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Cell & Developmental Biology

Discovery of a Natural Microsporidian Pathogen with a Broad Tissue Tropism in C. elegans. Luallen RJ, Reinke AW, Tong L, Botts MR, Félix MA, Troemel ER. PLoS Pathog. 2016 Jun 30;12(6):e1005724. doi: 10.1371/journal.ppat.1005724. eCollection 2016.

Abstract

Microbial pathogens often establish infection within particular niches of their host for replication. Determining how infection occurs preferentially in specific host tissues is a key aspect of understanding host-microbe interactions. Here, we describe the discovery of a natural microsporidian parasite of the nematode Caenorhabditis elegans that displays a unique tissue tropism compared to previously described parasites of this host. We characterize the life cycle of this new species, Nematocida displodere, including pathogen entry, intracellular replication, and exit. N. displodere can invade multiple host tissues, including the epidermis, muscle, neurons, and intestine of C. elegans. Despite robust invasion of the intestine very little replication occurs there, with the majority of replication occurring in the muscle and epidermis. This feature distinguishes N. displodere from two closely related microsporidian pathogens, N. parisii and N. sp. 1, which exclusively invade and replicate in the intestine. Comparison of the N. displodere genome with N. parisii and N. sp. 1 reveals that N. displodere is the earliest diverging species of the Nematocida genus. Over 10% of the proteins encoded by the N. displodere genome belong to a single species-specific family of RING-domain containing proteins of unknown function that may be mediating interactions with the host. Altogether, this system provides a powerful whole-animal model to investigate factors responsible for pathogen growth in different tissue niches.

Ecology, Behavior & Evolution

Biophysical mechanisms that maintain biodiversity through trade-offs. Justin R. Meyer, Ivana Gudelj, Robert Beardmore. Nature communications. 2015 Feb 19;6. doi:10.1038/ncomms7278

Abstract

Trade-offs are thought to arise from inevitable, biophysical limitations that prevent organisms from optimizing multiple traits simultaneously. A leading explanation for biodiversity maintenance is a theory that if the shape, or geometry, of a trade-off is right, then multiple species can coexist. Testing this theory, however, is difficult as trait data is usually too noisy to discern shape, or trade-offs necessary for the theory are not observed in vivo. To address this, we infer geometry directly from the biophysical mechanisms that cause trade-offs, deriving the geometry of two by studying nutrient uptake and metabolic properties common to all living cells. To test for their presence in vivo we isolated Escherichia coli mutants that vary in a nutrient transporter, LamB, and found evidence for both trade-offs. Consistent with data, population genetics models incorporating the trade-offs successfully predict the co-maintenance of three distinct genetic lineages, demonstrating that trade-off geometry can be deduced from fundamental principles of living cells and used to predict stable genetic polymorphisms.

Molecular Biology

Dynamic control of gene regulatory logic by seemingly redundant transcription factors. AkhavanAghdam Z, Sinha J, Tabbaa OP, Hao N. Elife. 2016 Sep 30;5. pii: e18458. doi: 10.7554/eLife.18458.PMID: 27690227.

Abstract

Many transcription factors co-express with their homologs to regulate identical target genes, however the advantages of such redundancies remain elusive. Using single-cell imaging and microfluidics, we study the yeast general stress response transcription factor Msn2 and its seemingly redundant homolog Msn4. We find that gene regulation by these two factors is analogous to logic gate systems. Target genes with fast activation kinetics can be fully induced by either factor, behaving as an 'OR' gate. In contrast, target genes with slow activation kinetics behave as an 'AND' gate, requiring distinct contributions from both factors, upon transient stimulation. Furthermore, such genes become an 'OR' gate when the input duration is prolonged, suggesting that the logic gate scheme is not static but rather dependent on the input dynamics. Therefore, Msn2 and Msn4 enable a time-based mode of combinatorial gene regulation that might be applicable to homologous transcription factors in other organisms.

Neurobiology

Hormonal Modulation of Pheromone Detection Enhances Male Courtship Success Lin HH, Cao DS, Sethi S, Zeng Z, Chin JS, Chakraborty TS, Shepherd AK, Nguyen CA, Yew JY, Su CY, Wang JW. Neuron. 2016 Jun 15;90(6):1272-85. doi: 10.1016/j.neuron.2016.05.004.

Abstract

During the lifespans of most animals, reproductive maturity and mating activity are highly coordinated. In Drosophila melanogaster, for instance, male fertility increases with age, and older males are known to have a copulation advantage over young ones. The molecular and neural basis of this age-related disparity in mating behavior is unknown. Here, we show that the Or47b odorant receptor is required for the copulation advantage of older males. Notably, the sensitivity of Or47b neurons to a stimulatory pheromone, palmitoleic acid, is low in young males but high in older ones, which accounts for older males' higher courtship intensity. Mechanistically, this age-related sensitization of Or47b neurons requires a reproductive hormone, juvenile hormone, as well as its binding protein Methoprene-tolerant in Or47b neurons. Together, our study identifies a direct neural substrate for juvenile hormone that permits coordination of courtship activity with reproductive maturity to maximize male reproductive fitness. Copyright © 2016 Elsevier Inc. All rights reserved.

Cell & Developmental Biology

Discovery of a Natural Microsporidian Pathogen with a Broad Tissue Tropism in C. elegans. Luallen RJ, Reinke AW, Tong L, Botts MR, Félix MA, Troemel ER. PLoS Pathog. 2016 Jun 30;12(6):e1005724. doi: 10.1371/journal.ppat.1005724. eCollection 2016.

