Biomedical subjects

Daniel L Hartl

Publications and source records attributed to Daniel L Hartl.

At least 19 recordsLinked to original sources

PubMed2007

Epigenetic memory at malaria virulence genes.

During its red blood cell stage, the malaria parasite Plasmodium falciparum can switch its variant surface proteins (P. falciparum erythrocyte membrane protein 1) to evade the host immune response. The var gene family encodes P. falciparum erythrocyte membrane protein 1, different versions of which have unique binding specificities to various human endothelial surface molecules. Individual parasites each contain approximately 60 var genes at various locations within their chromosomes; however, parasite isolates contain different complements of var genes, thus, the gene family is enormous with a virtually unlimited number of members. A single var gene is expressed by each parasite in a mutually exclusive manner. We report that control of var gene transcription and antigenic variation is associated with a chromatin memory that includes methylation of histone H3 at lysine K9 as an epigenetic mark. We also discuss how gene transcription memory may affect the mechanism of pathogenesis and immune evasion.

Animals↗

PubMed2006

A genome-wide map of diversity in Plasmodium falciparum.

Genetic variation allows the malaria parasite Plasmodium falciparum to overcome chemotherapeutic agents, vaccines and vector control strategies and remain a leading cause of global morbidity and mortality. Here we describe an initial survey of genetic variation across the P. falciparum genome. We performed extensive sequencing of 16 geographically diverse parasites and identified 46,937 SNPs, demonstrating rich diversity among P. falciparum parasites (pi = 1.16 x 10(-3)) and strong correlation with gene function. We identified multiple regions with signatures of selective sweeps in drug-resistant parasites, including a previously unidentified 160-kb region with extremely low polymorphism in pyrimethamine-resistant parasites. We further characterized 54 worldwide isolates by genotyping SNPs across 20 genomic regions. These data begin to define population structure among African, Asian and American groups and illustrate the degree of linkage disequilibrium, which extends over relatively short distances in African parasites but over longer distances in Asian parasites. We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite.

Africa↗

PubMed2006

Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum.

The density and distribution of single-nucleotide polymorphisms (SNPs) across the genome has important implications for linkage disequilibrium mapping and association studies, and the level of simple-sequence microsatellite polymorphisms has important implications for the use of oligonucleotide hybridization methods to genotype SNPs. To assess the density of these types of polymorphisms in P. falciparum, we sampled introns and noncoding DNA upstream and downstream of coding regions among a variety of geographically diverse parasites. Across 36,229 base pairs of noncoding sequence representing 41 genetic loci, a total of 307 polymorphisms including 248 polymorphic microsatellites and 39 SNPs were identified. We found a significant excess of microsatellite polymorphisms having a repeat unit length of one or two, compared to those with longer repeat lengths, as well as a nonrandom distribution of SNP polymorphisms. Almost half of the SNPs localized to only three of the 41 genetic loci sampled. Furthermore, we find significant differences in the frequency of polymorphisms across the two chromosomes (2 and 3) examined most extensively, with an excess of SNPs and a surplus of polymorphic microsatellites on chromosome 3 as compared to chromosome 2 (P=0.0001). Furthermore, at some individual genetic loci we also find a nonrandom distribution of polymorphisms between coding and flanking noncoding sequences, where completely monomorphic regions may flank highly polymorphic genes. These data, combined with our previous findings of nonrandom distribution of SNPs across chromosome 2, suggest that the Plasmodium falciparum genome may be a mosaic with regard to genetic diversity, containing chromosomal regions that are highly polymorphic interspersed with regions that are much less polymorphic.

Animals↗

PubMed2006

Duplication, gene conversion, and genetic diversity in the species-specific acyl-CoA synthetase gene family of Plasmodium falciparum.

