Honors & Awards
Pathway to Independence (K99/R00) Award, National Institutes of Health (2011-present)
Postdoctoral Fellowship, Damon Runyon Cancer Research Foundation (2008-2010)
Transition School/Early Entrance Program, University of Washington (1996-2001)
Ph.D., MIT, Biological Chemistry (2007)
B.S., University of Washington, Chemistry and Biochemistry (2001)
Current Research and Scholarly Interests
Survival in changing environments requires the acquisition of new heritable traits. However, mechanisms that safeguard the fidelity of DNA replication often limit the source of such novelty to relatively modest changes in the genetic code. Thus, the acquisition of new forms and functions is thought to be driven by rare variants that occur at random, and are enriched during times of stress. We have begun to study an intriguing alternative hypothesis: that intrinsic links between protein folding and virtually every biological trait provide multiple avenues through which environmental stress can directly elicit heritable variation that drives evolution, disease, and development.
Our aim is to identify and characterize these mechanisms at the molecular level, integrating our findings to gain insight into the interplay among genetic variation, phenotypic diversity, and environmental fluctuations in complex cellular systems. Much of our work centers on the specific influence of molecular chaperones, proteins that help other proteins fold. Other projects focus on the induction of epigenetic variation that can be passed from one generation to another via self-perpetuating changes in protein conformation. Our work employs multidisciplinary approaches including biochemistry, genome-scale analyses, high-throughput screening methodologies, live cell imaging, microfluidics, and quantitative genetic techniques. Ultimately we seek to not only to understand mechanisms that link environmental stress to the acquisition of biological novelty, but also to identify means of manipulating them for therapeutic benefit and harnessing their power to engineer synthetic signaling networks.
An Evolutionarily Conserved Prion-like Element Converts Wild Fungi from Metabolic Specialists to Generalists.
2014; 158 (5): 1072-1082
[GAR(+)] is a protein-based element of inheritance that allows yeast (Saccharomyces cerevisiae) to circumvent a hallmark of their biology: extreme metabolic specialization for glucose fermentation. When glucose is present, yeast will not use other carbon sources. [GAR(+)] allows cells to circumvent this "glucose repression." [GAR(+)] is induced in yeast by a factor secreted by bacteria inhabiting their environment. We report that de novo rates of [GAR(+)] appearance correlate with the yeast's ecological niche. Evolutionarily distant fungi possess similar epigenetic elements that are also induced by bacteria. As expected for a mechanism whose adaptive value originates from the selective pressures of life in biological communities, the ability of bacteria to induce [GAR(+)] and the ability of yeast to respond to bacterial signals have been extinguished repeatedly during the extended monoculture of domestication. Thus, [GAR(+)] is a broadly conserved adaptive strategy that links environmental and social cues to heritable changes in metabolism.
View details for DOI 10.1016/j.cell.2014.07.024
View details for PubMedID 25171408
Cross-kingdom chemical communication drives a heritable, mutually beneficial prion-based transformation of metabolism.
2014; 158 (5): 1083-1093
In experimental science, organisms are usually studied in isolation, but in the wild, they compete and cooperate in complex communities. We report a system for cross-kingdom communication by which bacteria heritably transform yeast metabolism. An ancient biological circuit blocks yeast from using other carbon sources in the presence of glucose. [GAR(+)], a protein-based epigenetic element, allows yeast to circumvent this "glucose repression" and use multiple carbon sources in the presence of glucose. Some bacteria secrete a chemical factor that induces [GAR(+)]. [GAR(+)] is advantageous to bacteria because yeast cells make less ethanol and is advantageous to yeast because their growth and long-term viability is improved in complex carbon sources. This cross-kingdom communication is broadly conserved, providing a compelling argument for its adaptive value. By heritably transforming growth and survival strategies in response to the selective pressures of life in a biological community, [GAR(+)] presents a unique example of Lamarckian inheritance.