Abstract

Microbial pathogens often establish infection within particular niches of their host for replication. Determining how infection occurs preferentially in specific host tissues is a key aspect of understanding host-microbe interactions. Here, we describe the discovery of a natural microsporidian parasite of the nematode Caenorhabditis elegans that displays a unique tissue tropism compared to previously described parasites of this host. We characterize the life cycle of this new species, Nematocida displodere, including pathogen entry, intracellular replication, and exit. N. displodere can invade multiple host tissues, including the epidermis, muscle, neurons, and intestine of C. elegans. Despite robust invasion of the intestine very little replication occurs there, with the majority of replication occurring in the muscle and epidermis. This feature distinguishes N. displodere from two closely related microsporidian pathogens, N. parisii and N. sp. 1, which exclusively invade and replicate in the intestine. Comparison of the N. displodere genome with N. parisii and N. sp. 1 reveals that N. displodere is the earliest diverging species of the Nematocida genus. Over 10% of the proteins encoded by the N. displodere genome belong to a single species-specific family of RING-domain containing proteins of unknown function that may be mediating interactions with the host. Altogether, this system provides a powerful whole-animal model to investigate factors responsible for pathogen growth in different tissue niches.

The dawn of active genetics Gantz VM, Bier E. Bioessays. 2015 Dec 10. doi: 10.1002/bies.201500102.

Abstract

On December 18, 2014, a yellow female fly quietly emerged from her pupal case. What made her unique was that she had only one parent carrying a mutant allele of this classic recessive locus. Then, one generation later, after mating with a wild-type male, all her offspring displayed the same recessive yellow phenotype. Further analysis of other such yellow females revealed that the construct causing the mutation was converting the opposing chromosome with 95% efficiency. These simple results, seen also in mosquitoes and yeast, open the door to a new era of genetics wherein the laws of traditional Mendelian inheritance can be bypassed for a broad variety of purposes. Here, we consider the implications of this fundamentally new form of "active genetics," its applications for gene drives, reversal and amplification strategies, its potential for contributing to cell and gene therapy strategies, and ethical/biosafety considerations associated with such active genetic elements. Also watch the Video Abstract.

Video Abstract

Gonadal Mosaicism Induced by Chemical Treatment of Sperm in Drosophila melanogaster Lindsley DL, Hardy R, Ripoll P, Lindsley D. genetics.115.178046; Early online July 9, 2015, doi:10.1534/genetics.115.178046

Abstract

Accurate interpretation of forward genetic screens of chromosomes exposed in mature spermatozoa to a mutagenic chemical requires understanding-incomplete to date-of how exposed chromosomes and their replicas proceed through early development stages from the fertilized ovum to establishment of the germ line of the treated male's offspring. We describe a model for early embryonic development and establishment of the germ line of Drosophila melanogaster and a model-validating experiment. Our model proposes that, barring repair, DNA strands modified by treatment with alkylating agents are stable and mutagenic. Each replication of an alkylated strand can result in misreplication and a mutant-bearing daughter nucleus. Daughter nuclei thenceforth replicate faithfully and their descendants comprise the embryonic syncytium. Of the 256 nuclei present after the eighth division, several migrate into the polar plasm at the posterior end of the embryo to found the germ line. Based upon distribution of descendants of the alkylated strands, the misreplication rate, and the number of nuclei selected as germline progenitors, the frequency of gonadal mosaicism is predictable. Experimentally, we tracked chromosomes 2 and 3 from EMS-treated sperm through a number of generations, to characterize autosomal recessive lethal mutations and infer gonadal genetic content of the sons of treated males. Over 50% of 106 sons bore germ lines that were singly, doubly, or triply mosaic for chromosome 2 or chromosome 3. These findings were consistent with our model, assuming a rate of misreplication between .65 and .80 at each replication of an alkylated strand. Crossing treated males to mismatch-repair-deficient females had no apparent effect on mutation rate.

Anent the Genomics of Spermatogenesis in Drosophila melanogaster Lindsley DL, Roote J, Kennison JA. PLoS One. 2013;8(2):e55915. doi: 10.1371/journal.pone.0055915. Epub 2013 Feb 7.

Abstract

An appreciable fraction of the Drosophila melanogaster genome is dedicated to male fertility. One approach to characterizing this subset of the genome is through the study of male-sterile mutations. We studied the relation between vital and male-fertility genes in three large autosomal regions that were saturated for lethal and male-sterile mutations. The majority of male-sterile mutations affect genes that are exclusively expressed in males. These genes are required only for male fertility, and several mutant alleles of each such gene were encountered. A few male-sterile mutations were alleles of vital genes that are expressed in both males and females. About one-fifth of the genes in Drosophila melanogaster show male-specific expression in adults. Although some earlier studies found a paucity of genes on the X chromosome showing male-biased expression, we did not find any significant differences between the X chromosome and the autosomes either in the relative frequencies of mutations to male sterility or in the frequencies of genes with male-specific expression in adults. Our results suggest that as much as 25% of the Drosophila genome may be dedicated to male fertility.

Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth. Cuomo CA, Desjardins CA, Bakowski MA, Goldberg J, Ma AT, Becnel JJ, Didier ES, Fan L, Heiman DI, Levin JZ, Young S, Zeng Q, Troemel ER. Genome Res. 2012 Dec;22(12):2478-88. doi: 10.1101/gr.142802.112. Epub 2012 Jul 18.

Abstract

Microsporidia comprise a large phylum of obligate intracellular eukaryotes that are fungal-related parasites responsible for widespread disease, and here we address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed deep sequencing of transcripts from a time course of N. parisii infection. Examination of pathogen gene expression revealed compact transcripts and a dramatic takeover of host cells by Nematocida. We also performed phylogenomic analyses of Nematocida and other microsporidian genomes to refine microsporidian phylogeny and identify evolutionary events of gene loss, acquisition, and modification. In particular, we found that all microsporidia lost the tumor-suppressor gene retinoblastoma, which we speculate could accelerate the parasite cell cycle and increase the mutation rate. We also found that microsporidia acquired transporters that could import nucleosides to fuel rapid growth. In addition, microsporidian hexokinases gained secretion signal sequences, and in a functional assay these were sufficient to export proteins out of the cell; thus hexokinase may be targeted into the host cell to reprogram it toward biosynthesis. Similar molecular changes appear during formation of cancer cells and may be evolutionary strategies adopted independently by microsporidia to proliferate rapidly within host cells. Finally, analysis of genome polymorphisms revealed evidence for a sexual cycle that may provide genetic diversity to alleviate problems caused by clonal growth. Together these events may explain the emergence and success of these diverse intracellular parasites.

