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PubMed2003

Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand.

Self-incompatibility in crucifers is effected by allele-specific interactions between the highly polymorphic stigmatic S locus receptor kinase (SRK) and its pollen ligand, the S locus cysteine-rich protein (SCR). Here we show that specificity in SCR function is determined by four contiguous amino acids in one variant, indicating that the minimum sequence requirement for gaining a new specificity can be low. We also provide evidence for an extraordinarily high degree of evolutionary flexibility in SCR, whereby SCR can tolerate extensive amino acid changes within the limits of maintaining the same predicted overall structure. This remarkable adaptability suggests a hypothesis for generation of new self-incompatibility specificities by gradual modification of SRK-SCR affinities and, more generally, for functional specialization within families of homologous ligands and receptors.

Amino Acid Sequence↗
PubMed1981

Somatic diversification is required to generate the V kappa genes of MOPC 511 and MOPC 167 myeloma proteins.

The immune response to phosphocholine in BALB/c mice involves one group of heavy chain variable region (VH) genes and at least three groups of light chain variable region (V kappa) genes, represented by the gene products of the myelomas TEPC 15, MOPC 603, and MOPC 167/MOPC 511. The amino acid sequences of BALB/c myeloma kappa chains MOPC 167 and MOPC 511 are known, and they differ by six amino acids. We have isolated several closely related V region genes of immunoglobulin light chains from a mouse sperm DNA phage library, selecting clones that cross-hybridize with a cDNA plasmid probe encoding the light chain of MOPC 167. We identified six strongly hybridizing clones, representing three separate cloning events. We determined the sequence of the coding and immediate flanking regions of three clones, representing the three separate cloning events, and they proved to be identical. This germ-line sequence encoded the amino acid sequence of neither MOPC 167 nor MOPC 511, but required four base pair changes to generate the V kappa M167 cDNA sequence and five base pair changes to generate the V kappa M511 gene. By Southern hybridization experiments, we demonstrated that neither MOPC 511 nor MOPC 167 germ-line genes exist. We conclude that the V kappa M167 and V kappa M511 genes are created somatically.

Antibody Diversity↗
PubMed1984

Somatic diversification of immunoglobulins.

A series of three IgM, kappa monoclonal antibodies arising from a fusion of BALB/c spleen cells from mice immunized with beta-(1,6)-galactan-containing antigens have been analyzed. These three lines were found (i) to have homologous protein sequences in the heavy chain D region and at the sites of recombination between the heavy chain variable and D segment (VH-D) and the D and joining segment (D-JH), although amino acid substitutions were observed in both the heavy and light chain variable regions; (ii) to use identical heavy and light chain joining segments; and (iii) to demonstrate two identical (productive and nonproductive) kappa-chain rearrangements. A likely explanation for these observations is that the three lines are clonally related (arise from a common precursor) and that the observed heavy and light chain variable segment substitutions represent somatic point mutations. Because these antibodies are all of the IgM class, the results indicate that a somatic mutational mechanism is activated early in B-cell ontogeny and operates at both the heavy and light chain loci. Furthermore, the somatic mutation process appears to continue during the development of a given cell line, but is independent of class switching.

Amino Acid Sequence↗
PubMed1985

Complete nucleotide sequences of three VH genes in Caiman, a phylogenetically ancient reptile: evolutionary diversification in coding segments and variation in the structure and organization of recombination elements.

Complete nucleotide sequences are described for three caiman (Caiman crocodylus crocodylus) immunoglobulin VH genes (C3, E1, and G4) that hybridize with a murine VH probe. The E1 and G4 genes are physically linked (intergenic distance, approximately equal to 6.5 kilobases) in the same transcriptional orientation but are not directly contiguous with the C3 gene. When the coding segments, including both framework and complementarity-determining regions, of these genes and the murine probe sequences are compared by metric analysis, it is apparent that the caiman genes are only slightly more related to each other than to the mammalian sequence, consistent with significant preservation of nucleotide sequence over an extended period of phylogenetic time. Based on the presence of transcriptionally critical 5' sequences and the absence of terminator codons, frameshift mutations, or other recognizable alterations, the genes do not appear to be pseudogenes. The E1 gene, however, is distinguished from other VH genes because (i) the spacer region within the 3' recombination signal sequence is 12 base pairs, typical of VK genes but not of VH genes, which possess 22- to 23-base-pair spacers and (ii) a near-perfect VH recombination signal sequence is present within the intervening sequence that splits the segment encoding the leader. These studies establish VH gene multiplicity in a species that arose prior to mammalian radiation and provide a description of differences in the configuration and location of recombination elements associated with an otherwise potentially functional gene.