View details for DOI 10.1016/j.cell.2014.07.025
View details for PubMedID 25171409
- Pernicious pathogens or expedient elements of inheritance: the significance of yeast prions. PLoS pathogens 2014; 10 (4)
Cryptic Variation in Morphological Evolution: HSP90 as a Capacitor for Loss of Eyes in Cavefish
2013; 342 (6164): 1372-1375
In the process of morphological evolution, the extent to which cryptic, preexisting variation provides a substrate for natural selection has been controversial. We provide evidence that heat shock protein 90 (HSP90) phenotypically masks standing eye-size variation in surface populations of the cavefish Astyanax mexicanus. This variation is exposed by HSP90 inhibition and can be selected for, ultimately yielding a reduced-eye phenotype even in the presence of full HSP90 activity. Raising surface fish under conditions found in caves taxes the HSP90 system, unmasking the same phenotypic variation as does direct inhibition of HSP90. These results suggest that cryptic variation played a role in the evolution of eye loss in cavefish and provide the first evidence for HSP90 as a capacitor for morphological evolution in a natural setting.
View details for DOI 10.1126/science.1240276
View details for Web of Science ID 000328196000051
View details for PubMedID 24337296
Prions are a common mechanism for phenotypic inheritance in wild yeasts
2012; 482 (7385): 363-U1507
The self-templating conformations of yeast prion proteins act as epigenetic elements of inheritance. Yeast prions might provide a mechanism for generating heritable phenotypic diversity that promotes survival in fluctuating environments and the evolution of new traits. However, this hypothesis is highly controversial. Prions that create new traits have not been found in wild strains, leading to the perception that they are rare 'diseases' of laboratory cultivation. Here we biochemically test approximately 700 wild strains of Saccharomyces for [PSI(+)] or [MOT3(+)], and find these prions in many. They conferred diverse phenotypes that were frequently beneficial under selective conditions. Simple meiotic re-assortment of the variation harboured within a strain readily fixed one such trait, making it robust and prion-independent. Finally, we genetically screened for unknown prion elements. Fully one-third of wild strains harboured them. These, too, created diverse, often beneficial phenotypes. Thus, prions broadly govern heritable traits in nature, in a manner that could profoundly expand adaptive opportunities.
View details for DOI 10.1038/nature10875
View details for Web of Science ID 000300287100038
View details for PubMedID 22337056
Hsp90 and Environmental Stress Transform the Adaptive Value of Natural Genetic Variation
2010; 330 (6012): 1820-1824
How can species remain unaltered for long periods yet also undergo rapid diversification? By linking genetic variation to phenotypic variation via environmental stress, the Hsp90 protein-folding reservoir might promote both stasis and change. However, the nature and adaptive value of Hsp90-contingent traits remain uncertain. In ecologically and genetically diverse yeasts, we find such traits to be both common and frequently adaptive. Most are based on preexisting variation, with causative polymorphisms occurring in coding and regulatory sequences alike. A common temperature stress alters phenotypes similarly. Both selective inhibition of Hsp90 and temperature stress increase correlations between genotype and phenotype. This system broadly determines the adaptive value of standing genetic variation and, in so doing, has influenced the evolution of current genomes.
View details for DOI 10.1126/science.1195487
View details for Web of Science ID 000285603700040
View details for PubMedID 21205668
Protein Homeostasis and the Phenotypic Manifestation of Genetic Diversity: Principles and Mechanisms
ANNUAL REVIEW OF GENETICS, VOL 44
2010; 44: 189-216
Changing a single nucleotide in a genome can have profound consequences under some conditions, but the same change can have no consequences under others. Indeed, organisms can be surprisingly robust to environmental and genetic perturbations. Yet, the mechanisms underlying such robustness are controversial. Moreover, how they might affect evolutionary change remains enigmatic. Here, we review the recently appreciated central role of protein homeostasis in buffering and potentiating genetic variation and discuss how these processes mediate the critical influence of the environment on the relationship between genotype and phenotype. Deciphering how robustness emerges from biological organization and the mechanisms by which it is overcome in changing environments will lead to a more complete understanding of both fundamental evolutionary processes and diverse human diseases.
