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PubMed2003

Field sports and conservation in the United Kingdom.

Many natural habitats exist on privately owned land outside protected areas, but few governments can afford to enforce or subsidize conservation of this biodiversity. Even in some developed countries, conservation subsidy schemes have only achieved limited success. Fortunately, some landowners may be willing to accept management costs in return for other benefits, although this remains controversial when it involves the killing of charismatic species. For example, participants in British field sports, such as fox hunting and game-bird shooting, may voluntarily conserve important habitats that are required by quarry species. Here we report results from a multidisciplinary study that addressed this issue by focusing on three sites across central England. We found that landowners participating in field sports maintained the most established woodland and planted more new woodland and hedgerows than those who did not, despite the equal availability of subsidies. Therefore, voluntary habitat management appears to be important for biodiversity conservation in Britain. Current debates on the future of field sports in Britain, and similar activities globally, may benefit from considering their utility as incentives to conserve additional habitat on private land.

Conservation of Natural Resources↗

PubMed2006

Global distribution and conservation of rare and threatened vertebrates.

Global conservation strategies commonly assume that different taxonomic groups show congruent geographical patterns of diversity, and that the distribution of extinction-prone species in one group can therefore act as a surrogate for vulnerable species in other groups when conservation decisions are being made. The validity of these assumptions remains unclear, however, because previous tests have been limited in both geographical and taxonomic extent. Here we use a database on the global distribution of 19,349 living bird, mammal and amphibian species to show that, although the distribution of overall species richness is very similar among these groups, congruence in the distribution of rare and threatened species is markedly lower. Congruence is especially low among the very rarest species. Cross-taxon congruence is also highly scale dependent, being particularly low at the finer spatial resolutions relevant to real protected areas. 'Hotspots' of rarity and threat are therefore largely non-overlapping across groups, as are areas chosen to maximize species complementarity. Overall, our results indicate that 'silver-bullet' conservation strategies alone will not deliver efficient conservation solutions. Instead, priority areas for biodiversity conservation must be based on high-resolution data from multiple taxa.

Animals↗

PubMed2004

The expansion of conservation genetics.

The 'crisis discipline' of conservation biology has voraciously incorporated many technologies to speed up and increase the accuracy of conservation decision-making. Genetic approaches to characterizing endangered species or areas that contain endangered species are prime examples of this. Technical advances in areas such as high-throughput sequencing, microsatellite analysis and non-invasive DNA sampling have led to a much-expanded role for genetics in conservation. Such expansion will allow for more precise conservation decisions to be made and, more importantly, will allow conservation genetics to contribute to area- and landscape-based decision-making processes.

Animals↗

PubMed2001

Inhibition of breast and brain cancer cell growth by BCCIPalpha, an evolutionarily conserved nuclear protein that interacts with BRCA2.

BRCA2 is a tumor suppressor gene involved in mammary tumorigenesis. Although important functions have been assigned to a few conserved domains of BRCA2, little is known about the longest internal conserved domain encoded by exons 14-24. We identified a novel protein, designated BCCIPalpha, that interacts with part of the internal conserved region of human BRCA2. Human BCCIP represents a family of proteins that are evolutionarily conserved, and contain three distinct domains: an N-terminus acidic domain (NAD) of 30-60 amino acids, an internal conserved domain (ICD) of 180-220 amino acids, and a C-terminus variable domain (CVD) of 30-60 amino acids. The N-terminal half of the human BCCIP ICD shares moderate homology with regions of calmodulin and M-calpain, suggesting that BCCIP may also bind Ca. Human cells express both a longer, BCCIPalpha, and a shorter, BCCIPbeta, form of the protein, which differ in their CVD. BCCIP is a nuclear protein highly expressed in testis. Although BCCIPbeta expression is relatively consistent in cancer cells, the expression of BCCIPalpha varies in cancer cell lines. The BCCIPalpha gene is located at chromosome 10q25.3-26.2, a region frequently altered in brain and other cancers. Furthermore, expression of BCCIPalpha inhibits breast and brain cancer cell growth, but fails to inhibit HT1080 cells and a non-transformed human skin fibroblast. These results suggest that BCCIPalpha is an important cofactor for BRCA2 in tumor suppression.