Alligators and Crocodiles↗
PubMed1987

Somatic diversification of S107 from an antiphosphocholine to an anti-DNA autoantibody is due to a single base change in its heavy chain variable region.

The S107 myeloma cell line expresses the germ-line sequence of the T15 antiphosphocholine (P-Cho) antibody, which is the major antibody made by BALB/c mice in response to P-Cho, either on a variety of bacterial polysaccharides or when attached to a protein carrier. We have previously reported that a somatic mutant of the S107 cell line produces an antibody that has lost the ability to bind P-Cho and has acquired binding for double-stranded DNA. This antibody has a substitution of an alanine for a glutamic acid at residue 35 in the heavy chain variable region. We now show that this amino acid substitution is due to a single A-C transversion, which is the only nucleotide change in the heavy and light chain variable regions. Further, it appears that this change is due to somatic mutation rather than to gene conversion.

Animals↗
PubMed1990

Somatic diversification of chicken immunoglobulin light chains by point mutations.

The light-chain locus of chicken has 1 functional V lambda 1 gene, 1 J gene, and 25 pseudo-V lambda-genes (where V = variable and J = joining). A major problem is which somatic mechanisms expand this extremely limited germ-line information to generate many different antibodies. Weill's group [Reynaud, C. A., Anquez, V., Grimal, H. & Weill, J. C. (1987) Cell 48, 379-388] has shown that the pseudo-V lambda-genes diversify the rearranged V lambda 1 by gene conversion. Here we demonstrate that chicken light chains are further diversified by somatic point mutations and by V lambda 1-J flexible joining. Somatic point mutations were identified in the J and 3' noncoding DNA of rearranged light-chain genes of chicken. These regions were analyzed because point mutations in V lambda 1 are obscured by gene conversion; the J and 3' noncoding DNA are presented in one copy per haploid genome and are not subject to gene conversion. In rodents point mutations occur as frequently in the V-J coding regions as in the adjacent flanking DNA. Therefore, we conclude that somatic point mutations diversify the V lambda 1 of chicken. The frequency (0-1%) and distribution of the mutations (decreasing in number with increased distance from the V lambda 1 segment) in chicken were as observed in rodents. Sequence variability at the V lambda 1-J junctions could be attributed to imprecise joining of the V lambda 1 and J genes. The modification by gene conversion of rearranged V lambda 1 genes in the bursa was similar in chicken aged 3 months (9.5%) or 3 weeks (9.1%)--i.e., gene conversion that generates the preimmune repertoire in the bursa seems to level off around 3 weeks of age. This preimmune repertoire can be further diversified by somatic point mutations that presumably lead to the formation of antibodies with increased affinity. A segment with structural features of a matrix association region [(A + T)-rich and four topoisomerase II binding sites] was identified in the middle of the J-C lambda intron (where C = constant).

Animals↗
PubMed1992

High rate of diversification and reversal among subclones of neoplastically transformed NIH 3T3 clones.

NIH 3T3 cells undergo neoplastic transformation when exposed to conditions of moderate physiological growth constraint. One of several characteristics of this transformation that indicates its adaptational nature is its gradual reversibility under conditions of unconstrained growth. We explored the origins of reversibility by isolating cells from each of three highly transformed foci and comparing their focus-forming capacity with that of derivative clones and subclones. A high proportion of the parental cells made dense foci. Six of the nine clones obtained from the three foci produced foci, though the percentage varied widely. The other three clones produced no foci at all. The transformed clones were subcloned and analyzed to evaluate the possibility that the negative clones were genuine revertants, rather than being derived from a small minority of nontransformed cells surrounding or underlying the original foci. In each case the subclones varied widely in the percentage of focus-forming cells and the average was much lower than the parental clone from which they were derived. Indeed, 15 of the 53 subclonal populations produced no foci. The high degree of heterogeneity, including complete reversal of focus-forming capacity, provides additional support for the hypothesis that "spontaneous" transformation is driven by an adaptive response to moderate growth constraint rather than by one or more effectively irreversible mutations.