While genes encoding antigens and other highly polymorphic proteins are commonly found in subtelomeres, it is unusual to find a small family of housekeeping genes in these regions. We found that in the species Plasmodium falciparum only, a non-subtelomeric acyl-CoA synthetase (ACS) gene has expanded into a family of duplicated genes mainly located in the subtelomeres of the genome. We identified the putative parent of the duplicated family by analysis of synteny and phylogeny relative to other Plasmodium ACS genes. All ten ACS paralogs are transcribed in erythrocytic stages of laboratory and field isolates. We identified and confirmed a recent double gene conversion event involving ACS genes on three different chromosomes of isolate 3D7, resulting in the creation of a new hybrid gene. Southern hybridization analysis of geographically diverse P. falciparum isolates provides evidence for the strikingly global conservation of the ACS gene family, but also for some chromosomal events, including deletion and recombination, involving the duplicated paralogs. We found a dramatically higher rate of non-synonymous substitutions per non-synonymous site than synonymous substitutions per synonymous site in the closely related ACS paralogs we sequenced, suggesting that these genes are under a form of selection that favors change in the state of the protein. We also found that the gene encoding acyl-CoA binding protein has expanded and diversified in P. falciparum. We have described a new class of subtelomeric gene family with a unique capacity for diversity in P. falciparum.

Animals↗

PubMed2006

Plasmodium falciparum: worldwide sequence diversity and evolution of the malaria vaccine candidate merozoite surface protein-2 (MSP-2).

We examined patterns and putative mechanisms of sequence diversification in the merozoite surface protein-2 (MSP-2) of Plasmodium falciparum, a major dimorphic malaria vaccine candidate antigen, by analyzing 448 msp-2 alleles from all continents. We describe several nucleotide replacements, insertion and deletion events, frameshift mutations, and proliferations of repeat units that generate the extraordinary diversity found in msp-2 alleles. We discuss the role of positive selection exerted by naturally acquired type- and variant-specific immunity in maintaining the observed levels of polymorphism and suggest that this is the most likely explanation for the significant excess of nonsynonymous nucleotide replacements found in dimorphic msp-2 domains. Hybrid sequences created by meiotic recombination between alleles of different dimorphic types were observed in few (3.1%) isolates, mostly from Africa. We found no evidence for an extremely ancient origin of allelic dimorphism at the msp-2 locus, predating P. falciparum speciation, in contrast with recent findings for other surface malarial antigens.

Alleles↗

PubMed2006

The evolution of the novel Sdic gene cluster in Drosophila melanogaster.

The origin of new genes and of new functions for existing genes are fundamental processes in molecular evolution. Sdic is a newly evolved gene that arose recently in the D. melanogaster lineage. The gene encodes a novel sperm motility protein. It is a chimeric gene formed by duplication of two other genes followed by multiple deletions and other sequence rearrangements. The Sdic gene exists in several copies in the X chromosome, and is presumed to have undergone several duplications to form a tandemly arrayed gene cluster. Given the very recent origin of the gene and the gene cluster, the analysis of the composition of this gene cluster represents an excellent opportunity to study the origin and evolution of new gene functions and the fate of gene duplications. We have analyzed the nucleotide sequence of this region and reconstructed the evolutionary history of this gene cluster. We found that the cluster is composed by four tandem copies of Sdic; these duplicates are very similar but can be distinguished by the unique pattern of insertions, deletions, and point mutations in each copy. The oldest gene copy in the array has a 3' exon that has undergone accelerated diversification, and also shows divergent regulatory sequences. Moreover, there is evidence that this might be the only gene copy in the tandem array that is transcribed at a significant level, expressing a novel sperm-specific protein. There is also a retrotransposon located at the 3' end of each Sdic gene copy. We argue that this gene cluster was formed in the last two million years by at least three tandem duplications and one retrotransposition event.

3' Untranslated Regions↗

PubMed2006

Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number.

We compared intron positions in conserved regions of 3479 orthologous gene pairs from Plasmodium falciparum and Plasmodium yoelii, which likely diverged >or=100 million years ago (Mya). Only 27 out of 2212 positions were specific to one of the two species. Intron presence in related species shows that at least 19 and possibly 26 of the changes are due to intron loss, depending on phylogeny. The implied intron loss and gain rates are much lower than previously estimated for nematodes, arthropods, fungi, and plants, and are comparable only with the rates in vertebrates. That all observed changes were exact, occurring without loss or gain of flanking coding sequence, suggests intron loss via an mRNA intermediate, as does a nonsignificant trend toward loss of introns at adjacent positions. Many of the intron changes occurred in genes encoding proteins involved in nucleic acid-related processes, as previously found for intron gains in nematodes. Two changes occurred in the chloroquine resistance transporter, suggesting a role for positive selection in intron loss in Plasmodium. The dearth of intron loss and gain could be explained by the lack of known transposable elements in Plasmodium, since transposable elements and/or reverse transcriptase are thought to be necessary for both processes. The observed pattern suggests that the availability of stochastic intron loss and gain mutations can be a major determinant of changes in intron number.

