into two groups on the basis of nucleotide sequence homology, which we have referred to here as alleles A and B. We sequenced the NS genes of eight additional avian influenza A viruses in order to define the differences between these two alleles more thoroughly. Four of the viruses had NS gene sequences which resembled that of A/FPV/Rostock/34 and belonged to allele A while the other four viruses had NS gene sequences more similar to that of A/Duck/Alberta/76 and belonged to allele B. There was approximately 90% sequence homology within alleles and 72% homology between alleles. As previously reported the NS genes of human influenza A viruses belong to allele A. We constructed single gene avian-human reassortant influenza A viruses containing an allele A or B NS gene segment from an avian influenza A virus and all other genes from a human influenza A virus and tested these reassortants for their ability to grow in the respiratory tract of a nonhuman primate. Reassortants containing an avian NS gene segment of allele B were significantly restricted in growth in the respiratory tract of squirrel monkeys while reassortants with an allele A NS gene segment were not. The divergent evolution of the B NS allele in birds may have resulted in gene products which do not function optimally in cooperation with genes from a human virus in viral replication in primate respiratory epithelium.

Alleles↗
PubMed1992

Possible use of similar framework region amino acid sequences between human and mouse immunoglobulins for humanizing mouse antibodies.

We have previously noted that a specific amino acid sequence could form the second framework region of human, mouse and rabbit immunoglobulin light chains, suggesting that this sequence has been preserved for 80 million years. Through divergent evolution, each species has acquired a different set of framework region sequences; however, these sets still share a few similar or identical amino acid sequences. In the present study, we have identified such sequences for all four framework regions between human and mouse immunoglobulin light and heavy chains. They may be useful in humanizing or reshaping mouse or rat antibodies for therapeutic applications in human patients.

Amino Acid Sequence↗
PubMed1993

Nucleotide sequence of sweet clover necrotic mosaic dianthovirus RNA-1.

The complete nucleotide sequence of sweet clover necrotic mosaic dianthovirus (SCNMV) RNA-1 has been determined. RNA-1 consists of 3876 nucleotides in length, containing three large open reading frames (ORFs). The 5'-proximal, internal and 3'-terminal ORFs potentially encode 27-kDa, 57-kDa and 37-kDa proteins, respectively. The frameshift event between the C-terminus of the 27-kDa protein and extension of the N-terminus of the 57-kDa protein may result in the formation of a 88-kDa protein which is presumed to be a replicase. The 37-kDa coat protein ORF is located immediately downstream of the 57-kDa ORF. The same genome organization and high similarity (80-92%) of both the nucleotide sequences and the deduced amino acid sequences between red clover necrotic mosaic dianthovirus and SCNMV suggest that they originate from a common progenitor, but have divergent evolution later. Striking similarity was detected between the putative RNA-dependent RNA polymerase of SCNMV and that of the tombus-, carmo-, necro-, machlomo- and luteoviruses, supporting a proposal that they belong to the same virus supergroup although there is a relatively low degree of coat protein sequence similarity in these viruses.

Amino Acid Sequence↗
PubMed1995

Genomic structure of SAS, a member of the transmembrane 4 superfamily amplified in human sarcomas.

SAS is a recently identified member of the transmembrane 4 superfamily (TM4SF) that is frequently amplified in human sarcomas. To further its characterization and to confirm its classification, the genomic structure of the SAS gene was determined. The SAS gene covers approximately 3.2 kb of DNA. It contains six exons within its translated region, three of which are highly conserved in the TM4SF. 5' to the translation start site are two putative transcription start sites, two CCAAT consensus sequences, and potential binding sites for both Sp1 and ATF transcription factors. Comparison of SAS organization to human ME491, CD9, and CD53 and murine CD53 and TAPA-1 confirms that SAS is a member of this family of genes and is consistent with the theory that these genes arose through duplication and divergent evolution.

Amino Acid Sequence↗
PubMed1993

The 12-transmembrane helix transporters.

From the hydropathic profiles of their amino acid sequences many transport proteins are conceived to comprise 12-transmembrane alpha-helices. In only a few examples, however, is there genetical and/or biochemical evidence to support the 12-helix structure or illuminate the molecular mechanism of the transport process. A number of these transport proteins occur in evolutionarily related families, and sometimes superfamilies, indicating divergent evolution of the 12-helix structure. Other individual members or families of transport proteins are sufficiently different in amino acid sequence for their evolution to have taken place by convergence from independent ancestral origins.

Amino Acid Sequence↗
PubMed1993

Topological similarities in TGF-beta 2, PDGF-BB and NGF define a superfamily of polypeptide growth factors.