Amino Acid Sequence↗

PubMed2004

Marsupial BRCA1: conserved regions in mammals and the potential effect of missense changes.

More than half of the reported missense changes in the breast cancer susceptibility protein BRCA1 occur in exon 11, but none has been clearly identified as disease associated and only 28 are designated 'probable' neutral polymorphisms. Previously, in a comparison of sequences from 57 eutherian mammal species, we found seven 'highly conserved regions' between amino acids 282 and 1103, and identified 38 missense changes as likely to disrupt gene function. These conserved regions were also present in birds and amphibians and included only six of the mutations predicted to affect function. In this new analysis, we hypothesized that using 37 ancestral sequences derived from the 57 GenBank sequences and including eight marsupial sequences would allow us to identify regions unique to mammals and refine our predictions of disease-associated missense changes. We identified 13 conserved regions, three of which appear to be unique to mammals, and 21 likely disease-associated missense changes, 11 of which occur in conserved regions. Seven regions identified in this analysis, including the three found only in mammalian sequences, and nine missense changes predicted to affect function are in the putative STAT1-interaction domain, suggesting that the role of STAT1 in immune response is important to mammary function. The reduction in the number of missense changes predicted to be disease associated and the identification of conserved regions specific to mammals can facilitate the further study of the role of missense changes in BRCA1-associated breast cancers.

Amino Acid Sequence↗

PubMed1999

Trans-dominant mutations in the 3'-terminal region of the rpoB gene define highly conserved, essential residues in the beta subunit of RNA polymerase: the GEME motif.

BACKGROUND: The multimeric DNA-dependent RNA polymerases are widespread throughout nature. The RNA polymerase of Escherichia coli, which is the most well characterized, consists of a holoenzyme with subunit stoichiometry of alpha2betabeta'sigma. The beta subunit is conserved and has been implicated in all stages of transcription. The extreme C-terminus of the beta subunit, which includes two well-conserved sequence segments, contributes to the active centre and has been proposed to act in transcriptional termination. We describe a genetic system for further characterizing the role of the extreme C-terminus of the beta subunit of E. coli RNA polymerase. This involves random, PCR (Polymerase Chain Reaction)-mediated mutagenesis of the 3' region of rpoB encoding the C-terminal 116 amino acids of beta, followed by the isolation and characterization of trans-dominant-negative mutations. RESULTS: Substitutions of conserved residues in this region were obtained that exhibited different degrees of growth inhibition in a host expressing the chromosomal-encoded wild-type form of the beta subunit. A number of different substitutions were isolated within the highly conserved sequence motif GEME (residues 1271-->1274 of the E. coli beta subunit). In addition, substitutions were obtained in the extreme C-terminal (surface-exposed) region of beta and at two residues previously proposed to be in the active site (H1237, K1242). The properties of the purified mutant holoenzymes, assessed by transcription assays in vitro, suggested a promoter blockading action. CONCLUSIONS: We have identified an important, highly conserved motif in the beta subunit, GEME (residues 1271-->1274). The nature and effect of the amino acid substitutions at the Gly residue in GEME emphasize the importance of a small, uncharged residue at this position. The in vitro properties of the most extreme trans dominant-negative mutants altered in the GEME motif (and the mutant characteristics in vivo) were similar to those of certain previously identified active-site mutants, suggesting that the altered RNA polymerases were capable of promoter binding and RNA chain initiation but were deficient in the subsequent transcriptional stage.

Amino Acid Sequence↗

PubMed1999

Preserving genes, species, or ecosystems? Healing the fractured foundations of conservation policy.

