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PubMed2003

The EBG system of E. coli: origin and evolution of a novel beta-galactosidase for the metabolism of lactose.

The EBG system of E. coli has served as a model for the evolution of novel functions. This paper reviews the experimental evolution of the catabolism of beta-galactoside sugars in strains of E. coli that carry deletions of the classical lacZ beta-galactosidase gene. Evolution of the ebgA encoded Ebg beta-galactosidase for an expanded substrate range, evolution of the ebgR encoded Ebg repressor for sensitivity to an expanded range of inducers, the amino acid replacements responsible for those changes, and the evolutionary potential of the system are discussed. The EBG system has also served as a model for studying the detailed catalytic consequences of experimental evolution at the physical-chemical level. The analysis of free-energy profiles for the wildtype and all of the various evolved Ebg enzymes has permitted rejection of the Albery-Knowles hypothesis that relates likely changes in free-energy profiles to evolutionary change.

Crosses, Genetic↗
PubMed1982

Glucocorticoid regulation of the mouse metallothionein I gene is selectively lost following amplification of the gene.

The mouse metallothionein I (MT-I) gene is regulated by both heavy metals and glucocorticoid hormones. We selected cadmium-resistant variants of the mouse sarcoma cell line, S180, in which the metallothionein I gene has been amplified 10-fold and found that the amplified genes are regulated by cadmium in a manner identical with that observed for the original MT-I gene in unselected S180 cells. However, the amplified metallothionein I genes appear to be essentially nonresponsive to glucocorticoids even though at least 18 kilobases of DNA flanking the 5' side of the metallothionein I gene are amplified in these cells. The same result has been observed in nine clonal lines derived from the cadmium-resistant (CdR) population. The implications of this result both for models of steroid hormone action and for gene evolution are discussed.

Animals↗
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↗
PubMed2005

Genes "waiting" for recruitment by the adaptive immune system: the insights from amphioxus.

In seeking evidence of the existence of adaptive immune system (AIS) in ancient chordate, cDNA clones of six libraries from a protochordate, the Chinese amphioxus, were sequenced. Although the key molecules such as TCR, MHC, Ig, and RAG in AIS have not been identified from our database, we demonstrated in this study the extensive molecular evidence for the presence of genes homologous to many genes that are involved in AIS directly or indirectly, including some of which may represent the putative precursors of vertebrate AIS-related genes. The comparative analyses of these genes in different model organisms revealed the different fates of these genes during evolution. Their gene expression pattern suggested that the primitive digestive system is the pivotal place of the origin and evolution of the AIS. Our studies support the general statement that AIS appears after the jawless/jawed vertebrate split. However our study further reveals the fact that AIS is in its twilight in amphioxus and the evolution of the molecules in amphioxus are waiting for recruitment by the emergence of AIS.

Amino Acid Sequence↗
PubMed2005

Sequencing and mapping hemoglobin gene clusters in the Australian model dasyurid marsupial Sminthopsis macroura.

Comparing globin genes and their flanking sequences across many species has allowed globin gene evolution to be reconstructed in great detail. Marsupial globin sequences have proved to be of exceptional significance. A previous finding of a beta(beta)-like omega(omega) gene in the alpha(alpha) cluster in the tammar wallaby suggested that the alpha and beta cluster evolved via genome duplication and loss rather than tandem duplication. To confirm and extend this important finding we isolated and sequenced BACs containing the alpha and beta loci from the distantly related Australian marsupial Sminthopsis macroura. We report that the alpha gene lies in the same BAC as the beta-like omega gene, implying that the alpha-omega juxtaposition is likely to be conserved in all marsupials. The LUC7L gene was found 3' of the S. macroura alpha locus, a gene order shared with humans but not mouse, chicken or fugu. Sequencing a BAC contig that contained the S. macroura beta globin and epsilon globin loci showed that the globin cluster is flanked by olfactory genes, demonstrating a gene arrangement conserved for over 180 MY. Analysis of the region 5' to the S. macroura epsilon (epsilon) globin gene revealed a region similar to the eutherian LCR, containing sequences and potential transcription factor binding sites with homology to eutherian hypersensitive sites 1 to 5. FISH mapping of BACs containing S. macroura alpha and beta globin genes located the beta globin cluster on chromosome 3q and the alpha locus close to the centromere on 1q, resolving contradictory map locations obtained by previous radioactive in situ hybridization.

Animals↗
PubMed2001

Mesophyll-specific, light and metabolic regulation of the C4 PPCZm1 promoter in transgenic maize.

