Recovery from TBT pollution in English Channel environments: A problem solved?

Following recognition of effects in the 1980s, tributyltin (TBT) has been monitored at sites in the English Channel to evaluate the prognosis for biota - spanning the introduction of restrictions on TBT use on small boats and the recent phase-out on the global fleet. We describe how persistence and impact of TBT in clams Scrobicularia plana has changed during this period in Southampton Water and Poole Harbour. TBT contamination (and loss) in water, sediment and clams reflects the abundance and type of vessel activity: half-times in sediment (up to 8y in Poole, 33y in Southampton) are longest near commercial shipping. Recovery of clam populations - slowest in TBT-contaminated deposits - provides a useful biological measure of legislative efficacy in estuaries. On rocky shores, recovery from imposex in Nucella lapillus is evident at many sites but, near ports, is prolonged by shipping impacts, including sediment legacy, for example, in the Fal.

Phylogeography of the invasive weed Hypochaeris radicata (Asteraceae): from Moroccan origin to worldwide introduced populations.

In an attempt to delineate the area of origin and migratory expansion of the highly successful invasive weedy species Hypochaeris radicata, we analysed amplified fragment length polymorphisms from samples taken from 44 populations. Population sampling focused on the central and western Mediterranean area, but also included sites from Northern Spain, Western and Central Europe, Southeast Asia and South America. The six primer combinations applied to 213 individuals generated a total of 517 fragments of which 513 (99.2%) were polymorphic. The neighbour-joining tree presented five clusters and these divisions were supported by the results of Bayesian analyses: plants in the Moroccan, Betic Sierras (Southern Spain), and central Mediterranean clusters are all heterocarpic. The north and central Spanish, southwestern Sierra Morena, and Central European, Asian and South American cluster contain both heterocarpic (southwestern Sierra Morena) and homocarpic populations (all other populations). The Doñana cluster includes two homocarpic populations. Analyses of fragment parameters indicate that the oldest populations of H. radicata are located in Morocco and that the species expanded from this area in the Late Quaternary via at least three migratory routes, the earliest of which seems to have been to the southwestern Iberian Peninsula, with subsequent colonizations to the central Mediterranean area and the Betic Sierras. Homocarpic populations originated in the southwestern Iberian Peninsula and subsequently spread across north and central Spain, Central Europe and worldwide, where they became a highly successful weed.

Recovery of polluted ecosystems: the case for long-term studies.

Recovery of marine ecosystems from pollution has tended to receive less attention than the study of new or continuing impacts, but such studies are important in charting recovery from acute incidents and following legislation to deal with chronic contamination. Recovery is inevitably a long-term process, and where such studies have been made they are often too short-lived. Interest quickly wanes following an acute incident and governmental bodies rapidly switch to new legislative priorities for chronic inputs. We review three case studies: recovery of dogwhelk populations after local extinction by tributyl tin leachates from anti-fouling paints; recovery of rocky shore communities from oil spills; and recovery of estuarine ecosystems from industrial and urban development. We then make some generalisations about recovery processes before making a plea for long-term studies of polluted areas.

Genetic control of self-incompatibility in Anagallis monelli (Primulaceae: Myrsinaceae).

The genetic control of self-incompatibility (SI) was studied in the Mediterranean short-lived perennial species Anagallis monelli (Primulaceae: Myrsinaceae). Arrays of siblings, including families derived from reciprocal crosses, were cross-pollinated in full diallels, and compatibility groups were assesssed from a census of fruit-set. Two, three and four intercompatible and intraincompatible groups were found. These crossing relationships fit the model for gametophytic SI controlled by a single polymorphic gene locus in families derived from parents with one or no S alleles in common (two vs. four compatibility groups), whilst one genotype was presumed to be missing in the small families that showed only three compatibility groups.

Evidence for a second function for Saccharomyces cerevisiae Rev1p.