View details for DOI 10.1146/annurev.genet.40.110405.090412
View details for Web of Science ID 000286042600009
View details for PubMedID 21047258
A single amino acid governs enhanced activity of DinB DNA polymerases on damaged templates
2006; 439 (7073): 225-228
Translesion synthesis (TLS) by Y-family DNA polymerases is a chief mechanism of DNA damage tolerance. Such TLS can be accurate or error-prone, as it is for bypass of a cyclobutane pyrimidine dimer by DNA polymerase eta (XP-V or Rad30) or bypass of a (6-4) TT photoproduct by DNA polymerase V (UmuD'2C), respectively. Although DinB is the only Y-family DNA polymerase conserved among all domains of life, the biological rationale for this striking conservation has remained enigmatic. Here we report that the Escherichia coli dinB gene is required for resistance to some DNA-damaging agents that form adducts at the N2-position of deoxyguanosine (dG). We show that DinB (DNA polymerase IV) catalyses accurate TLS over one such N2-dG adduct (N2-furfuryl-dG), and that DinB and its mammalian orthologue, DNA polymerase kappa, insert deoxycytidine (dC) opposite N2-furfuryl-dG with 10-15-fold greater catalytic proficiency than opposite undamaged dG. We also show that mutating a single amino acid, the 'steric gate' residue of DinB (Phe13 --> Val) and that of its archaeal homologue Dbh (Phe12 --> Ala), separates the abilities of these enzymes to perform TLS over N2-dG adducts from their abilities to replicate an undamaged template. We propose that DinB and its orthologues are specialized to catalyse relatively accurate TLS over some N2-dG adducts that are ubiquitous in nature, that lesion bypass occurs more efficiently than synthesis on undamaged DNA, and that this specificity may be achieved at least in part through a lesion-induced conformational change.
View details for DOI 10.1038/nature04318
View details for Web of Science ID 000234538400045
View details for PubMedID 16407906
- Rebels with a cause: molecular features and physiological consequences of yeast prions FEMS YEAST RESEARCH 2014; 14 (1): 136-147
HSP90 at the hub of protein homeostasis: emerging mechanistic insights
NATURE REVIEWS MOLECULAR CELL BIOLOGY
2010; 11 (7): 515-528
Heat shock protein 90 (HSP90) is a highly conserved molecular chaperone that facilitates the maturation of a wide range of proteins (known as clients). Clients are enriched in signal transducers, including kinases and transcription factors. Therefore, HSP90 regulates diverse cellular functions and exerts marked effects on normal biology, disease and evolutionary processes. Recent structural and functional analyses have provided new insights on the transcriptional and biochemical regulation of HSP90 and the structural dynamics it uses to act on a diverse client repertoire. Comprehensive understanding of how HSP90 functions promises not only to provide new avenues for therapeutic intervention, but to shed light on fundamental biological questions.
View details for DOI 10.1038/nrm2918
View details for Web of Science ID 000280076000016
View details for PubMedID 20531426
A DinB variant reveals diverse physiological consequences of incomplete TLS extension by a Y-family DNA polymerase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2009; 106 (50): 21137-21142
The only Y-family DNA polymerase conserved among all domains of life, DinB and its mammalian ortholog pol kappa, catalyzes proficient bypass of damaged DNA in translesion synthesis (TLS). Y-family DNA polymerases, including DinB, have been implicated in diverse biological phenomena ranging from adaptive mutagenesis in bacteria to several human cancers. Complete TLS requires dNTP insertion opposite a replication blocking lesion and subsequent extension with several dNTP additions. Here we report remarkably proficient TLS extension by DinB from Escherichia coli. We also describe a TLS DNA polymerase variant generated by mutation of an evolutionarily conserved tyrosine (Y79). This mutant DinB protein is capable of catalyzing dNTP insertion opposite a replication-blocking lesion, but cannot complete TLS, stalling three nucleotides after an N(2)-dG adduct. Strikingly, expression of this variant transforms a bacteriostatic DNA damaging agent into a bactericidal drug, resulting in profound toxicity even in a dinB(+) background. We find that this phenomenon is not exclusively due to a futile cycle of abortive TLS followed by exonucleolytic reversal. Rather, gene products with roles in cell death and metal homeostasis modulate the toxicity of DinB(Y79L) expression. Together, these results indicate that DinB is specialized to perform remarkably proficient insertion and extension on damaged DNA, and also expose unexpected connections between TLS and cell fate.