To play an essential role in C4 photosynthesis, the maize C4 phosphoenolpyruvate carboxylase gene (PPCZm1) acquired many new expression features, such as leaf specificity, mesophyll specificity, light inducibility and high activity, that distinguish the unique C4 PPC from numerous non-C4 PPC genes in maize. We present here the first investigation of the developmental, cell-specific, light and metabolic regulation of the homologous C4 PPCZm1 promoter in stable transgenic maize plants. We demonstrate that the 1.7 kb of the 5'-flanking region of the PPCZm1 gene is sufficient to direct the C4-specific expression patterns of beta-glucuronidase (GUS) activity, as a reporter, in stable transformed maize plants. In light-grown shoots, GUS expression was strongest in all developing and mature mesophyll cells in the leaf, collar and sheath. GUS activity was also detected in mesophyll cells in the outer husks of ear shoots and in the outer glumes of staminate spikelets. We did not observe histological localization of GUS activity in light- or dark-grown callus, roots, silk, developing or mature kernels, the shoot apex, prop roots, or pollen. In addition, we used the stable expressing transformants to conduct and quantify physiological induction studies. Our results indicate that the expression of the C4 PPCZm1-GUS fusion gene is mesophyll-specific and influenced by development, light, glucose, acetate and chloroplast biogenesis in transgenic maize plants. These studies suggest that the adoption of DNA regulatory elements for C4-specific gene expression is a crucial step in C4 gene evolution.

Acetates↗
PubMed1988

Histone genes of Volvox carteri: DNA sequence and organization of two H3-H4 gene loci.

Two Volvox genomic clones each containing a pair of histone H3-H4 genes were sequenced. In both loci the H3 and H4 genes show outwardly divergent polarity, their coding regions being separated by short intercistronic sequences containing TATA boxes and a conserved 14-bp element. The 3' untranslated regions contain a characteristic motif with hyphenated dyad symmetry otherwise only found associated with animal histone genes. Derived amino acid sequences of histones H3 and H4 are highly conserved and identical between the two sets. The Volvox H3 genes both contain one intron whose relative position is shifted by one basepair. Sequence comparisons led to a new interpretation of intron sliding. The Volvox H3 gene structure combines the exon-intron organization of fungal H3 and vertebrate H3.3 genes with a termination signal typical for animal H3.1 genes. These features are discussed in view of histone gene evolution.

Alleles↗
PubMed1995

Sequence and evolution of the gene for the monomeric globin I and its linkage to genes coding for dimeric globins in the insect Chironomus thummi.

We isolated genomic clones containing sequences encoding globins I and IA from a Chironomus thummi thummi genomic library. Three clones contain globin IA (ctt-1A) genes, while one contains a globin I (ctt-1) gene. The coding regions of the four genes are identical except for the single base substitution accounting for the globin I/IA polymorphism. The noncoding DNA flanking the coding region is more than 98% similar, confirming a previous hypothesis that the globin ctt-1 and ctt-1A genes are alleles. Hemoglobins I and IA are monomeric in the insect hemolymph. Earlier in situ hybridization studies suggested that monomeric and dimeric globin genes are clustered at different chromosomal loci. In situ hybridization of ctt-1 DNA to polytene salivary gland chromosomes places the ctt-1 gene on the same band as genes for the dimeric globins II beta and VIIB, forcing revision of the earlier hypothesis that genes for monomeric and dimeric globin genes are at different loci. The evolution of the ctt-1 and ctt-1A alleles and of the two globin gene loci are discussed.

Amino Acid Sequence↗
PubMed1984

Evolution of anticodons.

Anticodons are trinucleotides in transfer RNA (tRNA) molecules. The latter carry amino acids for insertion into the polypeptide sequences of proteins during the translation of messenger RNA (mRNA) molecules. Messenger RNA molecules are transcribed from genes. Evolution of tRNA molecules has resulted in a set of anticodons for the 20 amino acids that are used in protein synthesis. This set of anticodons is slightly different in mitochondrial codes from the set that used in the nuclear "universal" code. Theories for the evolution of the code include frozen accident, doublet expansion, repeating triplets and coevolutionary distribution. The number of codons has always been fixed at 64 by mathematical rules, but because an anticodon may pair with more than one codon, the number of anticodons is only 54 in the universal code, is smaller in mitochondrial codes, and was probably even smaller in archetypal primitive codes. Evidence of anticodon evolution can be seen by comparing mitochondrial codes with the universal code. Codes used by very primitive organisms that are now extinct might have specified fewer amino acids than are now used.

Amino Acids↗
PubMed1990

Structure of class II genes in wild mouse Mus saxicola: functional and evolutionary implications.

