Sam O Purvine

Pacific Northwest National Laboratory | PNNL

Despite the promise of the gut microbiome to predict human health, few studies expose the molecular-scale processes underpinning such forecasts. We mined over 200,000 gut-derived genomes from cultivated and uncultivated microbial lineages to inventory the gut microorganisms and their gene content that control trimethylamine-induced cardiovascular d...

Energy status and nutrients regulate photosynthetic protein expression. The unicellular green alga Chromochloris zofingiensis switches off photosynthesis in the presence of exogenous glucose (+Glc) in a process that depends on hexokinase (HXK1). Here, we show that this response requires that cells lack sufficient iron (−Fe). Cells grown in −Fe+Glc...

Energy status and nutrients regulate photosynthetic protein expression. The unicellular green alga Chromochloris zofingiensis switches off photosynthesis in the presence of exogenous glucose (+Glc) in a process that depends on hexokinase (HXK1). Here, we show that this response requires that cells lack sufficient iron (−Fe). Cells grown in −Fe+Glc...

Marine algae are responsible for half of the world's primary productivity, but this critical carbon sink is often constrained by insufficient iron. One species of marine algae, Dunaliella tertiolecta, is remarkable for its ability to maintain photosynthesis and thrive in low-iron environments. A related species, Dunaliella salina Bardawil, shares t...

Growth of Chlamydomonas reinhardtii in zinc (Zn) limited medium leads to disruption of copper (Cu) homeostasis, resulting in up to 40-fold Cu over-accumulation relative to its typical Cu quota. We show that Chlamydomonas controls its Cu quota by balancing Cu import and export, which is disrupted in a Zn deficient cell, thus establishing a mechanist...

Marine algae are responsible for half of the world’s primary productivity, but this critical carbon sink is often constrained by insufficient iron. One species of marine algae, Dunaliella tertiolecta , is remarkable for its ability to maintain photosynthesis and thrive in low-iron environments. A related species, Dunaliella salina Bardawil, shares...

Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus matin...

Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despit...

Bacterial remineralization of algal organic matter is thought to fuel algal growth, but this has not been quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others, nor whether this is linked their incorporation. We quantified bacterial incorporation of algal-deri...

Despite the promise of the gut microbiome to forecast human health, few studies expose the microbial functions underpinning such predictions. To comprehensively inventory gut microorganisms and their gene content that control trimethylamine induced cardiovascular disease, we mined over 200,000 gut-derived genomes from cultivated and uncultivated mi...

Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus matin...

Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to global greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite t...

Background: Rivers serve as a nexus for nutrient transfer between terrestrial and marine ecosystems and as such, have a significant impact on global carbon and nitrogen cycles. In river ecosystems, the sediments found within the hyporheic zone are microbial hotspots that can account for a significant portion of ecosystem respiration and have profou...

Significance While peatlands have historically stored massive amounts of soil carbon, warming is expected to enhance decomposition, leading to a positive feedback with climate change. In this study, a unique whole-ecosystem warming experiment was conducted in northern Minnesota to warm peat profiles to 2 m deep while keeping water flow intact. Afte...

Plant organs and tissues contain multiple cell types, which are well organized in 3‐dimensional structure to efficiently perform physiological functions such as homeostasis and response to environmental perturbation and pathogen infection. It is critically important to perform molecular measurements at the cell‐type‐specific level to discover mecha...

Microorganisms play vital roles in modulating organic matter decomposition and nutrient cycling in soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered in anoxic peat leading to polyphenol accumulation, and consequently diminished microbial activity. This model assumes that polyphenols are microbially u...

Significance White-rot fungi play an essential role in global carbon cycling because of their extraordinary ability to extracellularly deconstruct lignin, a recalcitrant plant biopolymer. Despite this, the intracellular metabolism of lignin-deconstruction products by this fungal group has been largely overlooked, potentially due to a lack of geneti...

Significance Historically, it has been understood that for gene expression in eukaryotes, each messenger RNA encodes a single protein. With the recent development of technologies to sequence full-length transcripts en masse, we have discovered hundreds of examples in two species of green algae where two, three, or more proteins are translated from...

Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and manganese peroxidases in association with lignocellulose degradation, the mechanisms b...

Background: Crohn's disease (CD) is a chronic inflammatory intestinal disorder associated with intestinal dysbiosis. Diet modulates the intestinal microbiome and therefore has a therapeutic potential. The aim of this study is to determine the potential efficacy of three versions of the specific carbohydrate diet (SCD) in active Crohn's Disease. M...

In the last decade, extensive application of hydraulic fracturing technologies to unconventional low-permeability hydrocarbon-rich formations has significantly increased natural-gas production in the United States and abroad. The injection of surface-sourced fluids to generate fractures in the deep subsurface introduces microbial cells and substrat...

The hydraulic fracturing of deep-shale formations for hydrocarbon recovery accounts for approximately 60% of U.S. natural gas production. Microbial activity associated with this process is generally considered deleterious due to issues associated with sulfide production, microbially induced corrosion, and bioclogging in the subsurface. Here we demo...

The unicellular green alga Chlamydomonas reinhardtii displays metabolic flexibility in response to a changing environment. We analyzed expression patterns of its three genomes in cells grown under light–dark cycles. Nearly 85% of transcribed genes show differential expression, with different sets of transcripts being up-regulated over the course of...

Natural organic matter (NOM) is composed of a highly complex mixture of thousands of organic compounds which, historically, proved difficult to characterize. However, to understand the thermodynamic and kinetic controls on greenhouse gas (carbon dioxide [CO2] and methane [CH4]) production resulting from the decomposition of NOM, a molecular-level c...

Hurley et al. used new informatic tools and deep sampling to systematically investigate the proteomic and transcriptomic output of the circadian clock, uncovering broad post-transcriptional control of output, especially of metabolic pathways. The largest portion of circadian post-transcriptional regulation appears to be imparted at the level of tra...

The phylum Caldiserica was identified from the hot spring 16S rRNA gene lineage ‘OP5’ and named for the sole isolate Caldisericum exile, a hot spring sulfur-reducing chemoheterotroph. Here we characterize 7 Caldiserica metagenome-assembled genomes (MAGs) from a thawing permafrost site in Stordalen Mire, Arctic Sweden. By 16S rRNA and marker gene ph...

Metaproteomics conducted on soil is challenged by a low depth of protein coverage that can potentially result in an underrepresentation of the functional underpinnings of important biological processes and interactions. Typically, the utilization of an on-line two-dimensional chromatographic separation approach (2D LC-MS/MS) can significantly impro...

White‐rot fungi, such as Dichomitus squalens, degrade all wood components and inhabit mixed‐wood forests containing both soft‐ and hardwood species. In this study, we evaluated how D. squalens responded to the compositional differences in softwood (guaiacyl (G) lignin and higher mannan content) and hardwood (syringyl/guaiacyl (S/G) lignin and highe...

As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to reco...

Marine algae perform approximately half of global carbon fixation, but their growth is often limited by the availability of phosphate or other nutrients1,2. As oceans warm, the area of phosphate-limited surface waters is predicted to increase, resulting in ocean desertification3,4. Understanding the responses of key eukaryotic phytoplankton to nutr...

Significance Microorganisms persisting in hydraulically fractured shales must maintain osmotic balance in hypersaline fluids, gain energy in the absence of electron acceptors, and acquire carbon and nitrogen to synthesize cell building blocks. We provide evidence that that cofermentation of amino acids (Stickland reaction) meets all of these organi...

Ostreococcus tauri is an ancient phototrophic microalgae that possesses favorable genetic and cellular characteristics for reductionist studies probing biosystem design and dynamics. Here multimodal bioimaging and multi-omics techniques were combined to interrogate O. tauri cellular changes in response to variations in bioavailable nitrogen and car...

Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems-based approach, we examined dif...

Glutathione S-transferases (GSTs) comprise a diverse family of phase II drug metabolizing enzymes whose shared function is the conjugation of reduced glutathione (GSH) to endo- and xenobiotics. Although the conglomerate activity of these enzymes can be measured, the individual contribution from specific isoforms and their contribution to the metabo...

