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PubMed2004

Barriers built on claudins.

The fundamental functions of epithelia and endothelia in multicellular organisms are to separate compositionally distinct compartments and regulate the exchange of small solutes and other substances between them. Tight junctions (TJs) between adjacent cells constitute the barrier to the passage of ions and molecules through the paracellular pathway and function as a 'fence' within the plasma membrane to create and maintain apical and basolateral membrane domains. How TJs achieve this is only beginning to be understood. Recently identified components of TJs include the claudins, a family of four-transmembrane-span proteins that are prime candidates for molecules that function in TJ permeability. Their identification and characterization have provided new insight into the diversity of different TJs and heterogeneity of barrier functions in different epithelia and endothelia.

Amino Acid Motifs↗

PubMed2006

Trans-specificity at loci near the self-incompatibility loci in Arabidopsis.

We compared allele sequences of two loci near the Arabidopsis lyrata self-incompatibility (S) loci with sequences of A. thaliana orthologs and found high numbers of shared polymorphisms, even excluding singletons and sites likely to be highly mutable. This suggests maintenance of entire S-haplotypes for long evolutionary times and extreme recombination suppression in the region.

Alleles↗

PubMedDate not supplied

Genetic analyses of cis-acting sequences controlling expression of human immunodeficiency virus type 1 coreceptor-CCR5 gene in rabbits and CXCR4 gene in monkeys.

INTRODUCTION: Human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus all use chemokine receptors (CCR5, CXCR4, and minor receptors) to gain entry into a susceptible cell and establish infection successfully by way of membrane fusion. Many such chemokine receptors that can act as entry cofactors under in vitro conditions have been identified, but the roles of CCR5 and CXCR4 chemokine receptors in infection, tropism, and pathogenesis have been studied in greater detail. The promoter region of CCR5 gene is quite polymorphic in humans, and mutations that affect the progression of HIV-1 have been identified. STUDY DESIGN/METHODS: We studied the nature of mutations in the CCR5 promoter region in rabbits. Large number of mutations, deletions, substitutions, and point mutations were observed all along the 400 base pair region of the promoter. RESULTS: We show that rabbit CCR5 promoter possesses features common to both humans and monkeys and lacks the second highly polymorphic region B in the CCR5 promoter that was previously identified in monkeys. Besides providing important evolutionary information, our findings can directly make an impact on the known expression levels of CCR5 protein that can modulate the progression of HIV-1 in rabbits. The CXCR4 promoter of monkeys showed polymorphisms that were largely caused by single nucleotide changes when compared with humans. CONCLUSIONS: This distinctly different evolutionary pattern suggests a more important role for chemokine receptor-CCR5 in the host defense.

Animals↗

PubMed1995

The enigma PAI-2. Gene expression, evolutionary and functional aspects.

The type-2 plasminogen activator inhibitor (PAI-2) belongs to the ovalbumin subfamily of serpins. It exhibits close to 50% homology with several recently cloned protease inhibitors such as the leukocyte elastase inhibitor, the placental thrombin inhibitor and the squamous cell carcinoma antigen. PAI-2 exists in an intracellular, nonglycosylated form of 47 kDa and a secreted, glycosylated form of about 60 kDa. The PAI-2 gene does not have a signal peptide which might explain why the major portion of PAI-2 remains intracellularly. Several response elements have been identified in the promoter region which are necessary for constitutive and phorbol ester and retinoic acid induced expression of the gene. These include two AP-1 sites, and response elements for cAMP, glucocorticoids and retinoic acid. The physiological function of PAI-2 has not been clearly elucidated. It may have cytoprotective functions and appears to play a role in programmed cell death.

Amino Acid Sequence↗

PubMed2003

Comprehensive analysis of all triple helical repeats in beta-spectrins reveals patterns of selective evolutionary conservation.

The spectrin superfamily (spectrin, alpha-actinin, utrophin and dystrophin) has in common a triple helical repeating unit of ~106 amino acid residues. In spectrin, alpha and beta chains contain multiple copies of this repeat. beta-spectrin chains contain the majority of binding activities in spectrin and are essential for animal life. Canonical beta-spectrins have 17 repeats; beta-heavy spectrins have 30. Here, the repeats of five human beta-spectrins, plus beta-spectrins from several other vertebrates and invertebrates, have been analysed. Repeats 1, 2, 14 and 17 in canonical beta are highly conserved between invertebrates and vertebrates, and repeat 8 in some isoforms. This is consistent with conservation of critical functions, since repeats 1, 2 and 17 bind alpha-spectrin. Repeats 1 of beta-spectrins are not always detected by SMART or Pfam tools. A profile hidden Markov model of beta-spectrin repeat 1 detects alpha-actinins, but not utrophin or dystrophin. Novel examples of repeat 1 were detected in the spectraplakins MACF1, BPAG1 and plectin close to the actin-binding domain. Ankyrin binds to the C-terminal portion of repeat 14; the high conservation of this entire repeat may point to additional, undiscovered ligand-binding activities. This analysis indicates that the basic triple helical repeat pattern was adapted early in the evolution of the spectrin superfamily to encompass essential binding activities, which characterise individual repeats in proteins extant today.