Alternative Splicing↗

PubMed2006

On the abundance, amino acid composition, and evolutionary dynamics of low-complexity regions in proteins.

Protein sequences frequently contain regions composed of a reduced number of amino acids. Despite their presence in about half of all proteins and their unusual prevalence in the malaria parasite Plasmodium falciparum, the function and evolution of such low-complexity regions (LCRs) remain unclear. Here we show that LCR abundance and amino acid composition depend largely, but not exclusively, on genomic A+T content and obey power-law growth dynamics. Further, our results indicate that LCRs are analogous to microsatellites in that DNA replication slippage and unequal crossover recombination are important molecular mechanisms for LCR expansion. We support this hypothesis by demonstrating that the size of LCR insertions/deletions among orthologous genes depends upon length. Moreover, we show that LCRs enable intra-exonic recombination in a key family of cell-surface antigens in P. falciparum and thus likely facilitate the generation of antigenic diversity. We conclude with a mechanistic model for LCR evolution that links the pattern of LCRs within P. falciparum to its high genomic A+T content and recombination rate.

Amino Acids↗

PubMed2006

Position-specific polymorphism of Plasmodium falciparum Stuttering motif in a PHISTc PFI1780w.

Several genes of Plasmodium falciparum are positively selected due to the pressure from the host immune system. This is a pattern completely opposite to that found in most housekeeping genes, which have few synonymous mutations. The discrepancy is an important topic in Plasmodium biology. We searched for unique polymorphism patterns in P. falciparum and identified a repetitive Stuttering motif in PFI1780w which was recently grouped as a gene in the PHIST family. The repeat has a position-specific polymorphism pattern in the otherwise highly conserved gene. Its mutations are limited to only one small region, and they are not consistent with replication slippage or gene conversion commonly found in low complexity regions. The repeat variation was analyzed in different strains of P. falciparum. The PFI1780w Stuttering motif can be a model to study gene diversification and used as a tool for strain typing.

Amino Acid Sequence↗

PubMed2006

Darwinian evolution can follow only very few mutational paths to fitter proteins.

Five point mutations in a particular beta-lactamase allele jointly increase bacterial resistance to a clinically important antibiotic by a factor of approximately 100,000. In principle, evolution to this high-resistance beta-lactamase might follow any of the 120 mutational trajectories linking these alleles. However, we demonstrate that 102 trajectories are inaccessible to Darwinian selection and that many of the remaining trajectories have negligible probabilities of realization, because four of these five mutations fail to increase drug resistance in some combinations. Pervasive biophysical pleiotropy within the beta-lactamase seems to be responsible, and because such pleiotropy appears to be a general property of missense mutations, we conclude that much protein evolution will be similarly constrained. This implies that the protein tape of life may be largely reproducible and even predictable.

Alleles↗

PubMed2006

Variable SNP density in aspartyl-protease genes of the malaria parasite Plasmodium falciparum.

An analysis of the diversity of the aspartyl proteases of Plasmodium falciparum, known as plasmepsins (PMs), was completed in view of their possible role as drug targets. DNA sequence polymorphisms were identified in nine pm genes including their non-coding (introns and 5' flanking) sequences. All genes contained at least one single nucleotide polymorphism (SNP). Extensive microsatellite diversity was observed predominantly in non-coding sequences. All but one non-synonymous polymorphism (a conservative substitution) were mapped to the surface of the predicted protein, contradicting a possible role in enzymatic activity. The distribution of SNPs was found to be non-random among pm genes, with pm6 and pm10 having significantly higher SNP densities, suggesting they were under selection. For pm6 the majority of the SNPs were in introns and some of these may contribute to splice site variation. SNPs were found at a high density in both the coding and non-coding sequences of pm10. Recombination was important in generating additional diversity at this locus. Although direct selection for pm10 mutations could not be ruled out, the presence of balancing selection and a high density of SNPs in non-coding sequence led us to propose that another gene under selection may be influencing the diversity in the region. By sequencing short DNA tags in a 200 kb region flanking pm10 we show that a cluster of antigen genes, known to be under diversifying selection, may contribute to the observed diversity. We discuss the importance of diversity and local selection effects when choosing drug targets for intervention strategies.

