Author: biota

Stinchcombe JR, Izem R, Heschel MS, McGoey BV, Schmitt J

Evolution 2010 Oct;64(10):2887-903

PubMed PMID: 20662920

Abstract

Trade-offs can exist within and across environments, and constrain evolutionary trajectories. To examine the effects of competition and resource availability on trade-offs, we grew individuals of recombinant inbred lines of Impatiens capensis in a factorial combination of five densities with two light environments (full light and neutral shade) and used a Bayesian logistic growth analysis to estimate intrinsic growth rates. To estimate across-environment constraints, we developed a variance decomposition approach to principal components analysis, which accounted for sample size, model-fitting, and within-RIL variation prior to eigenanalysis. We detected negative across-environment genetic covariances in intrinsic growth rates, although only under full-light. To evaluate the potential importance of these covariances, we surveyed natural populations of I. capensis to measure the frequency of different density environments across space and time. We combined our empirical estimates of across-environment genetic variance-covariance matrices and frequency of selective environments with hypothetical (yet realistic) selection gradients to project evolutionary responses in multiple density environments. Selection in common environments can lead to correlated responses to selection in rare environments that oppose and counteract direct selection in those rare environments. Our results highlight the importance of considering both the frequency of selective environments and the across-environment genetic covariances in traits simultaneously.

Anderson JB, Funt J, Thompson DA, Prabhu S, Socha A, Sirjusingh C, Dettman JR, Parreiras L, Guttman DS, Regev A, Kohn LM

Curr. Biol. 2010 Aug;20(15):1383-8

PubMed PMID: 20637622

Abstract

Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here, whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations, six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt, two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose, one mutation occurred in MDS3, which modulates growth at high pH, and one in MKT1, a global regulator of mRNAs encoding mitochondrial proteins, the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong.

Morrow JM, Chang BS

Plasmid 2010 Nov;64(3):162-9

PubMed PMID: 20627111

Abstract

The heterologous expression of membrane proteins such as G protein-coupled receptors can be a notoriously difficult task. We have engineered an expression vector, p1D4-hrGFP II, in order to efficiently express visual pigments in mammalian cell culture. This expression vector is based on pIRES-hrGFP II (Stratagene), with the addition of a C-terminal 1D4 epitope tag for immunoblotting and immunoaffinity purification. This vector employs the CMV promoter and hrGFP II, a co-translated reporter gene. We measured the effectiveness of pIRES-hrGFP II in expressing bovine rhodopsin, and showed a 3.9- to 5.7-fold increase in expression as measured by absorbance spectroscopy as compared with the pMT vector, a common choice for visual pigment expression. We then expressed zebrafish RH2-1 using p1D4-hrGFP II in order to assess its utility in expressing cone opsins, known to be less stable and more difficult to express than bovine rhodopsin. We show a ?(280)/?(MAX) value of 3.3, one third of that reported in previous studies, suggesting increased expression levels and decreased levels of misfolded, non-functional visual pigment. Finally, we monitored HEK293T cell growth following transfection with pIRES-hrGFP II using fluorescence microscopy to illustrate the benefits of having a co-translated reporter during heterologous expression studies.

Migeon A, Blaudez D, Wilkins O, Montanini B, Campbell MM, Richaud P, Thomine S, Chalot M

Cell. Mol. Life Sci. 2010 Nov;67(22):3763-84

PubMed PMID: 20623158

Abstract

The specific transport of metal ions, mediated by membrane-localized metal transporters, is of fundamental importance in all eukaryotes. Genome-wide analysis of metal transporters was undertaken, making use of whole genome sequences of the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the lycophyte Selaginella moellendorffii, the monocots rice and sorghum, and the dicots Arabidopsis thaliana, poplar, grapevine, as well as of the yeast Saccharomyces cerevisiae. A repertoire of 430 metal transporters was found in total across eight photosynthetic plants, as well as in S. cerevisiae. Seventy-two full-length metal transporter genes were identified in the Populus genome alone, which is the largest number of metal transporters genes identified in any single species to date. Diversification of some transporter family gene clusters appears to have occurred in a lineage-specific manner. Expression analysis of Populus metal transporters indicates that some family members show tissue-specific transcript abundance. Taken together, the data provide a picture into the diversification of these important gene families.