Amino Acid Sequence↗

PubMed1998

Evolving views of protein glycosylation.

The composition, biosynthesis and known roles of oligosaccharides that are attached to glycoproteins suggest that multiple forces have driven the evolution of proteins that create and recognize these structures. The evolution of glycoprotein biosynthesis and recognition mechanisms can be best understood as a sequential development of functions associated with oligosaccharides.

Animals↗

PubMed1986

Protein structure and neutral theory of evolution.

The neutral theory of evolution is extended to the origin of protein molecules. Arguments are presented which suggest that the amino acid sequences of many globular proteins mainly represent "memorized" random sequences while biological evolution reduces to the "editing" these random sequences. Physical requirements for a functional globular protein are formulated and it is shown that many of these requirement do not involve strategical selection of amino acid sequences during biological evolution but are inherent also for typical random sequences. In particular, it is shown that random sequences of polar and amino acid residues can form alpha-helices and beta-strand with lengths and arrangement along the chain similar to those in real globular proteins. These alpha- and beta-regions in random sequences can form three-dimensional folding patterns also similar to those in proteins. The arguments are presented suggesting that even the tight packing of side groups inside protein core do not require very strong biological selection of amino acid sequences either. Thus many structural features of real proteins can exist also in random sequences and the biological selection is needed mainly for the creation of active site of protein and for their stability under physiological conditions.

Amino Acid Sequence↗

PubMed1990

Molecular evolution of the zinc-containing long-chain alcohol dehydrogenase genes.

Phylogenetic relationships and rates of nucleotide substitution were studied for alcohol dehydrogenase (ADH) genes by using DNA sequences from mammals and plants. Mammalian ADH sequences include the three class I genes and a class II gene from humans and one gene each from baboon, rat, and mouse. Plant sequences include two ADH genes each from maize and rice, three genes from barley, and one gene each from wheat and two dicots, Arabidopsis and pea. Phylogenetic trees show that relationships among ADH genes are generally consistent with taxonomic relationships: mammalian and plant ADH genes are classified into two distinct groups; primate class I genes are clustered; and two dicot sequences are clustered separately from monocot sequences. Accelerated evolution has been detected among the duplicated ADH genes in plants, in which synonymous substitutions occurred more often within the coenzyme-binding domain than within the catalytic domains.

Alcohol Dehydrogenase↗

PubMed2000

The molecular characterisation of mouse tspan-3.

The Tetraspanin/Transmembrane-4 Superfamily of cell surface molecules is defined by their four highly conserved transmembrane domains and is found in a wide variety of species and cell types. A common function for these molecules has yet to be discovered, however their broad expression patterns and conservation over evolution suggests that they will have an important general function relevant to many cell lineages. Here we describe the cloning and characterisation of the murine homologue of a recently described member of this superfamily, tspan-3. Murine tspan-3 was remarkably similar to the human molecule showing 88% identity at the nucleic acid level and 98% homology on the amino acid level. Northern blot analyses of mouse tspan-3 show a very broad pattern of expression, with expression readily detected in most organs including neural and bone marrow derived tissues.

Amino Acid Sequence↗

PubMed1999

Origin and evolution of the 1918 "Spanish" influenza virus hemagglutinin gene.

The "Spanish" influenza pandemic killed over 20 million people in 1918 and 1919, making it the worst infectious pandemic in history. Here, we report the complete sequence of the hemagglutinin (HA) gene of the 1918 virus. Influenza RNA for the analysis was isolated from a formalin-fixed, paraffin-embedded lung tissue sample prepared during the autopsy of a victim of the influenza pandemic in 1918. Influenza RNA was also isolated from lung tissue samples from two additional victims of the lethal 1918 influenza: one formalin-fixed, paraffin-embedded sample and one frozen sample obtained by in situ biopsy of the lung of a victim buried in permafrost since 1918. The complete coding sequence of the A/South Carolina/1/18 HA gene was obtained. The HA1 domain sequence was confirmed by using the two additional isolates (A/New York/1/18 and A/Brevig Mission/1/18). The sequences show little variation. Phylogenetic analyses suggest that the 1918 virus HA gene, although more closely related to avian strains than any other mammalian sequence, is mammalian and may have been adapting in humans before 1918.