View details for DOI 10.1073/pnas.0907257106
View details for Web of Science ID 000272795300025
View details for PubMedID 19948952
- Song: SOS (To the Tune of ABBA's "SOS"). Biochemistry and molecular biology education 2009; 37 (5): 316-?
UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB
2007; 28 (6): 1058-1070
DinB is the only translesion Y family DNA polymerase conserved among bacteria, archaea, and eukaryotes. DinB and its orthologs possess a specialized lesion bypass function but also display potentially deleterious -1 frameshift mutagenic phenotypes when overproduced. We show that the DNA damage-inducible proteins UmuD(2) and RecA act in concert to modulate this mutagenic activity. Structural modeling suggests that the relatively open active site of DinB is enclosed by interaction with these proteins, thereby preventing the template bulging responsible for -1 frameshift mutagenesis. Intriguingly, residues that define the UmuD(2)-interacting surface on DinB statistically covary throughout evolution, suggesting a driving force for the maintenance of a regulatory protein-protein interaction at this site. Together, these observations indicate that proteins like RecA and UmuD(2) may be responsible for managing the mutagenic potential of DinB orthologs throughout evolution.
View details for DOI 10.1016/j.molcel.2007.10.025
View details for Web of Science ID 000252170000012
View details for PubMedID 18158902
DNA polymerase V allows bypass of toxic guanine oxidation products in vivo
JOURNAL OF BIOLOGICAL CHEMISTRY
2007; 282 (17): 12741-12748
Reactive oxygen and nitrogen radicals produced during metabolic processes, such as respiration and inflammation, combine with DNA to form many lesions primarily at guanine sites. Understanding the roles of the polymerases responsible for the processing of these products to mutations could illuminate molecular mechanisms that correlate oxidative stress with cancer. Using M13 viral genomes engineered to contain single DNA lesions and Escherichia coli strains with specific polymerase (pol) knockouts, we show that pol V is required for efficient bypass of structurally diverse, highly mutagenic guanine oxidation products in vivo. We also find that pol IV participates in the bypass of two spiroiminodihydantoin lesions. Furthermore, we report that one lesion, 5-guanidino-4-nitroimidazole, is a substrate for multiple SOS polymerases, whereby pol II is necessary for error-free replication and pol V for error-prone replication past this lesion. The results spotlight a major role for pol V and minor roles for pol II and pol IV in the mechanism of guanine oxidation mutagenesis.
View details for DOI 10.1074/jbc.M700575200
View details for Web of Science ID 000245942800044
View details for PubMedID 17322566
Proficient and accurate bypass of persistent DNA lesions by DinB DNA polymerases
2007; 6 (7): 817-822
Despite nearly universal conservation through evolution, the precise function of the DinB/pol kappa branch of the Y-family of DNA polymerases has remained unclear. Recent results suggest that DinB orthologs from all domains of life proficiently bypass replication blocking lesions that may be recalcitrant to DNA repair mechanisms. Like other translesion DNA polymerases, the error frequency of DinB and its orthologs is higher than the DNA polymerases that replicate the majority of the genome. However, recent results suggest that some Y-family polymerases, including DinB and pol kappa, bypass certain types of DNA damage with greater proficiency than an undamaged template. Moreover, they do so relatively accurately. The ability to employ this mechanism to manage DNA damage may be especially important for types of DNA modification that elude repair mechanisms. For these lesions, translesion synthesis may represent a more important line of defense than for other types of DNA damage that are more easily dealt with by other more accurate mechanisms.