Wilkins O, Bräutigam K, Campbell MM

Plant J. 2010 Sep;63(5):715-27

PubMed PMID: 20553421

Abstract

Under natural conditions, it is common for plants to experience water deprivation (drought) for periods of days or longer. Plants respond to drought stress by reconfiguring their transcriptome activity. Transcriptome changes in response to drought are dynamic, and are shaped by mitigating factors like time during the diurnal cycle. To date, analyses of drought-induced transcriptome remodelling have concentrated on dynamic changes induced by rapid desiccation, or changes at a single time point following gradual water stress. To gain insights into the dynamics of transcriptome reconfiguration in response to gradual drying of the soil, the drought-induced transcriptomes of Arabidopsis thaliana were examined at four time points over a single diel period – midday, late day, midnight, and pre-dawn. Transcriptome reconfigurations were induced by drought in advance of changes to relative water content, leaf water loss, and chlorophyll content. Comparative analyses support the hypothesis that the drought-responsive transcriptomes were shaped by invocation of distinct hormonal and stress response pathways at different times of the day. While a core set of genes were drought responsive at multiple time points throughout the day, the magnitude of the response varied in a manner dependent on the time of day. Moreover, analysis of a single time point would fail to identify suites of drought-responsive genes that can only be detected through assessment of the dynamics of diurnal changes, emphasising the value of characterising multiple time-of-day-specific drought transcriptomes.

Hamanishi ET, Raj S, Wilkins O, Thomas BR, Mansfield SD, Plant AL, Campbell MM

Plant Cell Environ. 2010 Oct;33(10):1742-55

PubMed PMID: 20525001

Abstract

Drought is a major limitation to the growth and productivity of trees in the ecologically and economically important genus Populus. The ability of Populus trees to contend with drought is a function of genome responsiveness to this environmental insult, involving reconfiguration of the transcriptome to appropriately remodel growth, development and metabolism. Here we test hypotheses aimed at examining the extent of intraspecific variation in the drought transcriptome using six different Populus balsamifera L. genotypes and Affymetrix GeneChip technology. Within a given genotype there was a positive correlation between the magnitude of water-deficit induced changes in transcript abundance across the transcriptome, and the capacity of that genotype to maintain growth following water deficit. Genotypes that had more similar drought-responsive transcriptomes also had fewer genotypic differences, as determined by microarray-derived single feature polymorphism (SFP) analysis, suggesting that responses may be conserved across individuals that share a greater degree of genotypic similarity. This work highlights the fact that a core species-level response can be defined; however, the underpinning genotype-derived complexities of the drought response in Populus must be taken into consideration when defining both species- and genus-level responses.

Cutter AD, Choi JY

Genome Res. 2010 Aug;20(8):1103-11

PubMed PMID: 20508143

Abstract

The combined actions of natural selection, mutation, and recombination forge the landscape of genetic variation across genomes. One frequently observed manifestation of these processes is a positive association between neutral genetic variation and local recombination rates. Two selective mechanisms and/or recombination-associated mutation (RAM) could generate this pattern, and the relative importance of these alternative possibilities remains unresolved generally. Here we quantify nucleotide differences within populations, between populations, and between species to test for genome-wide effects of selection and RAM in the partially selfing nematode Caenorhabditis briggsae. We find that nearly half of genome-wide variation in nucleotide polymorphism is explained by differences in local recombination rates. By quantifying divergence between several reproductively isolated lineages, we demonstrate that ancestral polymorphism generates a spurious signal of RAM for closely related lineages, with implications for analyses of humans and primates; RAM is, at most, a minor factor in C. briggsae. We conclude that the positive relation between nucleotide polymorphism and the rate of crossover represents the footprint of natural selection across the C. briggsae genome and demonstrate that background selection against deleterious mutations is sufficient to explain this pattern. Hill-Robertson interference also leaves a signature of more effective purifying selection in high-recombination regions of the genome. Finally, we identify an emerging contrast between widespread adaptive hitchhiking effects in species with large outcrossing populations (e.g., Drosophila) versus pervasive background selection effects on the genomes of organisms with self-fertilizing lifestyles and/or small population sizes (e.g., Caenorhabditis elegans, C. briggsae, Arabidopsis thaliana, Lycopersicon, human). These results illustrate how recombination, mutation, selection, and population history interact in important ways to shape molecular heterogeneity within and between genomes.