Adult↗

PubMed1994

Concerted evolution at the population level: pupfish HindIII satellite DNA sequences.

The canonical monomers (approximately 170 bp) of an abundant (1.9 x 10(6) copies per diploid genome) satellite DNA sequence family in the genome of Cyprinodon variegatus, a "pupfish" that ranges along the Atlantic coast from Cape Cod to central Mexico, are divergent in base sequence in 10 of 12 samples collected from natural populations. The divergence involves substitutions, deletions, and insertions, is marked in scope (mean pairwise sequence similarity = 61.6%; range = 35-95.9%), is largely confined to the 3' half of the monomer, and is not correlated with the distance among collecting sites. Repetitive cloning and direct genomic sequencing experiments failed to detect intrapopulation and intraindividual variation, suggesting high levels of sequence homogeneity within populations. The satellite sequence has therefore undergone "concerted evolution," at the level of the local population. Concerted evolution has previously almost always been discussed in terms of the divergence of species or higher taxa; its intraspecific occurrence apparently has not been reported previously. The generality of the observation is difficult to evaluate, for although satellite DNAs from a large number of organisms have been studied in detail, there appear to be little or no other data on their sequence variation in natural populations. The relationship (if any) between concerted, population level, satellite DNA divergence and the extent of gene flow/genetic isolation among conspecific natural populations remains to be established.

Animals↗

PubMed1998

Biogenesis and function of IgM: the role of the conserved mu-chain tailpiece glycans.

The tailpiece of secretory Ig-mu-chains (mu(s)tp) is highly conserved throughout evolution: in particular, a carboxy-terminal cysteine residue (Cys575) and a glycan linked to Asn563 are found in all species sequenced so far. Here we show that the mu(s)tp oligosaccharide moieties are important for the binding of J-chains and for the process of IgM polymerization. In the absence of the mu(s)tp glycans, pentamers cannot be assembled and polymers containing six or more subunits are secreted. Despite their increased valency, these molecules have a lower association rate with antigen than wild-type polymers. Unexpectedly, the C-terminal oligosaccharides also affect kinetic parameters on unpolymerized subunits. Thus, monomers lacking the C-terminal sugars because of either site-directed mutagenesis or selective enzymatic deglycosylation with endoglycosidase H, have a lower k(on) for the antigen. Taken together, our results indicate that the C-terminal mu-chain glycans can shape the structure of mu(s2)L2 subunits and their further assembly into polymers.

Animals↗

PubMed1995

Significance of strand configuration in self-replicating RNA molecules.

The kinetic theory of replication has been extended to include dual mechanisms for conversion of self-annealed single-strand RNA to double-strand molecules, which do not replicate. An analysis of experimental results established that the replicate-template annealing reaction during transcription significantly retarded replication in vitro among three RNA variants copied by Q beta replicase. Annealing between complementary RNA strands free in solution had far less significance. The finding that an RNA variant can be replicated in a multiple hairpin configuration, but not as its single, long hairpin conformer, the correlation between stability of strand secondary structure and replicative fitness, and a lack of homology in the internal sequence of RNA variants copied by Q beta replicase support the conclusion that template competence depends on strand configuration, independent of most of the underlying base sequence. Occurrence of self-annealed strands in the Q beta replicase system was attributed to its reliance on RNA-driven strand separation, in the absence of enzyme catalysed strand unwinding. A 'configuration before sequence' path to self-replication exhibited a substantially lower combinatorial barrier than standard sequence-dependent evolution. RNA-dependent RNA synthesis in the Q beta system thus displays features of an RNA World and, interestingly, they reveal a rapid path for evolution of the first self-replicating molecule on Earth.

Base Sequence↗

PubMed1995

Nucleotide substitution type dependence of generation time effect of molecular evolution.

Using DNA sequence data of 18 genes from 14 mammals, we analyzed how the average molecular evolution rate per year per site (Vy) depends on the generation time (g). (I) Assuming the relation Vy varies; is directly proportional to g(-alpha), the index of generation time effect, (alpha) was estimated to be about 0.14 for amino acid replacement substitutions (A), and about 0.32 for synonymous substitutions (S). (II) Assuming the relation Vy = V(m)g g-1 + V(e)y, where V(m)g and V(e)y are constant independent of g, the fraction, r(e) = V(e)y/Vy, of the mutation rate independent part (V(e)y) in the total evolution rate (Vy) was estimated under the assumptions of the star phylogeny and the constancy of the mutation rate per generation. r(e) was smallest for mouse with the shortest generation time among our analyzed species, and it was estimated to be about 0.57 for A and 0.31 for S. Both results do not support the view that Vy is equal to the neutral mutation rate per site both for A and for S. They are in line with the thesis that, at least for A and probably even for S, the molecular evolution rate is influenced by some causes other than the mutation rate, such as changing environment.