3T3 Cells↗
PubMed1994

Somatic diversification in the heavy chain variable region genes expressed by human autoantibodies bearing a lupus-associated nephritogenic anti-DNA idiotype.

Monoclonal anti-DNA antibodies bearing a lupus nephritis-associated idiotype were derived from five patients with systemic lupus erythematosus (SLE). Genes encoding their heavy (H)-chain variable (VH) regions were cloned and sequenced. When compared with their closest VH germ-line gene relatives, these sequences exhibit a number of silent (S) and replacement (R) substitutions. The ratios of R/S mutations were much higher in the complementarity-determining regions (CDRs) of the antibodies than in the framework regions. Molecular amplification of genomic VH genes and Southern hybridization with somatic CDR2-specific oligonucleotide probes showed that the configuration of the VH genes corresponding to VH sequences in the nephritogenic antibodies is not present in the patient's own germ-line DNA, implying that the B-cell clones underwent somatic mutation in vivo. These findings, together with the characteristics of the diversity and junctional gene elements utilized to form the antibody, indicate that these autoantibodies have been driven through somatic selection processes reminiscent of those that govern antibody responses triggered by exogenous stimuli.

Amino Acid Sequence↗
PubMed1996

Conservation and diversification in homeodomain-DNA interactions: a comparative genetic analysis.

Nearly all metazoan homeodomains (HDs) possess DNA binding targets that are related by the presence of a TAAT sequence. We use an in vitro genetic DNA binding site selection assay to refine our understanding of the amino acid determinants for the recognition of the TAAT site. Superimposed upon the conserved ability of metazoan HDs to recognize a TAAT core is a difference in their preference for the bases that lie immediately 3' to it. Amino acid position 50 of the HD has been shown to discriminate among these base pairs, and structural studies have suggested that water-mediated hydrogen bonds and van der Waals contacts underlie for this ability. Here, we show that each of six amino acids tested at position 50 can confer a distinct DNA binding specificity.

Amino Acid Sequence↗
PubMed1998

Diversification, expression, and gamma delta T cell recognition of evolutionarily distant members of the MIC family of major histocompatibility complex class I-related molecules.

Distant relatives of major histocompatibility complex (MHC) class I molecules, human MICA and MICB, function as stress-induced antigens that are broadly recognized by intestinal epithelial gamma delta T cells. They may thus play a central role in the immune surveillance of damaged, infected, or otherwise stressed intestinal epithelial cells. However, the generality of this system in evolution and the mode of recognition of MICA and MICB are undefined. Analysis of cDNA sequences from various primate species defined translation products that are homologous to MICA and MICB. All of the MIC polypeptides have common characteristics, although they are extraordinarily diverse. The most notable alterations are several deletions and frequent amino acid substitutions in the putative alpha-helical regions of the alpha1 alpha2 domains. However, the primate MIC molecules were expressed on the surfaces of normal and transfected cells. Moreover, despite their sharing of relatively few identical amino acids in potentially accessible regions of their alpha1 alpha2 domains, they were recognized by diverse human intestinal epithelial gamma delta T cells that are restricted by MICA and MICB. Thus, MIC molecules represent a family of MHC proteins that are structurally diverse yet appear to be functionally conserved. The promiscuous mode of gamma delta T cell recognition of these antigens may be explained by their sharing of a single conserved interaction site.

Amino Acid Sequence↗
PubMed1999

A test of alternative models of diversification in tropical rainforests: ecological gradients vs. rainforest refugia.