Class II beta genes have been characterized from Mus saxicola, a wild mouse which diverged five millions years ago from the house mouse. The nucleotide sequences of the exons 2 and 3 of E beta 1, A beta 2 and E beta 2 genes have been determined in order to define the molecular mechanisms of interspecies variability. The E beta 1 and A beta 1 (J. X. She, personal communication) genes from Mus saxicola display extensive sequence variability in exon 2 when compared to those of the house mouse, in association with the variability of residues probably involved in antigen binding. On the other hand, most putative T cell contact residues from the I-E beta chain, and to a lesser extent from the I-A beta chain, were found conserved in mice. T cell contact residues from Mus saxicola I-A beta and I-E beta chains are identical to those of the b and q, and of the k haplotypes of the house mouse, respectively. Comparisons performed with A beta 2 and E beta 2 genes revealed that both are highly conserved and, in contrast to A beta 1 and E beta 1 genes, that a strong selective pressure for conservation occurs in the A beta 2 second exon. The different aspects of A beta 2 and E beta 2 genes evolution may correlate with the original function of their products. Comparisons of the intervening sequences revealed that the repeated motifs of the hotspot region present in the E beta 1b gene are also conserved in Mus saxicola. Recombinations may have occurred, in some cases in association with chi-like sequences.

Amino Acid Sequence↗
PubMed1996

Gene conversion and natural selection in the evolution of X-linked color vision genes in higher primates.

During higher primate evolution, gene conversion seems to have occurred often between the red and green photo-pigment genes, which are tandemly linked on the X chromosome. To understand this phenomenon better, intron 4 sequences of the red and green pigment genes of a male human (an Asian Indian), a male chimpanzee, and a male baboon were amplified by PCR and sequenced. The data show that the intron 4 sequences between the two genes have been strongly or completely homogenized in the three species studied. Apparently recent gene conversion events have occurred in introns 4 of the red and green pigment genes in humans and chimpanzees. Two or more conversion events may have occurred at different times in introns 4 of the two pigment genes in baboons. The divergence between the two genes is significantly lower in intron 4 than in exons 4 and 5 in each species, contrary to the usual situation that introns evolve faster than exons. It is most likely that strong natural selection for maintaining the distinct functions of exons 4 and 5 of the red and green pigment genes has acted against sequence homogenization of these exons.

Animals↗
PubMed1990

Tandemly duplicated Caenorhabditis elegans collagen genes differ in their modes of splicing.

Caenorhabditis elegans contains 50 to 150 collagen genes dispersed throughout its genome. We have determined the complete nucleotide sequences of two collagen genes, col-12 and col-13, that are separated by only 1800 bases and are transcribed in the same direction. The 951 nucleotides of their coding regions differ by only five nucleotides (99.5% identity). The amino acid sequences are identical except for two conservative amino acid changes within the putative secretory signal sequences, so the mature forms of the col-12 and col-13 collagens would be identical. The position and sequence of the intron (52 base-pairs) within the coding region of each gene are perfectly conserved. In contrast to the coding regions and the introns, the 5' and 3' flanking regions show little sequence similarity, col-12 and col-13 are expressed at similar levels at the same developmental stages, and appear to utilize conserved TATA boxes and transcription start sites. The major differences between the genes is that, preceding the initiator ATG, col-12 has a cis-spliced intron, while col-13 is transspliced. Thus, col-12 and col-13 are essentially identical in all aspects except that the col-12 mRNA has a 26-nucleotide cis-spliced leader at the same place where the col-13 mRNA has a 22-nucleotide trans-spliced leader. These results suggest that col-12 and col-13 are derived from a gene duplication and that sequence homology in the coding regions, but not in the flanking regions, has been maintained by gene conversion. The fact that the only significant difference between the two genes is in their modes of splicing suggests that cis and trans-splicing can be interchanged during gene evolution.

Amino Acid Sequence↗
PubMed1987

Structural diversity of murine serum amyloid A genes. Evolutionary implications.

Mouse serum amyloid A (SAA) gene family comprises four members that are closely linked in the chromosome 7. Two of these genes encoding major mouse SAA isotypes (SAA1 and SAA2) are highly homologous not only in exons but also in introns and flanking regions; this sequence homology extends 280 base pairs upstream of major cap sites and 430 base pairs downstream of polyadenylation sites, and the 5' boundary of this homology unit is marked by the CA/GT repeat. Sequence comparison also shows that one (SAA4) of the other two genes is related to the SAA1/2 gene, whereas the other gene (SAA3) evolved independently. Based on these results and the SAA gene arrangement, we discussed mouse SAA gene evolution.