View details for Web of Science ID 000245577800012
View details for PubMedID 17377496
Y-family DNA polymerases in Escherichia coli
TRENDS IN MICROBIOLOGY
2007; 15 (2): 70-77
The observation that mutations in the Escherichia coli genes umuC+ and umuD+ abolish mutagenesis induced by UV light strongly supported the counterintuitive notion that such mutagenesis is an active rather than passive process. Genetic and biochemical studies have revealed that umuC+ and its homolog dinB+ encode novel DNA polymerases with the ability to catalyze synthesis past DNA lesions that otherwise stall replication--a process termed translesion synthesis (TLS). Similar polymerases have been identified in nearly all organisms, constituting a new enzyme superfamily. Although typically viewed as unfaithful copiers of DNA, recent studies suggest that certain TLS polymerases can perform proficient and moderately accurate bypass of particular types of DNA damage. Moreover, various cellular factors can modulate their activity and mutagenic potential.
View details for DOI 10.1016/j.tim.2006.12.004
View details for Web of Science ID 000244535900004
View details for PubMedID 17207624
Y-family DNA polymerases respond to DNA damage-independent inhibition of replication fork progression
2006; 25 (4): 868-879
In Escherichia coli, the Y-family DNA polymerases Pol IV (DinB) and Pol V (UmuD2'C) enhance cell survival upon DNA damage by bypassing replication-blocking DNA lesions. We report a unique function for these polymerases when DNA replication fork progression is arrested not by exogenous DNA damage, but with hydroxyurea (HU), thereby inhibiting ribonucleotide reductase, and bringing about damage-independent DNA replication stalling. Remarkably, the umuC122::Tn5 allele of umuC, dinB, and certain forms of umuD gene products endow E. coli with the ability to withstand HU treatment (HUR). The catalytic activities of the UmuC122 and DinB proteins are both required for HUR. Moreover, the lethality brought about by such stalled replication forks in the wild-type derivatives appears to proceed through the toxin/antitoxin pairs mazEF and relBE. This novel function reveals a role for Y-family polymerases in enhancing cell survival under conditions of nucleotide starvation, in addition to their established functions in response to DNA damage.
View details for DOI 10.1038/sj.emboj.7600986
View details for Web of Science ID 000236225000020
View details for PubMedID 16482223
Characterization of Escherichia coli translesion synthesis polymerases and their accessory factors
DNA REPAIR, PT A
2006; 408: 318-340
Members of the Y family of DNA polymerases are specialized to replicate lesion-containing DNA. However, they lack 3'-5' exonuclease activity and have reduced fidelity compared to replicative polymerases when copying undamaged templates, and thus are potentially mutagenic. Y family polymerases must be tightly regulated to prevent aberrant mutations on undamaged DNA while permitting replication only under conditions of DNA damage. These polymerases provide a mechanism of DNA damage tolerance, confer cellular resistance to a variety of DNA-damaging agents, and have been implicated in bacterial persistence. The Y family polymerases are represented in all domains of life. Escherichia coli possesses two members of the Y family, DNA pol IV (DinB) and DNA pol V (UmuD'(2)C), and several regulatory factors, including those encoded by the umuD gene that influence the activity of UmuC. This chapter outlines procedures for in vivo and in vitro analysis of these proteins. Study of the E. coli Y family polymerases and their accessory factors is important for understanding the broad principles of DNA damage tolerance and mechanisms of mutagenesis throughout evolution. Furthermore, study of these enzymes and their role in stress-induced mutagenesis may also give insight into a variety of phenomena, including the growing problem of bacterial antibiotic resistance.
View details for DOI 10.1016/S0076-6879(06)08020-7
View details for Web of Science ID 000238224100020
View details for PubMedID 16793378