Comparison of mitochondrial and morphological divergence in eight populations of a widespread leaf-litter skink is used to determine the relative importance of geographic isolation and natural selection in generating phenotypic diversity in the Wet Tropics Rainforest region of Australia. The populations occur in two geographically isolated regions, and within each region, in two different habitats (closed rainforest and tall open forest) that span a well characterized ecological gradient. Morphological differences among ancient geographic isolates (separated for several million years, judging by their mitochondrial DNA sequence divergence) were slight, but morphological and life history differences among habitats were large and occurred despite moderate to high levels of mitochondrial gene flow. A field experiment identified avian predation as one potential agent of natural selection. These results indicate that natural selection operating across ecological gradients can be more important than geographic isolation in similar habitats in generating phenotypic diversity. In addition, our results indicate that selection is sufficiently strong to overcome the homogenizing effects of gene flow, a necessary first step toward speciation in continuously distributed populations. Because ecological gradients may be a source of evolutionary novelty, and perhaps new species, their conservation warrants greater attention. This is particularly true in tropical regions, where most reserves do not include ecological gradients and transitional habitats.

Animals↗
PubMed2002

Identification of residues in glutathione transferase capable of driving functional diversification in evolution. A novel approach to protein redesign.

Evolution of protein function can be driven by positive selection of advantageous nonsynonymous codon mutations that arise following gene duplication. By observing the presence and degree of site-specific positive selection for change between divergent paralogs, residue positions responsible for functional changes can be identified. We applied this analysis to genes encoding Mu class glutathione transferases, which differ widely in substrate specificities. Approximately 3% of the amino acid residue positions, both near to and distant from the active site, are under statistically significant positive selection for change. Relevant human glutathione transferase (GST) M1-1 and GST M2-2 codons were mutated. A chemically conservative threonine to serine mutation in GST M2-2 elicited a 1,000-fold increase in specific activity with the GST M1-1-specific substrate trans-stilbene oxide and a 30-fold increase with the alternative epoxide substrates styrene oxide and nitrophenyl glycidol. The reverse mutation in GST M1-1 resulted in reciprocal decreases in activity. Thus, identification of hypervariable codon positions can be a powerful aid in the redesign of protein function, lessening the requirement for extensive mutagenesis or structural knowledge and sometimes suggesting mutations that would otherwise be considered functionally conservative.

Evolution, Molecular↗
PubMed2002

Development and evolution of lateral line placodes in amphibians. - II. Evolutionary diversification.

The amphibian lateral line system develops from a series of lateral line placodes. The different phases of development from early induction, to pattern formation, differentiation, morphogenesis, and metamorphic fate were summarized in the first part of this review (Schlosser, 2002a). Here, a survey of the diversity of lateral line systems in amphibians is presented indicating that most phases of lateral line development have been subject to evolutionary changes. Several trends suggest important roles for both adaptive changes and internal constraints in amphibian lateral line evolution. Many of these trends involved the coordinated modification of different derivatives of lateral line placodes suggesting that these placodes are not only autonomous developmental modules, but also units of evolutionary variation that tend to be modified in a coherent and largely context-independent fashion.

Journal Article↗
PubMed2002

Power of eight tree shape statistics to detect nonrandom diversification: a comparison by simulation of two models of cladogenesis.

We used simulations to compare the relative power of eight statistical tests to detect imbalance in phylogenies that is too great to be ascribed to an equal-rates Markov null model. Three of these tests have never had their power assessed before. Our simulations are the first to assess performance under scenarios in which the speciation rates of various lineages can evolve independently. In one of the scenarios explored, rates depend upon the value of an evolving trait, whereas in the other the probability that a species will speciate declines with the time since it last did so. The results indicate that the relative performance of the methods depends upon how the imbalance is generated. Different types of processes lead to different imbalance signatures, i.e., different patterns of imbalance at different depths in the phylogeny, and the measures of tree shape differ in the depth of phylogeny at which they are most sensitive. Relative performance is also affected by tree size but does not appear to depend greatly upon the degree of speciation rate variation among lineages. Two of the indices (Colless's index I(c) and Shao and Sokal's Nmacr;) show reasonable performance throughout, but another (Shao and Sokal's B(2)) is never indicated to be a preferred method. Two tests that do not require completely resolved phylogenies, mean I' and mean I'(10), have reasonable power.

Biological Evolution↗