Animals↗

PubMed2006

Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes.

One of the most important aspects of the evolution of development and physiology is the interplay between gene expression and the environment, by which traits become altered in response to environmental triggers. This feature is known as phenotypic plasticity. When different genotypes show different levels of plasticity for a trait, then they show genotype-by-environment interaction, or GEI. It is now clear that gene expression plays an important role in organismic-level phenotypic plasticity, but we know very little about whether gene expression itself is subject to genetic variation for phenotypic plasticity (GEI). Given that gene regulation is likely to have evolved to respond to environmental changes, it is of central importance to understand how environmental and genetic variation interact to produce variation in gene expression. Here we investigate genetic variation for phenotypic plasticity in the yeast transcriptome for the whole genome. Six strains of Saccharomyces cerevisiae were grown in four different environments representing a continuum of rich and poor natural conditions. Using DNA-microarray data and an ANOVA analysis with a stringent criterion of significance, we found significant genetic variation for transcriptional plasticity (GEI) among strains for approximately 5% of the genes in the genome. There are about twice as many genes that show genetic variation for phenotypic plasticity as show genetic variation in transcription level independent of the environment. We also found that genes with genetic variation for plasticity were less likely to be essential and were significantly biased towards genes that have paralogs.

Adaptation, Physiological↗

PubMed2006

Ecological and evolutionary genomics of Saccharomyces cerevisiae.

Saccharomyces cerevisiae, the budding yeast, is the most thoroughly studied eukaryote at the cellular, molecular, and genetic levels. Yet, until recently, we knew very little about its ecology or population and evolutionary genetics. In recent years, it has been recognized that S. cerevisiae occupies numerous habitats and that populations harbour important genetic variation. There is therefore an increasing interest in understanding the evolutionary forces acting on the yeast genome. Several researchers have used the tools of functional genomics to study natural isolates of this unicellular fungus. Here, we review some of these studies, and show not only that budding yeast is a prime model system to address fundamental molecular and cellular biology questions, but also that it is becoming a powerful model species for ecological and evolutionary genomics studies as well.

Ecology↗

PubMed2005

Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis.

Hybrid dysgenesis in Drosophila is a syndrome of gonadal atrophy, sterility, and male recombination, and it occurs in the progeny of crosses between males that harbor certain transposable elements (TEs) and females that lack them. Known examples of hybrid dysgenesis in Drosophila melanogaster result from mobilization of individual families of TEs, such as the P element, the I element, or hobo. An example of hybrid dysgenesis in Drosophila virilis is unique in that multiple, unrelated families of TEs become mobilized, but a TE designated Penelope appears to play a major role. In all known examples of hybrid dysgenesis, the paternal germ line transmits the TEs in an active state, whereas the female germ line maintains repression of the TEs. The mechanism of maternal maintenance of repression is not known. Recent evidence suggests that the molecular machinery of RNA interference may function as an important host defense against TEs. This protection is mediated by the action of endogenous small interfering RNAs (siRNAs) composed of dsRNA molecules of 21-25 nt that can target complementary transcripts for destruction. In this paper, we demonstrate that endogenous siRNA derived from the Penelope element is maternally loaded in embryos through the female germ line in D. virilis. We also present evidence that the maternal inheritance of these endogenous siRNAs may contribute to maternal repression of Penelope.

Animals↗

PubMed2005

Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila.