The biochemical mechanism of auxin biosynthesis by an Arabidopsis YUCCA flavin-containing monooxygenase. Dai X, Mashiguchi K, Chen Q, Kasahara H, Kamiya Y, Ojha S, Dubois J, Ballou D, Zhao Y. J Biol Chem. 2013 Jan 18;288(3):1448-57. doi: 10.1074/jbc.M112.424077. Epub 2012 Nov 27.

Abstract

Auxin regulates every aspect of plant growth and development. Previous genetic studies demonstrated that YUCCA (YUC) flavin-containing monooxygenases (FMOs) catalyze a rate-limiting step in auxin biosynthesis and that YUCs are essential for many developmental processes. We proposed that YUCs convert indole-3-pyruvate (IPA) to indole-3-acetate (IAA). However, the exact biochemical mechanism of YUCs has remained elusive. Here we present the biochemical characterization of recombinant Arabidopsis YUC6. Expressed in and purified from E. coli, YUC6 contains FAD as a cofactor, which has peaks at 448 nm and 376 nm in the UV-Visible spectrum. We show that YUC6 uses NADPH and oxygen to convert IPA to IAA. The first step of the YUC6-catalyzed reaction is the reduction of the FAD cofactor to FADH by NADPH. Subsequently, FADH reacts with oxygen to form a flavin-C4a-(hydro)peroxy intermediate3, which we show has a maximum absorbance at 381 nm in its UV-Visible spectrum. The final chemical step is the reaction of the C4a-intermediate with IPA to produce IAA. Although the sequences of the YUC enzymes are related to those of the mammalian FMOs, which oxygenate nucleophilic substrates, YUC6 oxygenates an electrophilic substrate (IPA). Nevertheless, both classes of enzymes form quasi-stable C4a-(hydro)peroxyl FAD intermediates. The YUC6 intermediate has a half-life of ~20 s whereas that of some FMOs is more than 30 min. This work reveals the catalytic mechanism of the first known plant flavin monooxygenase and provides a foundation for further investigating how YUC activities are regulated in plants.

Identification of novel filament-forming proteins in Saccharomyces cerevisiae and Drosophila melanogaster. Noree C, Sato BK, Broyer RM, Wilhelm JE. J Cell Biol. 2010 Aug 23;190(4):541-51. doi: 10.1083/jcb.201003001. Epub 2010 Aug 16.

Abstract

The discovery of large supramolecular complexes such as the purinosome suggests that subcellular organization is central to enzyme regulation. A screen of the yeast GFP strain collection to identify proteins that assemble into visible structures identified four novel filament systems comprised of glutamate synthase, guanosine diphosphate-mannose pyrophosphorylase, cytidine triphosphate (CTP) synthase, or subunits of the eIF2/2B translation factor complex. Recruitment of CTP synthase to filaments and foci can be modulated by mutations and regulatory ligands that alter enzyme activity, arguing that the assembly of these structures is related to control of CTP synthase activity. CTP synthase filaments are evolutionarily conserved and are restricted to axons in neurons. This spatial regulation suggests that these filaments have additional functions separate from the regulation of enzyme activity. The identification of four novel filaments greatly expands the number of known intracellular filament networks and has broad implications for our understanding of how cells organize biochemical activities in the cytoplasm.

Drosophila Mtm and class II PI3K coregulate a PI(3)P pool with cortical and endolysosomal functions. Michaella Velichkova, Joe Juan, Pavan Kadandale, Steve Jean, Inês Ribeiro, Vignesh Raman, Chris Stefan, and Amy A. Kiger. J Cell Biol. 2010 Aug 9;190(3):407-25. doi: 10.1083/jcb.200911020.

Abstract

Reversible phosphoinositide phosphorylation provides a dynamic membrane code that balances opposing cell functions. However, in vivo regulatory relationships between specific kinases, phosphatases, and phosphoinositide subpools are not clear. We identified myotubularin (mtm), a Drosophila melanogaster MTM1/ MTMR2 phosphoinositide phosphatase, as necessary and sufficient for immune cell protrusion formation and recruitment to wounds. Mtm-mediated turnover of endosomal phosphatidylinositol 3-phosphate (PI(3)P) pools generated by both class II and III phosphatidylinositol 3-kinases (Pi3K68D and Vps34, respectively) is needed to down-regulate membrane influx, promote efflux, and maintain endolysosomal homeostasis. Endocytosis, but not endolysosomal size, contributes to cortical remodeling by mtm function. We propose that Mtm-dependent regulation of an endosomal PI(3)P pool has separable consequences for endolysosomal homeostasis and cortical remodeling. Pi3K68D depletion (but not Vps34) rescues protrusion and distribution defects in mtm-deficient immune cells and restores functions in other tissues essential for viability. The broad interactions between mtm and class II Pi3K68D suggest a novel strategy for rebalancing PI(3)P-mediated cell functions in MTM-related human disease.

Cryptochrome mediates circadian regulation of cAMP signaling and hepatic gluconeogenesis. Nat Med. 2010 Oct;16(10):1152-6. Epub 2010 Sep 19. Zhang EE, Liu Y, Dentin R, Pongsawakul PY, Liu AC, Hirota T, Nusinow DA, Sun X, Landais S, Kodama Y, Brenner DA, Montminy M, Kay SA.