The scientific foundations of conservation policy are the subject of a recent tripolar debate, with systematists arguing for the primacy of phylogenetic rankings, ecologists arguing for protection at the level of populations or ecosystems, and evolutionary biologists urging more attention for the factors that enhance adaptation and biodiversity. In the field of conservation genetics, this controversy is manifested in the diverse viewpoints of molecular systematists, population biologists, and evolutionary (and quantitative) geneticists. A resolution of these viewpoints is proposed here, based on the premise that preserving particular objects (genes, species, or ecosystems) is not the ultimate goal of conservation. In order to be successful, conservation efforts must preserve the processes of life. This task requires the identification and protection of diverse branches in the tree of life (phylogenetics), the maintenance of life-support systems for organisms (ecology), and the continued adaptation of organisms to changing environments (evolution). None of these objectives alone is sufficient to preserve the threads of life across time. Under this temporal perspective, molecular genetic technologies have applications in all three conservation agendas; DNA sequence comparisons serve the phylogenetic goals, population genetic markers serve the ecological goals, quantitative genetics and genome explorations serve the evolutionary goals.

Animals↗

PubMed1998

Functional and structural conservation in the mechanosensitive channel MscL implicates elements crucial for mechanosensation.

mscL encodes a channel in Escherichia coli that is opened by membrane stretch force, probably serving as an osmotic gauge. Sequences more or less similar to mscL are found in other bacteria, but the degree of conserved function has been unclear. We subcloned and expressed these putative homologues in E. coli and examined their products under patch clamp. Here, we show that each indeed encodes a conserved mechanosensitive channel activity, consistent with the interpretation that this is an important and primary function of the protein in a wide range of bacteria. Although similar, channels of different bacteria differ in kinetics and their degree of mechanosensitivity. Comparison of the primary sequence of these proteins reveals two highly conserved regions, corresponding to domains previously shown to be important for the function of the wild-type E. coli channel, and a C-terminal region that is not conserved in all species. This structural conservation is providing insight into regions of this molecule that are vital to its role as a mechanosensitive channel and may have broader implications for the understanding of other mechanosensitive systems.

Amino Acid Sequence↗

PubMed2001

Conservation strategies for Africa's large mammals.

Africa's large mammals are conserved for their aesthetic, scientific and economic values. Many of these species face a gloomy future precipitated by a combination of factors directly and indirectly influenced by the activities of man, including habitat loss, overexploitation, poor management of designated protected areas, and the vulnerability of small isolated populations. Africa's designated protected areas and biodiversity hotspots are also under threat, highlighting the importance of embracing community participation to address accelerating poverty and malnutrition. Innovative strategies are required for the conservation of Africa's mammals, such as the integration of a wide range of species in the production landscape, including the farming community. Transfrontier conservation areas (TFCAs) have been established with the combined objectives of conserving biodiversity, creating new jobs in the tourism and wildlife industry, and promoting a culture of peace. These areas extend far beyond traditional national parks, providing opportunities for integrating large mammals into sustainable land-use practices, at the same time as addressing some of the continent's more pressing socioeconomic needs. Research on African mammals will inevitably have to change direction to accommodate the growing threats and changed circumstances. Priorities will include the identification of corridors associated with TFCA establishment, the determination of the economic value of certain species in consumptive use programmes, research on contraception as a management option in restricted areas, and further work on the indirect use value of species. There will also be worthwhile opportunities to be pursued with ex situ conservation programmes, but these need to be focussed more efficiently.

Africa↗

PubMed2003

Wilderness and biodiversity conservation.

Human pressure threatens many species and ecosystems, so conservation efforts necessarily prioritize saving them. However, conservation should clearly be proactive wherever possible. In this article, we assess the biodiversity conservation value, and specifically the irreplaceability in terms of species endemism, of those of the planet's ecosystems that remain intact. We find that 24 wilderness areas, all > or = 1 million hectares, are > or = 70% intact and have human densities of less than or equal to five people per km2. This wilderness covers 44% of all land but is inhabited by only 3% of people. Given this sparse population, wilderness conservation is cost-effective, especially if ecosystem service value is incorporated. Soberingly, however, most wilderness is not speciose: only 18% of plants and 10% of terrestrial vertebrates are endemic to individual wildernesses, the majority restricted to Amazonia, Congo, New Guinea, the Miombo-Mopane woodlands, and the North American deserts. Global conservation strategy must target these five wildernesses while continuing to prioritize threatened biodiversity hotspots.