Although thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for t...

Fungi generate a wide range of extracellular hydrolytic and oxidative enzymes and reactive metabolites, collectively known as the secretome, that synergistically drive plant litter decomposition in the environment. While secretome studies of model organisms have greatly expanded our knowledge of these enzymes, few have extended secretome characteri...

Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica...

The yeast Yarrowia lipolytica is a potent accumulator of lipids, and lipogenesis in this organism can be influenced by a variety of factors, such as genetics and environmental conditions. Using a multifactorial study, we elucidated the effects of both genetic and environmental factors on regulation of lipogenesis in Y. lipolytica and identified how...

Current proteomic approaches are comprised of both broad discovery measurements and quantitative targeted analyses. In many cases, discovery measurements are initially used to identify potentially important proteins (e.g., candidate biomarkers) and then targeted studies are employed to quantify a limited number of selected proteins. Both approaches...

Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cel-lulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that syner-gistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatl...

Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote (<2 μm diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using tripl...

Full genome-based predicted secretome of A. alternata (1352 proteins). (XLSX)

Proteins unique to Pyrenochaeta sp. experimental secretome (381 proteins). (XLSX)

Full genome-based predicted secretome of P. sporulosum (1604 proteins). (XLSX)

Full genome-based predicted secretome of Pyrenochaeta sp. (1404 proteins). (XLSX)

Proteins unique to Stagonospora sp. experimental secretome (562 proteins). (XLSX)

Oxygenic Photosynthesis clusters. This table contains information regarding the clusters that were either enriched or contained genes from the Oxygenic Photosynthesis (OP) pathway, including gene name, as well as GO term and EC number annotations. Note, EC numbers were annotated using Pathway Tools, as described in the Materials and Methods section...

All proteins experimentally identified in secretomes of A. alternata, P. sporulosum, Pyrenochaeta sp., and Stagonospora sp. (XLSX)

Full genome-based predicted secretome of Stagonospora sp. (1527 proteins). (XLSX)

Proteins unique to A. alternata experimental secretome (412 proteins). (XLSX)

Proteins unique to P. sporulosum experimental secretome (578 proteins). (XLSX)

Supplementary Information. This file contains supplementary methods, as well as supplementary figures A-U, and tables A-J. (DOCX)

Progressive differential protein expression. This table contains a detailed list of differentially expressed genes, as determined by a progressive scan where protein expression from one time point was compared with data from the subsequent time point just prior to it, e.g. T2 compared with T3. In the case of T4, this was compared with the data from...

Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification. We gene...

Background Yarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen. While the enzymatic pathways responsible for neutral lipid accumulation in Y. lipolytica are well characterized, regulation of these pathways has received little attention. We therefore sought to characterize the response to ni...

Pandemic influenza viruses modulate proinflammatory responses that can lead to immunopathogenesis. We present an extensive and systematic profiling of lipids, metabolites, and proteins in respiratory compartments of ferrets infected with either 1918 or 2009 human pandemic H1N1 influenza viruses. Integrative analysis of high-throughput omics data wi...

Leaf-cutter ants are prolific and conspicuous constituents of Neotropical ecosystems that derive energy from specialized fungus gardens they cultivate using prodigious amounts of foliar biomass. The basidiomycetous cultivar of the ants, Leucoagaricus gongylophorus, produces specialized hyphal swellings called gongylidia that serve as the primary fo...

This Data Descriptor announces the submission to public repositories of the PNNL Biodiversity Library, a large collection of global proteomics data for 112 bacterial and archaeal organisms. The data comprises 35,162 tandem mass spectrometry (MS/MS) datasets from ~10 years of research. All data has been searched, annotated and organized in a consist...

Hypoxic areas are a common feature of rapidly growing malignant tumors and their metastases, and are typically spatially heterogeneous. Hypoxia has a strong impact on tumor cell biology and contributes to tumor progression in multiple ways. To date, only a few molecular key players in tumor hypoxia, such as for example hypoxia-inducible factor-1 (H...