Wilton M, Desveaux D

Plant Signal Behav 2010 Jun;5(6):746-8

PubMed PMID: 20505348

Abstract

The Gram negative bacterial phytopathogen Pseudomonas syringae employs a molecular syringe termed the Type III secretion system (TTSS) to deliver an array of Type III secreted effector (TTSE) proteins into plant cells. The major function ascribed to type III effectors of P. syringae is their ability to suppress plant immunity. Because individual pathovars of P. syringae can possess over 30 TTSEs, functional redundancy can provide a hurdle to ascribing functions by TTSE-deletion or -overexpression in such TTSE-rich backgrounds. Approaches to overcome functional redundancy have included the deletion of multiple TTSEs from individual pathovars as well as engineering the plant commensal P. fluorescens strain to express the P. syringae TTSS and deliver P. syringae TTSEs. As we describe here, transgenic Arabidopsis plants expressing individual TTSEs have also be used to overcome problems of functional redundancy and provide invaluable insights into TTSE virulence functions.

Dang LT, Tropepe V

Neural Dev 2010;5:13

PubMed PMID: 20459606

Abstract

BACKGROUND: Mouse definitive neural stem cells (NSCs) are derived from a population of LIF-responsive primitive neural stem cells (pNSCs) within the neurectoderm, yet details on the early signaling and transcriptional mechanisms that control this lineage transition are lacking. Here we tested whether FGF and Wnt signaling pathways can regulate Zfhx1b expression to control early neural stem cell development.

RESULTS: By microinjecting FGF8b into the pro-amniotic cavity ex vivo at 7.0 days post-coitum (dpc) and culturing whole embryos, we demonstrate that neurectoderm-specific gene expression (for example, Sox2, Nestin, Zfhx1b) is increased, whereas Wnt3a represses neurectoderm gene expression. To determine whether FGF signaling also mediates the lineage transition from a pNSC to a NSC, 7.0-dpc embryos were microinjected with either FGF8b or inhibitors of the FGF receptor-MAP kinase signaling pathway ex vivo, cultured as whole embryos to approximately 8.5 dpc and assayed for clonal NSC colony formation. We show that pre-activation of FGF signaling in the anterior neurectoderm causes an increase in the number of colony forming NSCs derived later from the anterior neural plate, whereas inhibition of FGF signaling significantly reduces the number of NSC colonies. Interestingly, inhibition of FGF signaling causes the persistence of LIF-responsive pNSCs within the anterior neural plate and over-expression of Zfhx1b in these cells is sufficient to rescue the transition from a LIF-responsive pNSC to an FGF-responsive NSC.

CONCLUSION: Our data suggest that definitive NSC fate specification in the mouse neurectoderm is facilitated by FGF activation of Zfhx1b.

Cutter AD, Agrawal AF

Genetics 2010 Jun;185(2):685-93

PubMed PMID: 20382830

Abstract

Genes in nematode and ascidian genomes frequently occur in operons–multiple genes sharing a common promoter to generate a polycistronic primary transcript–and such genes comprise 15-20% of the coding genome for Caenorhabditis elegans and Ciona intestinalis. Recent work in nematodes has demonstrated that the identity of genes within operons is highly conserved among species and that the unifying feature of genes within operons is that they are expressed in germline tissue. However, it is generally unknown what processes are responsible for generating the distribution of operon sizes across the genome, which are composed of up to eight genes per operon. Here we investigate several models for operon evolution to better understand their abundance, distribution of sizes, and evolutionary dynamics over time. We find that birth-death models of operon evolution reasonably describe the relative abundance of operons of different sizes in the C. elegans and Ciona genomes and generate predictions about the number of monocistronic, nonoperon genes that likely participate in the birth-death process. This theory, and applications to C. elegans and Ciona, motivates several new and testable hypotheses about eukaryote operon evolution.