Animals↗

PubMed1997

The I/LWEQ module: a conserved sequence that signifies F-actin binding in functionally diverse proteins from yeast to mammals.

Talin is an actin-binding protein involved in integrin-mediated cell adhesion and spreading. The C-terminal 197 amino acids of vertebrate talin are 45% similar to the C-terminal residues of Sla2, a yeast protein implicated in polarized assembly of the yeast actin cytoskeleton. Talin is also homologous in this region to nematode talin, cellular slime mold filopodin, and an Sla2 homolog from nematode. Analysis of the conserved C-terminal sequences of these five proteins with BLOCK MAKER reveals a series of four blocks, which we name the I/LWEQ module after the conserved initial residues in each block. Experiments presented here show that the conserved protein domain represented by the I/LWEQ module competes quantitatively with native talin for binding to F-actin in vitro. Furthermore, the corresponding domain of Sla2 binds to both yeast and vertebrate F-actin in vitro. Mutation of one of the conserved residues in the fourth conserved block abolishes the interaction of the Sla2 I/LWEQ module with F-actin. These results establish the location of an F-actin binding domain in native talin, demonstrate that direct interaction of Sla2 with actin is a possible basis for its effect on the actin cytoskeleton in vivo, and define the I/LWEQ consensus as a new actin-binding motif.

Actins↗

PubMed1999

Conservation of the expression and function of apterous orthologs in Drosophila and mammals.

The Drosophila apterous (ap) gene encodes a protein of the LIM-homeodomain family. Many transcription factors of this class have been conserved during evolution; however, the functional significance of their structural conservation is generally not known. ap is best known for its fundamental role as a dorsal selector gene required for patterning and growth of the wing, but it also has other important functions required for neuronal fasciculation, fertility, and normal viability. We isolated mouse (mLhx2) and human (hLhx2) ap orthologs, and we used transgenic animals and rescue assays to investigate the conservation of the Ap protein during evolution. We found that the human protein LHX2 is able to regulate correctly ap target genes in the fly, causes the same phenotypes as Ap when ectopically produced, and most importantly rescues ap mutant phenotypes as efficiently as the fly protein. In addition, we found striking similarities in the expression patterns of the Drosophila and murine genes. Both mLhx2 and ap are expressed in the respective nerve cords, eyes, olfactory organs, brain, and limbs. These results demonstrate the conservation of Ap protein function across phyla and argue that aspects of its expression pattern have also been conserved from a common ancestor of insects and vertebrates.

Amino Acid Sequence↗

PubMed1995

Segmental conservation of sapA sequences in type B Campylobacter fetus cells.

Campylobacter fetus cells may exist as either of two defined serogroups (type A or B) based on their lipopolysaccharide (LPS) composition. Wild-type strains contain surface array proteins (S-layer proteins) that have partial antigenic cross-reactivity but bind exclusively to LPS from homologous (type A or B) cells. Type A cells possess 8 homologs of sapA, which encodes a 97-kDa S-layer protein; the gene products of these homologs have a conserved N terminus of 184 amino acids. To further explore the structural relationships between the C. fetus S-layer proteins and their encoding genes, we sought to clone and express an S-layer protein from type B strain 84-91. The cloned type B gene (sapB) was similar in structure to the previously cloned type A gene (sapA) and encoded a full-length 936-amino acid (97-kDa) S-layer protein. Sequence analysis of sapB indicated that the conserved N-terminal encoding region in sapA was absent but that the remainder of the ORF (encoding 751 amino acids) was identical to that of sapA in spite of the nonconserved nature of this region among sapA homologs. Noncoding sequences both 300 base pairs 5' and 1000 base pairs 3' to the sapB and sapA ORFs, including the sapA promoter and transcriptional terminator sequences, were essentially identical. Southern analyses revealed that the sapB N-terminal encoding region was conserved in multiple copies in type B strains but was absent in type A strains. Recombinant sapA and sapB products bound to a substantially greater degree to cells of the homologous LPS type compared with the heterologous LPS type, indicating that the conserved sapA- and sapB-encoded N termini are critical for LPS binding specificity. The parallel genetic organization and identity at the nucleotide level in both coding and noncoding regions for sap homologs in types A and B cells indicates the necessity of both homolog conservation and high fidelity DNA replication in the biology of sap diversity.