The function of the Saccharomyces cerevisiae REV1 gene is required for translesion replication and mutagenesis induced by a wide variety of DNA-damaging agents. We showed previously that Rev1p possesses a deoxycytidyl transferase activity, which incorporates dCMP opposite abasic sites in the DNA template, and that dCMP insertion is the major event during bypass of an abasic site in vivo. However, we now find that Rev1p function is needed for the bypass of a T-T (6-4) UV photoproduct, a process in which dCMP incorporation occurs only very rarely, indicating that Rev1p possesses a second function. In addition, we find that Rev1p function is, as expected, required for bypass of an abasic site. However, replication past this lesion was also much reduced in the G-193R rev1-1 mutant, which we find retains substantial levels of deoxycytidyl transferase activity. This mutant is, therefore, presumably deficient principally in the second, at present poorly defined, function. The bypass of an abasic site and T-T (6-4) lesion also depended on REV3 function, but neither it nor REV1 was required for replication past the T-T dimer; bypass of this lesion presumably depends on another enzyme.

The function of the human homolog of Saccharomyces cerevisiae REV1 is required for mutagenesis induced by UV light.

In Saccharomyces cerevisiae, most mutations induced by a wide range of mutagens arise during translesion replication employing the REV1 gene product and DNA polymerase zeta. As part of an effort to investigate mammalian mutagenic mechanisms, we have identified cDNA clones of the human homologs of the yeast REV genes and examined their function in UV mutagenesis. Previously, we described the isolation of a human homolog of yeast REV3, the catalytic subunit of pol zeta, and here report the identification and sequence of a human homolog of yeast REV1. This gene was isolated by identifying an expressed sequence tag encoding a peptide with similarity to the C terminus of yeast Rev1p, followed by sequencing of the clone and retrieval of the remaining cDNA by 5' rapid amplification of cDNA ends. The human gene encodes an expected protein of 1,251 residues, compared with 985 residues in the yeast protein. The proteins share two amino-terminal regions of approximately 100 residues with 41% and 20% identity, a region of approximately 320 residues with 31% identity, and a central motif in which 11 of 13 residues are identical. Human cells expressing high levels of an hREV1 antisense RNA grew normally, and were not more sensitive to the cytotoxic effect of 254 nm UV radiation than cells lacking antisense RNA. However, the frequencies of 6-thioguanine resistance mutants induced by UV in the cells expressing antisense hREV1 RNA were significantly lower than in the control (P = 0.01), suggesting that the human gene has a function similar to that of the yeast homolog.

The molecular clock runs at different rates among closely related members of a gene family.

The serum albumin gene family is composed of four members that have arisen by a series of duplications from a common ancestor. From sequence differences between members of the gene family, we infer that a gene duplication some 580 Myr ago gave rise to the vitamin D-binding protein (DBP) gene and a second lineage, which reduplicated about 295 Myr ago to give the albumin (ALB) gene and a common precursor to alpha-fetoprotein (AFP) and alpha-albumin (ALF). This precursor itself duplicated about 250 Myr ago, giving rise to the youngest family members, AFP and ALF. It should be possible to correlate these dates with the phylogenetic distribution of members of the gene family among different species. All four genes are found in mammals, but AFP and ALF are not found in amphibia, which diverged from reptiles about 360 Myr ago, before the divergence of the AFP-ALF progenitor from albumin. Although individual family members display an approximate clock-like evolution, there are significant deviations-the rates of divergence for AFP differ by a factor of 7, the rates for ALB differ by a factor of 2.1. Since the progenitor of this gene family itself arose by triplication of a smaller gene, the rates of evolution of individual domains were also calculated and were shown to vary within and between family members. The great variation in the rates of the molecular clock raises questions concerning whether it can be used to infer evolutionary time from contemporary sequence differences.

A human homolog of the Saccharomyces cerevisiae REV3 gene, which encodes the catalytic subunit of DNA polymerase zeta.

To get a better understanding of mutagenic mechanisms in humans, we have cloned and sequenced the human homolog of the Saccharomyces cerevisiae REV3 gene. The yeast gene encodes the catalytic subunit of DNA polymerase zeta, a nonessential enzyme that is thought to carry out translesion replication and is responsible for virtually all DNA damage-induced mutagenesis and the majority of spontaneous mutagenesis. The human gene encodes an expected protein of 3,130 residues, about twice the size of the yeast protein (1,504 aa). The two proteins are 29% identical in an amino-terminal region of approximately 340 residues, 39% identical in a carboxyl-terminal region of approximately 850 residues, and 29% identical in a 55-residue region in the middle of the two genes. The sequence of the expected protein strongly predicts that it is the catalytic subunit of a DNA polymerase of the pol zeta type; the carboxyl-terminal domain possesses, in the right order, the six motifs characteristic of eukaryotic DNA polymerases, most closely resembles yeast pol zeta among all polymerases in the GenBank database, and is different from the human alpha, delta, and epsilon enzymes. Human cells expressing high levels of an hsREV3 antisense RNA fragment grow normally, but show little or no UV-induced mutagenesis and are slightly more sensitive to killing by UV. The human gene therefore appears to carry out a function similar to that of its yeast counterpart.