BACKGROUND: The development of functional diversity through gene duplication and subsequent divergent evolution can give rise to proteins that have little or no sequence similarity, but retain similar topologies. RESULTS: The crystal structures of nerve growth factor, transforming growth factor-beta 2 and platelet-derived growth factor-BB show that all three are based on a cystine-knot plus beta-strands topology. There is very little sequence identity between the three proteins and the relationship between the structures had not been deduced from sequence comparisons. Each growth factor is usually active as a dimer; each exists as a dimer in the crystal, but the relative orientations of the protomers are different in each case. CONCLUSION: The structural motif of disulphide bonds and hydrogen-bonded beta-strands unexpectedly found in these three growth factors acts as a stable framework for elaboration of loops of low sequence similarity that contain the specificity for receptor interaction.

Amino Acid Sequence↗
PubMed2004

A 14-3-3 protein of Chlamydomonas reinhardtii associated with the endoplasmic reticulum: nucleotide sequence of the cDNA and the corresponding gene and derived amino acid sequence.

Two major 14-3-3 proteins of the unicellular green alga Chlamydomonas reinhardtii were purified and partially sequenced. The obtained data show that the 30-kDa isoform predominant in the cytosol is encoded by a previously cloned and sequenced 14-3-3 cDNA whereas the 27-kDa isoform represents a new 14-3-3 protein which is largely associated with the endoplasmic reticulum (ER). Therefore, the corresponding cDNA was cloned and sequenced. The nucleotide sequence of this new cDNA species and the derived amino acid sequence differ considerably from the previously cloned Chlamydomonas 14-3-3 cDNA. The conclusion that the divergent evolution of the corresponding genes must have started rather early as compared to the 14-3-3 genes of other organisms was corroborated by their different genomic organization. The amino acid sequences of both 14-3-3 isoforms were comparatively analysed to find differences which might be responsible for their differential binding to the ER.

14-3-3 Proteins↗
PubMed2003

Comparison of glycosyltransferase families using the profile hidden Markov model.

In order to investigate the relationship between glycosyltransferase families and the motif for them, we classified 47 glycosyltransferase families in the CAZy database into four superfamilies, GTS-A, -B, -C, and -D, using a profile Hidden Markov Model method. On the basis of the classification and the similarity between GTS-A and nucleotidylyltransferase family catalyzing the synthesis of nucleotide-sugar, we proposed that ancient oligosaccharide might have been synthesized by the origin of GTS-B whereas the origin of GTS-A might be the gene encoding for synthesis of nucleotide-sugar as the donor and have evolved to glycosyltransferases to catalyze the synthesis of divergent carbohydrates. We also suggested that the divergent evolution of each superfamily in the corresponding subcellular component has increased the complexities of eukaryotic carbohydrate structure.

Amino Acid Sequence↗
PubMed2005

Comparative analysis of the distribution of choline acetyltransferase in the central nervous system of cyprinids.

The general organization of the cholinergic system in the central nervous system is similar among vertebrates, though fish show higher variability. Thus, in zebrafish, cholinergic cells are absent from the habenula and the rhombencephalic reticular formation, where such neurons are present in most vertebrate species analyzed. In this work, we compared the distribution of choline acetyltransferase in the central nervous system of both zebrafish and tench, in order to investigate whether these divergences in the distribution of cholinergic cells in zebrafish are species-specific, or a feature shared by members of the cyprinid family. Our data show that these two cyprinid possess in common some peculiarities in their cholinergic system that are not present in the rest of fish analyzed (e.g. absence of cholinergic cells in the habenula and their presence in the descendent octaval nucleus). Nonetheless, some cholinergic cells were observed in the dorsal thalamus and rhombencephalic reticular nuclei of the tench, which were absent in the same regions in zebrafish. The comparative analysis suggests a divergent evolution of the cholinergic system among close-related cyprinid species.

Animals↗
PubMed2005

Mycoplasma bovis shares insertion sequences with Mycoplasma agalactiae and Mycoplasma mycoides subsp. mycoides SC: Evolutionary and developmental aspects.

Three new insertion elements, ISMbov1, ISMbov2 and ISMbov3, which are closely related to ISMag1 (Mycoplasma agalactiae), ISMmy1 and IS1634 (both Mycoplasma mycoides subsp. mycoides SC), respectively, have been discovered in Mycoplasma bovis, an important pathogen of cattle. Southern blotting showed that the genome of M. bovis harbours 6-12 copies of ISMbov1, 11-15 copies of ISMbov2 and 4-10 copies of ISMbov3, depending on the strain. A fourth insertion element, the IS30-like element, is present in 4-8 copies. This high number of IS elements in M. bovis, which represent a substantial part of its genome, and their relatedness with IS elements of both M. agalactiae and M. mycoides subsp. mycoides SC suggest the occurrence of two evolutionary events: (i) a divergent evolution into M. agalactiae and M. bovis upon infection of different hosts; (ii) a horizontal transfer of IS elements during co-infection with M. mycoides subsp. mycoides SC and M. bovis of a same bovine host.