Abstract

During fasting, mammals maintain normal glucose homeostasis by stimulating hepatic gluconeogenesis. Elevations in circulating glucagon and epinephrine, two hormones that activate hepatic gluconeogenesis, trigger the cAMP-mediated phosphorylation of cAMP response element-binding protein (Creb) and dephosphorylation of the Creb-regulated transcription coactivator-2 (Crtc2)-two key transcriptional regulators of this process. Although the underlying mechanism is unclear, hepatic gluconeogenesis is also regulated by the circadian clock, which coordinates glucose metabolism with changes in the external environment. Circadian control of gene expression is achieved by two transcriptional activators, Clock and Bmal1, which stimulate cryptochrome (Cry1 and Cry2) and Period (Per1, Per2 and Per3) repressors that feed back on Clock-Bmal1 activity. Here we show that Creb activity during fasting is modulated by Cry1 and Cry2, which are rhythmically expressed in the liver. Cry1 expression was elevated during the night-day transition, when it reduced fasting gluconeogenic gene expression by blocking glucagon-mediated increases in intracellular cAMP concentrations and in the protein kinase A-mediated phosphorylation of Creb. In biochemical reconstitution studies, we found that Cry1 inhibited accumulation of cAMP in response to G protein-coupled receptor (GPCR) activation but not to forskolin, a direct activator of adenyl cyclase. Cry proteins seemed to modulate GPCR activity directly through interaction with G(s)α. As hepatic overexpression of Cry1 lowered blood glucose concentrations and improved insulin sensitivity in insulin-resistant db/db mice, our results suggest that compounds that enhance cryptochrome activity may provide therapeutic benefit to individuals with type 2 diabetes.

PMID: 20852621

Ecology, Behavior & Evolution

Biophysical mechanisms that maintain biodiversity through trade-offs. Justin R. Meyer, Ivana Gudelj, Robert Beardmore. Nature communications. 2015 Feb 19;6. doi:10.1038/ncomms7278

Abstract

Trade-offs are thought to arise from inevitable, biophysical limitations that prevent organisms from optimizing multiple traits simultaneously. A leading explanation for biodiversity maintenance is a theory that if the shape, or geometry, of a trade-off is right, then multiple species can coexist. Testing this theory, however, is difficult as trait data is usually too noisy to discern shape, or trade-offs necessary for the theory are not observed in vivo. To address this, we infer geometry directly from the biophysical mechanisms that cause trade-offs, deriving the geometry of two by studying nutrient uptake and metabolic properties common to all living cells. To test for their presence in vivo we isolated Escherichia coli mutants that vary in a nutrient transporter, LamB, and found evidence for both trade-offs. Consistent with data, population genetics models incorporating the trade-offs successfully predict the co-maintenance of three distinct genetic lineages, demonstrating that trade-off geometry can be deduced from fundamental principles of living cells and used to predict stable genetic polymorphisms.

Warming experiments underpredict plant phenological responses to climate change. Wolkovich EM, Cook BI, Allen JM, Crimmins TM, Betancourt JL, Travers SE, Pau S, Regetz J, Davies TJ, Kraft NJ, Ault TR, Bolmgren K, Mazer SJ, McCabe GJ,McGill BJ, Parmesan C, Salamin N, Schwartz MD, Cleland EE.  2012 May 2;485(7399):494-7. doi: 10.1038/nature11014.

Abstract

Warming experiments are increasingly relied on to estimate plant responses to global climate change. For experiments to provide meaningful predictions of future responses, they should reflect the empirical record of responses to temperature variability and recent warming, including advances in the timing of flowering and leafing. We compared phenology (the timing of recurring life history events) in observational studies and warming experiments spanning four continents and 1,634 plant species using a common measure of temperature sensitivity (change in days per degree Celsius). We show that warming experiments underpredict advances in the timing of flowering and leafing by 8.5-fold and 4.0-fold, respectively, compared with long-term observations. For species that were common to both study types, the experimental results did not match the observational data in sign or magnitude. The observational data also showed that species that flower earliest in the spring have the highest temperature sensitivities, but this trend was not reflected in the experimental data. These significant mismatches seem to be unrelated to the study length or to the degree of manipulated warming in experiments. The discrepancy between experiments and observations, however, could arise from complex interactions among multiple drivers in the observational data, or it could arise from remediable artefacts in the experiments that result in lower irradiance and drier soils, thus dampening the phenological responses to manipulated warming. Our results introduce uncertainty into ecosystem models that are informed solely by experiments and suggest that responses to climate change that are predicted using such models should be re-evaluated.

Species selection maintains self-incompatibility. Goldberg EE, Kohn JR, Lande R, Robertson KA, Smith SA, Igić B. Science. 2010 Oct 22;330(6003):493-5.

Abstract

Identifying traits that affect rates of speciation and extinction and, hence, explain differences in species diversity among clades is a major goal of evolutionary biology. Detecting such traits is especially difficult when they undergo frequent transitions between states. Self-incompatibility, the ability of hermaphrodites to enforce outcrossing, is frequently lost in flowering plants, enabling self-fertilization. We show, however, that in the nightshade plant family (Solanaceae), species with functional self-incompatibility diversify at a significantly higher rate than those without it. The apparent short-term advantages of potentially self-fertilizing individuals are therefore offset by strong species selection, which favors obligate outcrossing.

PMID: 20966249 [PubMed - indexed for MEDLINE]

Multiple mechanisms underlie displacement of solitary Hawaiian Hymenoptera by an invasive social wasp. Wilson EE, Holway DA. Ecology. 2010 Nov;91(11):3294-302.

Abstract

Variation in invasion success may result from the divergent evolutionary histories of introduced species compared to those of native taxa. The vulnerability of native biotas to ecological disruption may be especially great on oceanic islands invaded by continental species with unique ecological traits. In part because Hawaii lacks native eusocial insects, social invaders may threaten endemic taxa that are ecologically similar but solitary. Using a combination of field manipulations, molecular analyses, physiological data, and behavioral assays, we identify the mechanisms underlying the displacement of two genera of native solitary Hymenoptera in Hawaii by a social continental invader, the western yellowjacket (Vespula pensylvanica). Experimental removal of V. pensylvanica colonies resulted in increased densities of native Hymenoptera. Endemic Hylaeus bees directly suffer through predation by yellowjackets, and perhaps as a consequence, avoid floral resources occupied by V. pensylvanica. Native Nesodynerus wasps also avoid V. pensylvanica but are negatively affected by yellowjackets not through predation, but through exploitative competition for caterpillar prey. Displacement of native solitary Hymenoptera may be heightened by the ability of V. pensylvanica to prey upon and scavenge honey bees and to rob their honey stores, resources unavailable to endemic bees and wasps because of their specialized niches. Our study provides a unique example of an ecologically generalized social invader that restructures native assemblages of solitary Hymenoptera by interacting with endemic taxa on multiple trophic levels.