The chimpanzee alpha-fetoprotein-encoding gene shows structural similarity to that of gorilla but distinct differences from that of human.

The chimpanzee (Pan troglodytes) alpha-fetoprotein (AFP)-encoding gene (AFP) spans 18,867 bp from the transcription start point to the polyadenylation site, and the nucleotide (nt) sequence reveals that the gene is composed of 15 exons, which are symmetrically placed within three domains of AFP. In addition, we report 3121 bp of 5'-flanking sequence and 4886 bp of 3'-flanking sequence. The entire 26,874 bp of contiguous DNA reported here was determined from three overlapping lambda phage clones. The deduced polypeptide chain is composed of a 19-amino-acid (aa) putative leader peptide, followed by 590 aa of the mature protein. The sequence of chimpanzee AFP was compared with those of the previously published human AFP [Gibbs et al., Biochemistry 26 (1987) 1332-1343] and gorilla AFP [Ryan et al., Genomics 9 (1991) 60-72]. At the aa level, the human AFP differs from the chimpanzee at 6 aa positions and from the gorilla at 4 aa positions; the chimpanzee and gorilla differ at 8 aa positions. There are four types of repetitive sequence elements (X, Alu, Xba and Kpn) in the introns and flanking regions of chimpanzee AFP, and they are located in orthologous positions in the human and gorilla AFP. However, one specific Alu and one Xba repeat in introns 4 and 7, respectively, found in human AFP, are absent from orthologous positions in chimpanzee and gorilla AFP. These two repeats represent human-specific novelties that arose from recent DNA transpositions in primate phylogeny.

Novel mutagenic properties of abasic sites in Saccharomyces cerevisiae.

Abasic sites are particularly important in mutation research because they are frequently the ultimate lesion in chemical mutagenesis, and because they are believed to be a paradigm for non-pairing lesions. Although preferential insertion of dAMP ("A-rule") opposite the lesion has been observed in almost all previous studies with other organisms, we find that in budding yeast, Saccharomyces cerevisiae, the preferred nucleotide is dCMP, suggesting that yeast has a "C-rule", at least with respect to the vector constructs used. These constructs contained a single abasic site specifically located within a 28 nucleotide single-stranded region in an otherwise duplex vector. Nucleotide insertions were determined by sequence analysis of replicated vectors taken from a random set of yeast transformants. In three different sequence contexts, the frequencies of dCMP and dAMP insertion were 83% and 13%, 62% and 31%, and 85% and 8%, respectively. A similar bias in favor of cytosine insertion was found using vectors that were entirely single-stranded. However, a preference for dAMP insertion was found when Escherichia coli, rather than yeast, was transfected with samples of the same gapped duplex vector DNA. Preferential insertion of dCMP is not likely to have arisen by previously proposed mechanisms, but is also unlikely to have occurred by a primer/template misalignment mechanism, in which a nearby template guanine directs the insertion of cytosine. Predominant dCMP insertion was observed even when template guanine bases were excluded from a region extending 19 nucleotides 5', and 13 nucleotides 3', to the abasic site.

The T-T pyrimidine (6-4) pyrimidinone UV photoproduct is much less mutagenic in yeast than in Escherichia coli.

We have examined the mutagenic properties of the T-T pyrimidine (6-4) pyrimidinone UV photoproduct in Saccharomyces cerevisiae, transforming the yeast cells either with single-stranded vectors that carried this adduct at a unique site or with gapped duplex vectors in which the adduct was located within a 28 nt single-stranded region. In an earlier study with SOS-induced Escherichia coli, we found that this photoproduct is highly mutagenic, specifically generating 3' T-->C substitutions in >85% of replicated molecules, and ascribed this specificity to the formation of a stable guanine-pyrimidinone mispair via hydrogen bonds at N-3 and O-2. In contrast, this adduct is very much less mutagenic in yeast, with 60-70% of molecules being replicated accurately and only 12-20% of them exhibiting 3' T-->C substitutions. The enhanced accuracy may reflect the ability of a yeast DNA polymerase, but not E.coli DNA polymerase III, to trap the adduct in a configuration favorable for the formation of an adenine-pyrimidinone base pair.