Animals↗
PubMed2002

Evidence for the murine IgH mu locus acting as a hot spot for intrachromosomal homologous recombination.

Homologous recombination accomplishes the exchange of genetic information between two similar or identical DNA duplexes. It can occur either by gene conversion, a process of unidirectional genetic exchange, or by reciprocal crossing over. Homologous recombination is well known for its role in generating genetic diversity in meiosis and, in mitosis, as a DNA repair mechanism. In the immune system, the evidence suggests a role for homologous recombination in Ig gene evolution and in the diversification of Ab function. Previously, we reported the occurrence of homologous recombination between repeated, donor and recipient alleles of the Ig H chain mu gene C (Cmu) region residing at the Ig mu locus in mouse hybridoma cells. In this study, we constructed mouse hybridoma cell lines bearing Cmu region heteroalleles to learn more about the intrachromosomal homologous recombination process. A high frequency of homologous recombination (gene conversion) was observed for markers spanning the entire recipient Cmu region, suggesting that recombination might initiate at random sites within the Cmu region. The Cmu region heteroalleles were equally proficient as either conversion donors or recipients. Remarkably, when the same Cmu heteroalleles were tested for recombination in ectopic genomic positions, the mean frequency of gene conversion was reduced by at least 65-fold. These results are consistent with the murine IgH mu locus behaving as a hot spot for intrachromosomal homologous recombination.

Alleles↗
PubMed1992

New gene assignments to rabbit chromosomes; implications for chromosome evolution.

The genes for SOD1 and SOD2 (superoxide dismutases 1 and 2), RB1 (retinoblastoma), TYMS (thymidylate synthase), and TK1 (thymidine kinase) were mapped by in situ hybridization using biotinylated probes to rabbit chromosomes 6, 12, 8, 9, and 19, respectively. This confirms their proposed homoeologies with human chromosomes 21, 6, 13, 18, and 17, respectively, and provides additional information on the modification of these chromosomes during evolution.

Animals↗
PubMed1980

Nucleotide sequence of genes coding for tRNAPhe and tRNATyr from a repeating unit of X. laevis DNA.

A cloned 3.18 kb repeating unit of Xenopus laevis DNA, known to contain two tRNA1Met genes, has been partially sequenced. The sequenced region could potentially code for two more tRNA species. One is a phenylalanine tRNA with the same primary sequence as that found in a variety of mammals. The other is a tyrosine tRNA with a 13 bp intervening sequence located immediately adjacent or very close to the 3' nucleotide of the anticodon. The two putative genes have opposite polarity and the sequences encoding the 5' nucleotides of the mature tRNAs are separated by only 72 bp of DNA. Homologous GC-rich sequences of dyad symmetry precede each gene. Neither gene codes for the 3' terminal CCA expected in the nature tRNAs. A short T cluster is present in the noncoding strand 3 bp away from the 3' end of the tRNATyr gene. A similar short T cluster is located 26 bp downstream of the tRNAPhe sequence. The nucleotides in between are very GC-rich and are capable of forming a stable RNA hairpin. The possible significance of these features for tRNA gene evolution, RNA splicing and transcription is discussed.

Animals↗
PubMedDate not supplied

Expression of Pax gene family members in the anthozoan cnidarian, Nematostella vectensis.

Pax genes are a family of homeodomain transcription factors that have been isolated from protostomes (e.g., eight in Drosophilia) and deuterostomes (e.g., nine in vertebrates) as well as outside the Bilateria, from sponges, a placozoan, and several classes of cnidarians. The genome of an anthozoan cnidarian, the starlet sea anemone, Nematostella vectensis, has been surveyed by both degenerate polymerase chain reaction and in silico for the presence of Pax genes. N. vectensis possesses seven Pax genes, which are orthologous to cnidarian Pax genes (A,B,C, and D) previously identified in another anthozoan, a coral, Acropora millepora. Phylogenetic analyses including data from nonchordate deuterostomes indicates that there were five Pax gene classes in the protostome-deuterostome ancestor, but only three in the cnidarian-bilaterian ancestor, with PaxD class genes lost in medusozoan cnidarians. Pax genes play diverse roles in bilaterians, including eye formation (e.g., Pax6), segmentation (e.g., Pax3/7 class genes), and neural patterning (e.g., Pox-neuro, Pax2/5/8). We show the first expression data for members of all four Pax classes in a single species of cnidarian. N. vectensis Pax genes are expressed in both a cell-type and region-specific manner during embryogenesis, and likely play a role in patterning specific components of the cnidarian ectodermal nerve net. The results of these patterns are discussed with respect to Pax gene evolution in the Bilateria.

Amino Acid Sequence↗