Animals↗

PubMed1998

Non-equilibrium thermodynamics of molecular evolution.

The evolution of the information complexity of a large database of protein sequences is investigated. The information entropy for protein sequences is determined from their algorithmic complexity and is found to change with evolutionary time at a constant rate. The information content of changed residues is always lower than the content of conserved residues. This indicates that sequences are becoming less random throughout evolution. It also shows that the system is being driven toward minimal complexity production. The change in information content per amino acid substitution is virtually identical for all the protein sequences studied. These results are interpreted with a statistical mechanical theory that ties sequence information to the thermodynamics of protein structure. Sequence evolution is viewed as a means to drive the system to minimum thermodynamic entropy production in a stable, non-equilibrium state. This theory provides a physical framework for understanding molecular evolution and incorporates features of both the neutralist and selectionist models.

Amino Acid Sequence↗

PubMed2003

The gene cassette metagenome is a basic resource for bacterial genome evolution.

Lateral gene transfer has been proposed as a fundamental process underlying bacterial diversity. Transposons, plasmids and phage are widespread and have been shown to significantly contribute to lateral gene transfer. However, the processes by which disparate genes are assembled and integrated into the host regulatory network to yield new phenotypes are poorly known. Recent discoveries about the integron/gene cassette system indicate it has the potential to play a role in this process. Gene cassettes are small mobile elements typically consisting of a promoterless orf and a recombination site. Integrons are capable of acquisition and re-arrangement of gene cassettes and of the expression of their associated genes. The potential of the integron/gene cassette system is thus largely determined by the diversity contained within the cassette pool and the rate at which integrons sample this pool. We show here using a polymerase chain reaction (PCR) approach by which the environmental gene cassette (EGC) metagenome can be directly sampled that this metagenome contains both protein-coding and non-protein coding genes. Environmental gene cassette-associated recombination sites showed greater diversity than previously seen in integron arrays. Class 1 integrons were shown to be capable of accessing this gene pool through tests of recombinational activity with a representative range of EGCs. We propose that gene cassettes represent a vast, prepackaged genetic resource that could be thought of as a metagenomic template for bacterial evolution.

Base Sequence↗

PubMed2002

Repeats with variations: accelerated evolution of the Pin2 family of proteinase inhibitors.

The Pin2 genes encode potato type II proteinase inhibitors that act against pathogenic attack. The first examples were found only in the Solanaceae family, but, using new EST and genomic data, we have found 11 homologous genes dispersed through almost the whole range of mono- and di-cotyledonous plants. In contrast to the repetitive precursor sequences of the Solanaceae Pin2 genes, the new homologs have only a single repeat unit. The gene family appears to have evolved from a single-domain ancestral gene through a series of gene-duplication and domain-duplication steps. A number of unequal cross-over and gene conversion events could explain the current gene and domain pattern of the Solanaceae Pin2 subfamily.

Amino Acid Sequence↗

PubMed2004

Expansion of quasispecies diversity but no evidence for adaptive evolution of SHIV during rapid serial transfers among seronegative macaques.

Four successive, rapid serial passages of the nonpathogenic, CCR5-tropic simian-human immunodeficiency virus SHIV(SF162) in rhesus macaques resulted in an increase in acute plasma viremia with each passage and the emergence of a pathogenic isolate SHIV(SF162P3) in one of the passage three transfer animals (macaque T353). To explore the mechanism(s) underlying increased virulence of SHIV(SF162) upon in vivo passage, the evolution of the HIV-1 envelope gene was characterized in plasma and PBMC samples obtained from animals before (week 1) and after (week 3) the time of virus transfer. We found no evidence in support of adaptive evolution of the HIV gp120 during rapid serial passage; however, the animals which later received passage virus had more diverse quasispecies. SHIV(SF162P3)-like gp120 sequences were first detected in macaque T353 at week 6, after seroconversion. These sequence changes increased in frequency and number at later time points. The first sequence change conferred neutralization escape but not an increase in viral infectivity that could account for the apparent increase in replicative capacity of the later passage viruses. Collectively, our data argue against any host-specific adaptation of the HIV-1 envelope gp120 as the basis for the generation of more aggressive SHIV variants during rapid serial transfers in seronegative macaques, and support the model of quasispecies diversity as a predictor of pathogenesis. Envelope sequence changes accumulate principally in response to immune pressure exerted by the host, generating viral variants that can persist in the presence of a strong host immune response.

Amino Acid Sequence↗