Cloning and sequence of REV7, a gene whose function is required for DNA damage-induced mutagenesis in Saccharomyces cerevisiae.

The function of the REV7 gene is required for DNA damage-induced mutagenesis in budding yeast, Saccharomyces cerevisiae, and is therefore thought to promote replication past sites of mutagen damage in the DNA template. We have cloned this gene by complementation of the rev7-2 mutant defect, and determined its sequence. REV7 encodes a predicted protein of M(r) 28,759 which is unlikely any other protein in the NCBI non-redundant protein sequence data base, and which is inessential for viability.

Reading the molecular clock from the decay of internal symmetry of a gene.

The closely related serum albumin, alpha-fetoprotein, and vitamin D-binding proteins are derived from a common ancestor, which itself was the result of a triplication of an ancestral gene. We have aligned the sequences of these proteins against themselves to assess the degree to which the ancestral 3-fold symmetry has been retained; in a dot plot, relics of the molecular symmetry appear as a series of alignments parallel to the main diagonal. The decay of internal symmetry reflects the rate of change of a gene in a single line of evolutionary descent. We examined 11 serum albumins, 2 ceruloplasmins, 3 alpha-fetoproteins, and 3 vitamin D-binding proteins. We have found that ceruloplasmin evolves at the same rate in human and rat, whereas albumin, alpha-fetoprotein, and vitamin D-binding protein evolve at different rates. The human genes had the highest alignment scores, indicating the most preserved ancestral features. We conclude that the molecular clock may run at different rates for the same gene in different species.

U-U and T-T cyclobutane dimers have different mutational properties.

We have examined the mutagenic properties in E. coli of single stranded vectors containing a uniquely placed cis-syn or trans-syn uracil-uracil cyclobutane dimer in the sequence 5' GCAAGUUGGAG 3', and compared these with the properties of the corresponding T-T dimers in the same sequence context. The frequencies with which U-U and T-T photoproducts were bypassed were similar in SOS induced cells, and each induced similar frequencies of mutations. However, although both U-U and T-T cis-syn dimers showed a preference for misincorporation in about 5-7% of the replication products, with T or G being incorporated in place of A, the ratios of these events differed, being > 4:1 for T-T cis-syn, but only 2:1 for U-U cis-syn. A shift towards G insertion opposite dimerized uracil was also found with the trans-syn dimers, but the difference was greater; T and G were misincorporated opposite the U-U trans-syn dimer in a ratio of 1:2, compared with 4:1 for its T-T counterpart. In addition, the U-U dimer induced only nucleotide substitutions, unlike the T-T photoproduct which induced single nucleotide deletions as well as substitutions. We conclude that even relatively minor differences in photoproduct structure, such as the presence of a methyl group at C-5, can alter mutational properties, and that such properties cannot depend only on the attributes of the DNA polymerase. Neither the efficiency of bypass, the error frequency nor the mutation spectrum of either U-U isomer is influenced by DNA uracil glycosylase. In vitro, the U-U cis-syn dimer is a substrate for DNA photolyase, but not for the glycosylase.

Complete structure of the human Gc gene: differences and similarities between members of the albumin gene family.

The sequence of the human Gc gene, including 4228 base pairs of the 5'-flanking region and 8514 base pairs of the 3' flanking region (55,136 in total), was determined from five overlapping lambda phage clones. The sequence spans 42,394 base pairs from the cap site to the polyadenylation site, and it reveals that the gene is composed of 13 exons, which are symmetrically placed within the three domains of the Gc protein. The first exon is partially untranslated, as is exon 12, which contains the termination codon TAG. Exon 13 is entirely untranslated, but contains the polyadenylation signal AATAAA. Ten central introns split the coding sequence between codon positions 2 and 3 and between codon positions 3 and 1 in an alternating pattern, exactly as has been observed in the structure of the albumin and alpha-fetoprotein genes. The Gc gene has several distinctive features which set it apart from the other members of the family. First, the gene is smaller by two exons, which results in a protein some 130 amino acids shorter than albumin or AFP. This decrease in size may result from the loss of two internal exons during the evolutionary history of the Gc gene. Second, exons 6, 8, 9, and 11 are smaller than their counterparts in albumin or AFP by a total of 8 codons (1, 4, 1, and 2, respectively). Although the mRNA and protein expressed from the Gc gene are significantly smaller, the gene itself is about 2.5 times larger than the other genes of the family.(ABSTRACT TRUNCATED AT 250 WORDS)

The frequency and accuracy of replication past a thymine-thymine cyclobutane dimer are very different in Saccharomyces cerevisiae and Escherichia coli.