PMID: 21141190 [PubMed - indexed for MEDLINE]

A Model for Damage Load and Its Implications for the Evolution of Bacterial Aging. PLoS Genet. 2010 Aug 26;6(8). pii: e1001076.
Chao L

Abstract

Deleterious mutations appearing in a population increase in frequency until stopped by natural selection. The ensuing equilibrium creates a stable frequency of deleterious mutations or the mutational load. Here I develop the comparable concept of a damage load, which is caused by harmful non-heritable changes to the phenotype. A damage load also ensues when the increase of damage is opposed by selection. The presence of a damage load favors the evolution of asymmetrical transmission of damage by a mother to her daughters. The asymmetry is beneficial because it increases fitness variance, but it also leads to aging or senescence. A mathematical model based on microbes reveals that a cell lineage dividing symmetrically is immortal if lifetime damage rates do not exceed a threshold. The evolution of asymmetry allows the lineage to persist above the threshold, but the lineage becomes mortal. In microbes with low genomic mutation rates, it is likely that the damage load is much greater than the mutational load. In metazoans with higher genomic mutation rates, the damage and the mutational load could be of the same magnitude. A fit of the model to experimental data shows that Escherichia coli cells experience a damage rate that is below the threshold and are immortal under the conditions examined. The model estimates the asymmetry level of E. coli to be low but sufficient for persisting at higher damage rates. The model also predicts that increasing asymmetry results in diminishing fitness returns, which may explain why the bacterium has not evolved higher asymmetry.

PMID: 20865171

Molecular Biology

Dynamic control of gene regulatory logic by seemingly redundant transcription factors. AkhavanAghdam Z, Sinha J, Tabbaa OP, Hao N. Elife. 2016 Sep 30;5. pii: e18458. doi: 10.7554/eLife.18458.PMID: 27690227.

Abstract

Many transcription factors co-express with their homologs to regulate identical target genes, however the advantages of such redundancies remain elusive. Using single-cell imaging and microfluidics, we study the yeast general stress response transcription factor Msn2 and its seemingly redundant homolog Msn4. We find that gene regulation by these two factors is analogous to logic gate systems. Target genes with fast activation kinetics can be fully induced by either factor, behaving as an 'OR' gate. In contrast, target genes with slow activation kinetics behave as an 'AND' gate, requiring distinct contributions from both factors, upon transient stimulation. Furthermore, such genes become an 'OR' gate when the input duration is prolonged, suggesting that the logic gate scheme is not static but rather dependent on the input dynamics. Therefore, Msn2 and Msn4 enable a time-based mode of combinatorial gene regulation that might be applicable to homologous transcription factors in other organisms.

Microbial pathogens often establish infection within particular niches of their host for replication. Determining how infection occurs preferentially in specific host tissues is a key aspect of understanding host-microbe interactions. Here, we describe the discovery of a natural microsporidian parasite of the nematode Caenorhabditis elegans that displays a unique tissue tropism compared to previously described parasites of this host. We characterize the life cycle of this new species, Nematocida displodere, including pathogen entry, intracellular replication, and exit. N. displodere can invade multiple host tissues, including the epidermis, muscle, neurons, and intestine of C. elegans. Despite robust invasion of the intestine very little replication occurs there, with the majority of replication occurring in the muscle and epidermis. This feature distinguishes N. displodere from two closely related microsporidian pathogens, N. parisii and N. sp. 1, which exclusively invade and replicate in the intestine. Comparison of the N. displodere genome with N. parisii and N. sp. 1 reveals that N. displodere is the earliest diverging species of the Nematocida genus. Over 10% of the proteins encoded by the N. displodere genome belong to a single species-specific family of RING-domain containing proteins of unknown function that may be mediating interactions with the host. Altogether, this system provides a powerful whole-animal model to investigate factors responsible for pathogen growth in different tissue niches.

New insights into the pathways by which normal immune cells may lead to lymphoma. Miyazaki M, Miyazaki K, Chen S, Chandra V, Wagatsuma K, Agata Y, Rodewald HR, Saito R, Chang AN, Varki N, Kawamoto H, Murre C. GGenes Dev. 2015 Feb 15;29(4):409-25. doi: 10.1101/gad.255331.114.

Abstract

Lymphomas are relatively common forms of cancer that develop in cells of the immune system. In this study, Cornelis Murre and colleagues identify a previously unsuspected population of immune cells. These cells are missing some of the standard features that define normal immune cells. In experiments performed in mice, it was found that loss of these features leads to the development of a malignancy very similar to human Burkitt lymphoma. This type of lymphoma, named after the scientist who first identified it in populations in Africa in the 1950s, is of particular interest because it is now known to also affect children and patients with weakened immune systems, including organ transplant patients whose immune systems must be actively suppressed to prevent rejection. The progress made in this study is important because it gives new insight into the pathways by which normal immune cells develop and mature and how, when disrupted, may lead to lymphoma.

TRF2 and the evolution of the bilateria. Duttke SH1, Doolittle RF2, Wang YL1, Kadonaga JT3. Genes Dev. 2014 Oct 1;28(19):2071-6. doi: 10.1101/gad.250563.114.