Hybrids between species are often characterized by novel gene-expression patterns. A recent study on allele-specific gene expression in hybrids between species of Drosophila revealed cases in which cis- and trans-regulatory elements within species had coevolved in such a way that changes in cis-regulatory elements are compensated by changes in trans-regulatory elements. We hypothesized that such coevolution should often lead to gene misexpression in the hybrid. To test this hypothesis, we estimated allele-specific expression and overall expression levels for 31 genes in D. melanogaster, D. simulans, and their F1 hybrid. We found that 13 genes with cis-trans compensatory evolution are in fact misexpressed in the hybrid. These represent candidate genes whose dysregulation might be the consequence of coevolution of cis- and trans-regulatory elements within species. Using a mathematical model for the regulation of gene expression, we explored the conditions under which cis-trans compensatory evolution can lead to misexpression in interspecific hybrids.

Alleles↗

PubMed2005

Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes.

We compared levels of sequence divergence between fourfold synonymous coding sites and noncoding sites from the intergenic and intronic regions of the Plasmodium falciparum and Plasmodium reichenowi genomes. We observed significant differences in the level of divergence between these classes of silent sites. Fourfold synonymous coding sites exhibited the highest level of sequence divergence, followed by introns, and then intergenic sequences. This pattern of relative divergence rates has been observed in primate genomes but was unexpected in Plasmodium due to a paucity of variation at silent sites in P. falciparum and the corollary hypothesis that silent sites in this genome may be subject to atypical selective constraints. Exclusion of hypermutable CpG dinucleotides reduces the divergence level of synonymous coding sites to that of intergenic sites but does not diminish the significantly higher divergence level of introns relative to intergenic sites. A greater than expected incidence of CpG dinucleotides in intergenic regions less than 500 bp from genes may indicate selective maintenance of regulatory motifs containing CpGs. Divergence rates of different classes of silent sites in these Plasmodium genomes are determined by a combination of mutational and selective pressures.

Animals↗

PubMed2005

Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineages.

We describe the complete opsin gene families from the sequenced fugu and Tetraodon pufferfish genomes. We report the convergent loss of function of an anciently duplicated, functionally divergent RH2 or "green-sensitive" opsin gene in both pufferfish lineages, designated RH2-2. In fugu, RH2-2 apparently ceased to function very recently following a transposon-induced deletion that truncated the N-terminal 115 amino acids from the translated protein. Although a lack of frameshift or nonsense mutations in the fugu RH2-2 pseudogene suggests that the gene was lost very recently in this lineage, we were unable to detect any evidence of a selective sweep associated with the fixation of the truncated allele from population data. Interspecific comparison of the remaining fugu RH2-2 coding sequence paradoxically indicates that the gene was under strong purifying selection until the truncation occurred.

Amino Acid Sequence↗

PubMed2005

Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions.

Organismic evolution requires that variation at distinct hierarchical levels and attributes be coherently integrated, often in the face of disparate environmental and genetic pressures. A central part of the evolutionary analysis of biological systems remains to decipher the causal connections between organism-wide (or genome-wide) attributes (e.g., mRNA abundance, protein length, codon bias, recombination rate, genomic position, mutation rate, etc) as well as their role-together with mutation, selection, and genetic drift-in shaping patterns of evolutionary variation in any of the attributes themselves. Here we combine genome-wide evolutionary analysis of protein and gene expression data to highlight fundamental relationships among genomic attributes and their associations with the evolution of both protein sequences and gene expression levels. Our results show that protein divergence is positively coupled with both gene expression polymorphism and divergence. We show moreover that although the number of protein-protein interactions in Drosophila is negatively associated with protein divergence as well as gene expression polymorphism and divergence, protein-protein interactions cannot account for the observed coupling between regulatory and structural evolution. Furthermore, we show that proteins with higher rates of amino acid substitutions tend to have larger sizes and tend to be expressed at lower mRNA abundances, whereas genes with higher levels of gene expression divergence and polymorphism tend to have shorter sizes and tend to be expressed at higher mRNA abundances. Finally, we show that protein length is negatively associated with both number of protein-protein interactions and mRNA abundance and that interacting proteins in Drosophila show similar amounts of divergence. We suggest that protein sequences and gene expression are subjected to similar evolutionary dynamics, possibly because of similarity in the fitness effect (i.e., strength of stabilizing selection) of disruptions in a gene's protein sequence or its mRNA expression. We conclude that, as more and better data accumulate, understanding the causal connections among biological traits and how they are integrated over time to constrain or promote structural and regulatory evolution may finally become possible.

Animals↗