We have compared the mutagenic properties of a T-T cyclobutane dimer in baker's yeast, Saccharomyces cerevisiae, with those in Escherichia coli by transforming each of these species with the same single-stranded shuttle vector carrying either the cis-syn or the trans-syn isomer of this UV photoproduct at a unique site. The mutagenic properties investigated were the frequency of replicational bypass of the photoproduct, the error rate of bypass, and the mutation spectrum. In SOS-induced E. coli, the cis-syn dimer was bypassed in approximately 16% of the vector molecules, and 7.6% of the bypass products had targeted mutations. In S. cerevisiae, however, bypass occurred in about 80% of these molecules, and the bypass was at least 19-fold more accurate (approximately 0.4% targeted mutations). Each of these yeast mutations was a single unique event, and none were like those in E. coli, suggesting that in fact the difference in error rate is much greater. Bypass of the trans-syn dimer occurred in about 17% of the vector molecules in both species, but with this isomer the error rate was higher in S. cerevisiae (21 to 36% targeted mutations) than in E. coli (13%). However, the spectra of mutations induced by the latter photoproduct were virtually identical in the two organisms. We conclude that bypass and error frequencies are determined both by the structure of the photoproduct-containing template and by the particular replication proteins concerned but that the types of mutations induced depend predominantly on the structure of the template. Unlike E. coli, bypass in S. cerevisiae did not require UV-induced functions.

Mutagenesis induced by single UV photoproducts in E. coli and yeast.

Data from experiments with single-stranded vectors that carry a site-specific cyclobutane dimer, pyrimidine (6-4) pyrimidone adduct, or abasic lesion, replicated in either E. coli or, in some cases, bakers' yeast, Saccharomyces cerevisiae, are used to examine two questions: (i) what factors are responsible for the lesion's mutagenicity? and (ii) what are the relative contributions of different photoproducts to the spectrum of UV-induced mutations? With respect to the first question, we suggest that the structure of the mutagen-modified template itself largely determines the kinds of mutations induced, but the relative frequencies of these mutations, the error frequency, and the bypass frequency are strongly dependent on the particular organism studied. With respect to the second question, we suggest that cyclobutane dimers may be responsible for most of the mutations in slowly replicating genomes because of the deamination of cytosine, and that the T-T, and to a lesser extent the T-C, (6-4) adducts play a greater role in the UV mutagenesis of quickly replicating viruses, such as M13 and lambda phage.

Evolution of legume seed storage proteins--a domain common to legumins and vicilins is duplicated in vicilins.

We examined the primary sequence of canavalin, the major storage protein of jack beans, and found that an ancient sequence duplication accounts for 80% of the amino acid residues. Evidence for such a duplication was also found in the orthologous proteins phaseolin and pea vicilin. This sequence duplication presumably accounts for a structural duplication in the canavalin monomer observed by crystallographic analysis. One copy of this repeat was found in a second storage-protein family, the legumins, where it encompasses almost the entire B-chain of the mature molecule. We propose that the vicilin and legumin families of legume seed proteins evolved from a common precursor, which consisted of one copy of the repeat in the vicilins.

Computer analysis of 1,25-dihydroxyvitamin D3-receptor regulated promoters: identification of a candidate D3-response element.

The receptor for the steroid hormone 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] belongs to a superfamily of steroid and triidothyronine (T3) receptors. As yet no 1,25(OH)2D3 response element (DRE) has been identified. Since the T3 and 1,25(OH)2D3 receptors are structurally homologous, we have used the nucleotide sequence of the T3 response element to carry out a computer search of the promoter region of several 1,25(OH)2D3 regulated genes. We report here one candidate DRE from the chick calbindin-D28K gene (AGCCCAATGGCTGAACA) and two candidate DRE's from the rat osteocalcin gene (TCCCCACTGGATGAGCG and CCTGCACTGGGTGAATGA).