Abstract

The development of a complex body plan requires a diversity of regulatory networks. Here we consider the concept of TATA-box-binding protein (TBP) family proteins as "system factors" that each supports a distinct set of transcriptional programs. For instance, TBP activates TATA-box-dependent core promoters, whereas TBP-related factor 2 (TRF2) activates TATA-less core promoters that are dependent on a TCT or downstream core promoter element (DPE) motif. These findings led us to investigate the evolution of TRF2. TBP occurs in Archaea and eukaryotes, but TRF2 evolved prior to the emergence of the bilateria and subsequent to the evolutionary split between bilaterians and nonbilaterian animals. Unlike TBP, TRF2 does not bind to the TATA box and could thus function as a new system factor that is largely independent of TBP. We postulate that this TRF2-based system served as the foundation for new transcriptional programs, such as those involved in triploblasty and body plan development, that facilitated the evolution of bilateria.

3D trajectories adopted by coding and regulatory DNA elements: first-passage times for genomic interactions. Lucas JS, Zhang Y, Dudko OK, Murre C. Cell. 2014 Jul 17;158(2):339-52. doi: 10.1016/j.cell.2014.05.036. Epub 2014 Jul 3.

Abstract

During B lymphocyte development, immunoglobulin heavy-chain variable (VH), diversity (DH), and joining (JH) segments assemble to generate a diverse antigen receptor repertoire. Here, we have marked the distal VH and DH-JH-Eμ regions with Tet-operator binding sites and traced their 3D trajectories in pro-B cells transduced with a retrovirus encoding Tet-repressor-EGFP. We found that these elements displayed fractional Langevin motion (fLm) due to the viscoelastic hindrance from the surrounding network of proteins and chromatin fibers. Using fractional Langevin dynamics modeling, we found that, with high probability, DHJH elements reach a VH element within minutes. Spatial confinement emerged as the dominant parameter that determined the frequency of such encounters. We propose that the viscoelastic nature of the nuclear environment causes coding elements and regulatory elements to bounce back and forth in a spring-like fashion until specific genomic interactions are established and that spatial confinement of topological domains largely controls first-passage times for genomic interactions.

Translational coregulation of 5'TOP mRNAs by TIA-1 and TIAR. Damgaard CK, Lykke-Andersen J. Genes Dev. 2011 Oct 1;25(19):2057-68. doi: 10.1101/gad.17355911.

Abstract

The response of cells to changes in their environment often requires coregulation of gene networks, but little is known about how this can occur at the post-transcriptional level. An important example of post-transcriptional coregulation is the selective translational regulation in response to growth conditions of mammalian mRNAs that encode protein biosynthesis factors and contain hallmark 5'-terminal oligopyrimidine tracts (5'TOP). However, the responsible trans-factors and the mechanism by which they coregulate 5'TOP mRNAs have remained elusive. Here we identify stress granule-associated TIA-1 and TIAR proteins as key factors in human 5'TOP mRNA regulation, which upon amino acid starvation assemble onto the 5' end of 5'TOP mRNAs and arrest translation at the initiation step, as evidenced by TIA-1/TIAR-dependent 5'TOP mRNA translation repression, polysome release, and accumulation in stress granules. This requires starvation-mediated activation of the GCN2 (general control nonderepressible 2) kinase and inactivation of the mTOR (mammalian target of rapamycin) signaling pathway. Our findings provide a mechanistic explanation to the long-standing question of how the network of 5'TOP mRNAs are coregulated according to amino acid availability, thereby allowing redirection of limited resources to mount a nutrient deprivation response. This presents a fundamental example of how a group of mRNAs can be translationally coregulated in response to changes in the cellular environment.

A phage tubulin assembles dynamic filaments by an atypical mechanism to center viral DNA within the host cell. Kraemer JA, Erb ML, Waddling CA, Montabana EA, Zehr EA, Wang H, Nguyen K, Pham DS, Agard DA, Pogliano J. Cell. 2012 Jun 22;149(7):1488-99. doi: 10.1016/j.cell.2012.04.034.

Abstract

Tubulins are essential for the reproduction of many eukaryotic viruses, but historically, bacteriophage were assumed not to require a cytoskeleton. Here, we identify a tubulin-like protein, PhuZ, from bacteriophage 201φ2-1 and show that it forms filaments in vivo and in vitro. The PhuZ structure has a conserved tubulin fold, with an unusual, extended C terminus that we demonstrate to be critical for polymerization in vitro and in vivo. Longitudinal packing in the crystal lattice mimics packing observed by EM of in-vitro-formed filaments, indicating how interactions between the C terminus and the following monomer drive polymerization. PhuZ forms a filamentous array that is required for positioning phage DNA within the bacterial cell. Correct positioning to the cell center and optimal phage reproduction only occur when the PhuZ filament is dynamic. Thus, we show that PhuZ assembles a spindle-like array that functions analogously to the microtubule-based spindles of eukaryotes.

Auto-regulation of miRNA biogenesis by let-7 and Argonaute. Zisoulis DG, Kai ZS, Chang RK, Pasquinelli AE. 2012 Jun 28;486(7404):541-4. doi: 10.1038/nature11134.

Abstract

MicroRNAs (miRNAs) comprise a large family of small RNA molecules that post-transcriptionally regulate gene expression in many biological pathways. Most miRNAs are derived from long primary transcripts that undergo processing by Drosha to produce ~65-nucleotide precursors that are then cleaved by Dicer, resulting in the mature 22-nucleotide forms. Serving as guides in Argonaute protein complexes, mature miRNAs use imperfect base pairing to recognize sequences in messenger RNA transcripts, leading to translational repression and destabilization of the target messenger RNAs. Here we show that the miRNA complex also targets and regulates non-coding RNAs that serve as substrates for the miRNA-processing pathway. We found that the Argonaute protein in Caenorhabditis elegans, ALG-1, binds to a specific site at the 3′ end of let-7 miRNA primary transcripts and promotes downstream processing events. This interaction is mediated by mature let-7 miRNA through a conserved complementary site in its own primary transcript, thus creating a positive-feedback loop. We further show that ALG-1 associates with let-7 primary transcripts in nuclear fractions. Argonaute also binds let-7 primary transcripts in human cells, demonstrating that the miRNA pathway targets non-coding RNAs in addition to protein-coding messenger RNAs across species. Moreover, our studies in C. elegans reveal a novel role for Argonaute in promoting biogenesis of a targeted transcript, expanding the functions of the miRNA pathway in gene regulation. This discovery of autoregulation of let-7 biogenesis establishes a new mechanism for controlling miRNA expression.