Amino Acid Sequence↗

PubMed1995

A conserved glutamate is responsible for ion selectivity and pH dependence of the mammalian anion exchangers AE1 and AE2.

The erythrocyte anion exchanger AE1 (band 3) serves as an important model for the study of the mechanism of ion transport. Chemical modification of human erythrocyte AE1 has previously suggested that glutamic acid residue 681 lies within the transport pathway and can cross the permeability barrier. This glutamate is conserved in all anion exchangers sequenced to date. We examined the effect on divalent (sulfate) and monovalent (chloride and bicarbonate) anion transport of mutating the corresponding glutamates in mouse AE1 and the closely related anion exchanger, AE2. Substitution of this conserved glutamate with uncharged or basic amino acids had a negligible effect on the maximal rate of sulfate-sulfate exchange in AE-reconstituted proteoliposomes, but largely abolished the steep pH dependence of sulfate transport observed in wild-type AE1 and AE2. In contrast, exchange of monovalent anions was undetectable in cells expressing these mutants. Replacement of the conserved glutamate with aspartate abolished both monovalent and divalent anion transport. These data suggest that the conserved glutamate residue plays a dual role in determining anion selectivity and in proton coupling to sulfate transport. A model explaining the role of the conserved glutamate in promoting ion selectivity and pH regulation is discussed.

Animals↗

PubMed1996

The effect of amino acid substitutions in the conserved aromatic region of subunit II of cytochrome c oxidase in Saccharomyces cerevisiae.

Mitochondrial encoded subunit II of cytochrome c oxidase carries the metal center, which acts as the initial acceptor of electrons from cytochrome c. Among the conserved features of this protein is a region in which five aromatic and three non-aromatic amino acids are conserved in a wide variety of organisms. This aromatic region has been postulated to be involved in transfer of electrons from the copper center in subunit II to the remaining metal centers of cytochrome oxidase in subunit I. To test the functional importance of two conserved, aromatic tryptophan residues and one conserved, non-aromatic glycine residue, yeast strains with alterations at these positions were characterized. The strains with altered codons were tested for their ability to carry out cellular respiration, for their growth rates on non-fermentable carbon sources, and for their cytochrome c oxidase activity. The results demonstrate that the aromatic character of the tryptophan residues appears necessary for subunit II function, while the conserved glycine can be replaced with other, small, uncharged residues.

Amino Acid Sequence↗

PubMed1997

Recognition of nonconserved bases in the P22 operator by P22 repressor requires specific interactions between repressor and conserved bases.

The ability of P22 repressor protein to distinguish between the six naturally occurring operator binding sites is critically important in determining whether the bacteriophage chooses to grow lytically or lysogenically. We have shown that changes in the highly conserved bases at P22 operator positions 3, 5, 6, and 7 prevent specific binding of P22 repressor. Moreover, studies of mutant proteins identified the three repressor amino acids that directly contact these conserved bases. The pattern of operator sequence conservation permits these direct amino acid-base pair interactions to occur in all except one of the 12 operator half-sites in the phage chromosome. Therefore, repressor differential affinity for these sites cannot be due to these highly conserved base pair-amino acid interactions. Our binding studies show that the nonconserved bases at positions 2 and 4 also play an important role in determining the relative affinity of the naturally occurring P22 operators for P22 repressor. Our data indicate that the direct contacts between the three solvent-exposed amino acids and the conserved bases in the binding site lock these amino acids in place, forming a scaffold allowing the rest of the amino acids side chains to form weaker interactions with the nonconserved bases in the binding site.