Animals↗
PubMed2004

Characterization of the Anaplasma marginale msp2 locus and its synteny with the omp1/p30 loci of Ehrlichia chaffeensis and E. canis.

Major surface protein 2 (MSP2) is an immunodominant and antigenically variant protein in the outer membrane of the rickettsia Anaplasma marginale. MSP2 variation is generated by recombination into a single operon-linked genomic expression site. The complete 5.6-kb msp2 locus was identified by sequencing a 90-kb region of the St. Maries strain of A. marginale. The locus encoded, in a 5' to 3' direction, a transcriptional regulator followed by five outer membrane proteins, OMP1, OpAG3, OpAG2, OpAG1, and MSP2. The sequences of this entire locus were analyzed using six genetically and phenotypically distinct strains of A. marginale. The overall locus structure was highly conserved with 100% identity among strains in the transcriptional regulator. Synonymous and nonsynonymous exchanges were infrequent in omp1 and rare in opag1 and opag2 among the six strains without strong bias for either type of exchange (neutral mutations). In contrast, mutations in opag3 seem to underlie purifying (negative) selection reflecting pressure to retain protein structure, in marked contrast to the highly antigenically variant MSP2. Interestingly, the 5' structure of this A. marginale msp2 locus is conserved in the omp1 gene locus of Ehrlichia chaffeensis and p30 gene locus of E. canis despite marked divergence between genera in the structure of the 3' region of the loci. This supports the hypothesis that the expression sites of these important immunogenic proteins are derived from a common precursor with later divergent evolution along genus lines.

Anaplasma marginale↗
PubMed2003

Apolipophorin III: a lipid-triggered molecular switch.

Apolipophorin III (apoLp-III) is a low molecular weight exchangeable apolipoprotein that plays an important role in the enhanced neutral lipid transport during insect flight. The protein exists in lipid-free and lipid-bound states. The lipid-bound state is the active form of the protein and occurs when apoLp-III associates with lipid-enriched lipophorins. ApoLp-III is well characterized in two evolutionally divergent species: Locusta migratoria and Manduca sexta. The two apolipoproteins interact in a similar manner with model phospholipid vesicles, and transform them into discoidal particles. Their low intrinsic stability in the lipid-free state likely facilitates interaction with lipid surfaces. Low solution pH also favors lipid binding interaction through increased exposure of hydrophobic surfaces on apoLp-III. While secondary structure is maintained under acidic conditions, apoLp-III tertiary structure is altered, adopting molten globule-like characteristics. In studies of apoLp-III interaction with natural lipoproteins, we found that apoLp-III is readily displaced from the surface of L. migratoria low-density lipophorin by recombinant apoLp-III proteins from either L. migratoria or M. sexta. Thus, despite important differences between these two apoLp-IIIs (amino acid sequence, presence of carbohydrate), their functional similarity is striking. This similarity is also illustrated by the recently published NMR solution structure of M. sexta apoLp-III wherein its molecular architecture closely parallels that of L. migratoria apoLp-III.

Animals↗
PubMed2006

Genospecies of Borrelia burgdorferi sensu lato in Ixodes ricinus ticks from the Autonomous Province of Trento, Italy.

Sequences of the variable intergenic spacer region 5S (rrfA) 23S (rrlB) rRNA were used to identify Borrelia genospecies present in Ixodes ricinus nymphs collected from the Lamar Lakes area of the Province of Trento, Italy (overall prevalence=6.3%). Four genospecies were identified, one for the first time in this Province (B. valaisiana), and three which have been noted previously (B. afzelii, B. garinii, and B. burgdorferi s.s.). In order to compare the genetic variability of these genospecies in Trento with that at a European level, our 21 sequences (15 new haplotypes) and all appropriate European Borrelia sequences registered in GenBank (up to the end of 2004) were subjected to a phylogenetic analysis (for a total of 73 sequences and 43 haplotypes). Clusters of sequences representing the five main European genospecies (afzelii, garinii, burgdorferi s.s., valaisiana, lusitaniae) are well-supported. At least two other groups of haplotypes (genospecies) are suggested by our analysis; moreover, divergent evolution may be occurring in several genospecies. The maximum uncorrected pairwise differences between sequences within genospecies ranges from 1.5% (B. burgdorferi s.s.), to 2.3% (B. garinii and B. valaisiana) to 4.7% (B. afzelii), and are not correlated with geographical distribution. Within the Province of Trento, these values for the same genospecies are 1.5%, 2.3%, 0.9%, 1.9%, respectively. These high mutation rates within genospecies suggest that the sequencing of haplotypes should continue if we are to fully understand and monitor the evolution and epidemiology of Borrelia.

Animals↗