Late Interlukin-6 escalates T follicular helper cell responses and controls chronic viral infection. Harker JA, Lewis GM, Mack L, Zuniga EI. Science. 2011 Nov 11;334(6057):825-9. doi: 10.1126/science.1208421. Epub 2011 Sep 29.

Abstract

Multiple inhibitory molecules create a profoundly immunuosuppressive environment during chronic viral infections in humans and mice. Therefore, eliciting effective immunity in this context represents a challenge. Here, we report that during a murine chronic viral infection, interleukin-6 (IL-6) was produced by irradiation-resistant cells in a biphasic manner, with late IL-6 being absolutely essential for viral control. The underlying mechanism involved IL-6 signaling on virus-specific CD4 T cells that caused up-regulation of the transcription factor Bcl6 and enhanced T follicular helper cell responses at late, but not early, stages of chronic viral infection. This resulted in escalation of germinal center reactions and improved antibody responses. Our results uncover an antiviral strategy that helps to safely resolve a persistent infection in vivo.

The roots of bioinformatics in protein evolution. Doolittle RF. Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, United States of America. rdoolittle@ucsd.edu

PLoS Comput Biol. 2010 Jul 29;6(7):e1000875. PMID: 20686682

Neurobiology

Hormonal Modulation of Pheromone Detection Enhances Male Courtship Success Lin HH, Cao DS, Sethi S, Zeng Z, Chin JS, Chakraborty TS, Shepherd AK, Nguyen CA, Yew JY, Su CY, Wang JW. Neuron. 2016 Jun 15;90(6):1272-85. doi: 10.1016/j.neuron.2016.05.004.

Abstract

During the lifespans of most animals, reproductive maturity and mating activity are highly coordinated. In Drosophila melanogaster, for instance, male fertility increases with age, and older males are known to have a copulation advantage over young ones. The molecular and neural basis of this age-related disparity in mating behavior is unknown. Here, we show that the Or47b odorant receptor is required for the copulation advantage of older males. Notably, the sensitivity of Or47b neurons to a stimulatory pheromone, palmitoleic acid, is low in young males but high in older ones, which accounts for older males' higher courtship intensity. Mechanistically, this age-related sensitization of Or47b neurons requires a reproductive hormone, juvenile hormone, as well as its binding protein Methoprene-tolerant in Or47b neurons. Together, our study identifies a direct neural substrate for juvenile hormone that permits coordination of courtship activity with reproductive maturity to maximize male reproductive fitness. Copyright © 2016 Elsevier Inc. All rights reserved.

Ryk controls remapping of motor cortex during functional recovery after spinal cord injury. Edmund R. Hollis, II, Nao Ishiko, Ting Yu, Chin-Chun Lu, Ariela Haimovich, Kristine Tolentino, Alisha Richman, Anna Tury, Shih-Hsiu Wang, Maysam Pessian, Euna Jo, Alex Kolodkin, Yimin Zou. Nature Neurosci. 2016 May;19(5):697-705.

Abstract

Limited functional recovery can be achieved with rehabilitation after incomplete spinal cord injury. Eliminating the function of a repulsive Wnt receptor, Ryk, by either conditional knockout in the motor cortex or monoclonal antibody infusion, resulted in increased corticospinal axon collateral branches with pre-synaptic puncta in the spinal cord and enhanced recovery of forelimb reaching and grasping function following a cervical dorsal column lesion. Using optical stimulation, we observed that motor cortical output maps underwent massive changes after injury and the hindlimb cortical areas were recruited to control the forelimb over time. Furthermore, a greater cortical area was dedicated to control the forelimb in Ryk cKO. In the absence of weekly task-specific training, recruitment of ectopic cortical areas was greatly reduced without significant functional recovery even in Ryk cKO. Our study provides evidence that maximal circuit reorganization and functional recovery can be achieved by combining molecular manipulation and task-specific training.

Hierarchy of orofacial rhythms revealed through whisking and breathing. Moore JD, Deschênes M, Furuta T, Huber D, Smear MC, Demers M, Kleinfeld D. Nature. 2013 May 9;497(7448):205-10. doi: 10.1038/nature12076. Epub 2013 Apr 28.

Abstract

Whisking and sniffing are predominant aspects of exploratory behaviour in rodents. Yet the neural mechanisms that generate and coordinate these and other orofacial motor patterns remain largely uncharacterized. Here we use anatomical, behavioural, electrophysiological and pharmacological tools to show that whisking and sniffing are coordinated by respiratory centres in the ventral medulla. We delineate a distinct region in the ventral medulla that provides rhythmic input to the facial motor neurons that drive protraction of the vibrissae. Neuronal output from this region is reset at each inspiration by direct input from the pre-Bötzinger complex, such that high-frequency sniffing has a one-to-one relationship with whisking, whereas basal respiration is accompanied by intervening whisks that occur between breaths. We conjecture that the respiratory nuclei, which project to other premotor regions for oral and facial control, function as a master clock for behaviours that coordinate with breathing.

Dynamic sensory representations in the olfactory bulb: modulation by wakefulness and experience. Kato HK, Chu MW, Isaacson JS, Komiyama T. 2012 Dec 6;76(5):962-75. doi: 10.1016/j.neuron.2012.09.037.

Abstract

How are sensory representations in the brain influenced by the state of an animal? Here we use chronic two-photon calcium imaging to explore how wakefulness and experience shape odor representations in the mouse olfactory bulb. Comparing the awake and anesthetized state, we show that wakefulness greatly enhances the activity of inhibitory granule cells and makes principal mitral cell odor responses more sparse and temporally dynamic. In awake mice, brief repeated odor experience leads to a gradual and long-lasting (months) weakening of mitral cell odor representations. This mitral cell plasticity is odor specific, recovers gradually over months, and can be repeated with different odors. Furthermore, the expression of this experience-dependent plasticity is prevented by anesthesia. Together, our results demonstrate the dynamic nature of mitral cell odor representations in awake animals, which is constantly shaped by recent odor experience.