Amino Acid Sequence↗

PubMed1998

Comparison of promoters for the murine and human P-selectin genes suggests species-specific and conserved mechanisms for transcriptional regulation in endothelial cells.

P-selectin, an adhesion receptor for leukocytes, is constitutively expressed in megakaryocytes and endothelial cells. Tumor necrosis factor-alpha (TNF-alpha) or lipopolysaccharide (LPS) increases synthesis of P-selectin in murine but not in human endothelial cells. To identify potential species-specific and conserved mechanisms for regulation of expression of P-selectin, we cloned the 5'-flanking region of the murine P-selectin gene and compared its features with those previously reported for the human gene. The murine and human genes shared conserved Stat-like, Hox, Ets, GATA, and GT-IIC elements. In the murine gene, a conserved GATA element bound to GATA-2 and functioned as a positive regulatory element, whereas a conserved Ets element bound to GA-binding protein and functioned as a negative regulatory element. Significantly, the murine P-selectin gene had several features not found in the human gene. These included an insertion from -987 to -649 that contained tandem GATA and tandem AP1-like sequences, which resembled enhancers in beta-globin locus control regions. Both tandem elements bound specifically to nuclear proteins. The murine gene lacked the unique kappaB site specific for p50 or p52 homodimers found in the human gene. Instead, it contained two tandem kappaB elements and a variant activating transcription factor/cAMP response element site, which closely resembled sites in the E-selectin gene that are required for TNF-alpha- or LPS-inducible expression. TNF-alpha or LPS augmented expression of a reporter gene driven by the murine, but not the human, P-selectin promoter in transfected endothelial cells. Deletional analysis of the murine 5'-flanking region revealed several sequences that were required for either constitutive or inducible expression. These data suggest that both species-specific and conserved mechanisms regulate transcription of the human and murine P-selectin genes.

Animals↗

PubMed1999

Chemical modification and site-directed mutagenesis of conserved HXXH and PP-loop motif arginines and histidines in the murine bifunctional ATP sulfurylase/adenosine 5'-phosphosulfate kinase.

The sulfurylase domain of the mouse bifunctional enzyme ATP sulfurylase/adenosine 5'-phosphosulfate (APS) kinase contains HXXH and PP-loop motifs. To elucidate the functional importance of these motifs and of conserved arginines and histidines, chemical modification and site-directed mutagenesis studies were performed. Chemical modification of arginines and histidines with phenylglyoxal and diethyl pyrocarbonate, respectively, renders the enzyme inactive in sulfurylase, kinase, and overall assays. Data base searches and sequence comparison of bifunctional ATP sulfurylase/APS kinase and monofunctional ATP sulfurylases shows a limited number of highly conserved arginines and histidines within the sulfurylase domain. Of these conserved residues, His-425, His-428, and Arg-421 are present within or near the HXXH motif whereas His-506, Arg-510, and Arg-522 residues are present in and around the PP-loop. The functional role of these conserved residues was further studied by site-directed mutagenesis. In the HXXH motif, none of the alanine mutants (H425A, H428A, and R421A) had sulfurylase or overall activity, whereas they all exhibited normal kinase activity. A slight improvement in reverse sulfurylase activity (<10% residual activity) and complete restoration of forward sulfurylase was observed with R421K. Mutants designed to probe the PP-loop requirements included H506A, R510A, R522A, R522K, and D523A. Of these, R510A exhibited normal sulfurylase and kinase activity, R522A and R522K showed no sulfurylase activity, and H506A had normal sulfurylase activity but produced an effect on kinase activity (<10% residual activity). The single aspartate, D523A, which is part of the highly conserved GRD sequence of the PP-loop, affected both sulfurylase and kinase activity. This mutational analysis indicates that the HXXH motif plays a role only in the sulfurylase activity, whereas the PP-loop is involved in both sulfurylase and kinase activities. Residues specific for sulfurylase activity have also been distinguished from those involved in kinase activity.

Amino Acid Sequence↗