Copyright © 2012 Elsevier Inc. All rights reserved.

Regulation of DLK-1 Kinase Activity by Calcium-Mediated Dissociation from an Inhibitory Isoform. Yan D, Jin Y. Neuron. 2012 Nov 8;76(3):534-48. doi: 10.1016/j.neuron.2012.08.043.

Abstract

MAPKKK dual leucine zipper-bearing kinases (DLKs) are regulators of synaptic development and axon regeneration. The mechanisms underlying their activation are not fully understood. Here, we show that C. elegans DLK-1 is activated by a Ca(2+)-dependent switch from inactive heteromeric to active homomeric protein complexes. We identify a DLK-1 isoform, DLK-1S, that shares identical kinase and leucine zipper domains with the previously described long isoform DLK-1L but acts to inhibit DLK-1 function by binding to DLK-1L. The switch between homo- or heteromeric DLK-1 complexes is influenced by Ca(2+) concentration. A conserved hexapeptide in the DLK-1L C terminus is essential for DLK-1 activity and is required for Ca(2+) regulation. The mammalian DLK-1 homolog MAP3K13 contains an identical C-terminal hexapeptide and can functionally complement dlk-1 mutants, suggesting that the DLK activation mechanism is conserved. The DLK activation mechanism is ideally suited for rapid and spatially controlled signal transduction in response to axonal injury and synaptic activity.

Copyright © 2012 Elsevier Inc. All rights reserved.

Piezo proteins are pore-forming subunits of mechanically activated channels. . Coste B, Xiao B, Santos JS, Syeda R, Grandl J, Spencer KS, Kim SE, Schmidt M, Mathur J, Dubin AE, Montal M, Patapoutian A., Nature. 2012 Feb 19;483(7388):176-81.

Abstract

Mechanotransduction has an important role in physiology. Biological processes including sensing touch and sound waves require as-yet-unidentified cation channels that detect pressure. Mouse Piezo1 (MmPiezo1) and MmPiezo2 (also called Fam38a and Fam38b, respectively) inducemechanically activated cationic currents in cells; however, it is unknown whether Piezo proteins are pore-forming ion channels or modulate ionchannels. Here we show that Drosophila melanogaster Piezo (DmPiezo, also called CG8486) also induces mechanically activated currents in cells, but through channels with remarkably distinct pore properties including sensitivity to the pore blocker ruthenium red and single channel conductances. MmPiezo1 assembles as a ∼1.2-million-dalton homo-oligomer, with no evidence of other proteins in this complex. Purified MmPiezo1 reconstituted into asymmetric lipid bilayers and liposomes forms ruthenium-red-sensitive ion channels. These data demonstrate that Piezo proteinsare an evolutionarily conserved ion channel family involved in mechanotransduction.

PMID: 22343900

The spatial periodicity of grid cells is not sustained during reduced theta oscillations. Koenig J, Linder AN, Leutgeb JK, Leutgeb S. Science, 332:592-595.

Abstract

Grid cells in parahippocampal cortices fire at vertices of a periodic triangular grid that spans the entire recording environment. Such precise neural computations in space have been proposed to emerge from equally precise temporal oscillations within cells or within the local neural circuitry. We found that grid-like firing patterns in the entorhinal cortex vanished when theta oscillations were reduced after intraseptal lidocaine infusions in rats. Other spatially modulated cells in the same cortical region and place cells in the hippocampus retained their spatial firing patterns to a larger extent during these periods without well-organized oscillatory neuronal activity. Precisely timed neural activity within single cells or local networks is thus required for periodic spatial firing but not for single place fields.

PMID: 21458672 [PubMed - in process]

Presynaptic facilitation by neuropeptide signaling mediates odor-driven food search. Root CM, Ko KI, Jafari A, Wang JW. Cell. 2011 Apr 1;145(1):133-44.

Abstract

Internal physiological states influence behavioral decisions. We have investigated the underlying cellular and molecular mechanisms at the first olfactory synapse for starvation modulation of food-search behavior in Drosophila. We found that a local signal by short neuropeptide F (sNPF) and a global metabolic cue by insulin are integrated at specific odorant receptor neurons (ORNs) to modulate olfactory sensitivity. Results from two-photon calcium imaging show that starvation increases presynaptic activity via intraglomerular sNPF signaling. Expression of sNPF and its receptor (sNPFR1) in Or42b neurons is necessary for starvation-induced food-search behavior. Presynaptic facilitation in Or42b neurons is sufficient to mimic starvation-like behavior in fed flies. Furthermore, starvation elevates the transcription level of sNPFR1 but not that of sNPF, and insulin signaling suppresses sNPFR1 expression. Thus, starvation increases expression of sNPFR1 to change the odor map, resulting in more robust food-search behavior.

PMID: 21458672 [PubMed - in process]

Lateral competition for cortical space by layer-specific horizontal circuits. Adesnik H, Scanziani M. Nature. 2010 Apr 22;464(7292):1155-60.

Abstract

The cerebral cortex constructs a coherent representation of the world by integrating distinct features of the sensory environment. Although these features are processed vertically across cortical layers, horizontal projections interconnecting neighbouring cortical domains allow these features to be processed in a context-dependent manner. Despite the wealth of physiological and psychophysical studies addressing the function of horizontal projections, how they coordinate activity among cortical domains remains poorly understood. We addressed this question by selectively activating horizontal projection neurons in mouse somatosensory cortex, and determined how the resulting spatial pattern of excitation and inhibition affects cortical activity. We found that horizontal projections suppress superficial layers while simultaneously activating deeper cortical output layers. This layer-specific modulation does not result from a spatial separation of excitation and inhibition, but from a layer-specific ratio between these two opposing conductances. Through this mechanism, cortical domains exploit horizontal projections to compete for cortical space.

PMID: 20414303