Dermacentor andersoni, known as the Rocky Mountain wood tick, is found in the western United States and transmits pathogens that cause diseases of veterinary and public health importance including Rocky Mountain spotted fever, tularemia, Colorado tick fever and bovine anaplasmosis. Tick saliva is known to modulate both innate and acquired immune re...

Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity (1). In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic pla...

Protein stable isotope probing (protein-SIP) has strong potential for revealing key metabolizing taxa in complex microbial communities. While most protein-SIP work to date has been performed under controlled laboratory conditions to allow extensive isotope labeling of the target organism(s), a key application will be in situ studies of microbial co...

S-glutathionylation (SSG) is an important regulatory posttranslational modification on protein cysteine (Cys) thiols, yet the role of specific cysteine residues as targets of modification is poorly understood. We report a novel quantitative mass spectrometry (MS)-based proteomic method for site-specific identification and quantification of S-glutat...

Lignocellulosic biomass has great promise as a highly abundant and renewable source for the production of biofuels. However, the recalcitrant nature of lignocellulose toward hydrolysis into soluble sugars remains a significant challenge to harnessing the potential of this source of bioenergy. A primary method for deconstructing lignocellulose is vi...

Characterization of microbial protein expression provides information necessary to better understand the unique biological pathways that occur within soil microbial communities that contribute to atmospheric CO2 levels and the Earth's changing climate. A significant challenge in studying the soil microbial community proteome is the initial dissocia...

The potential for commensal microorganisms indigenous to a host (the 'microbiome' or 'microbiota') to alter infection outcome by influencing host-pathogen interplay is largely unknown. We used a multi-omics "systems" approach, incorporating proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular interplay between the murine...

Expression of fuc genes in vivo following Salmonella infection. qRT-PCR analysis revealed increased expression of genes in the fuc regulon of S. Typhimurium during infection. Data presented as fold change over expression in uninfected animals. (PDF)

Fucose and high mannose glycan detection in individual biological replicates. (A) Five fucosylated glycan moieties that were observed at each time point were selected for analysis. These fucosylated glycans increased during infection in both (B) experimental group 1 and (C) experimental group 2, in comparison to control animals. Data from infected...

All filter-passing protein identifications. (A) Mouse-derived, (B) microbiota-derived, and (C) Salmonella-derived protein identifications. (PDF)

Selected mouse proteins identified during infection. The immune response to gastrointestinal S. Typhimurium infection in humans is characterized by an inflammatory response and neutrophil activation. Proteomic results support a similar host response in 129/SvJ mice, which includes (but is not limited to) expression of neutrophil-related proteins, c...

16S rDNA analysis of the Salmonella and other non-Salmonella Proteobacterial genera through time. (A) Raw data shows the proliferation of Salmonella during infection and clearance by day 28. (B) Other Proteobacteria are present at very low levels (note axis scale in A and B), and do not significantly contribute to observed Proteobacteria increase i...

S. Typhimurium infection induces metabolite changes in the gut environment. GC-MS metabolite analysis of soluble factors in fecal samples revealed that (A,B) the profile of metabolites in infected animals (right panel, red) is distinct from that of control animals (left panel, black). Chromatograms presented here, with early time points in the fore...

Inability to utilize fucose demonstrates in vivo phenotype. WT and Δfuc strains were mixed at a 1∶1 ratio and used to orally infect 129/SvJ mice. Quantification of each strain in the shed feces demonstrated a slight growth advantage in vivo of the Δfuc strain. Two replicate experiments were performed, shown in (A) and (B). Each filled circle repres...

Proteins determined to be statistically significantly different in control and infected mice. (PDF)

Primer sequences used for 16s community profiling. Primer sequences are listed for each sample, including four experimental groups (control 1, control 2, infected 1, and infected 2), with eight time points per group (−1, 1, 3, 6, 10, 14, 21, and 18 days post-infection). (XLSX)

Salmonella infection disrupts the commensal microbial community at the genus level. Presentation of the top 10 most abundant genera (each representing greater than 0.5% of the total population as determined by 16s rDNA sequencing) reveals a pre-infection microbial population composed of primarily Barnesiella (green), with a small fraction of Blauti...

Plants represent a large reservoir of organic carbon comprised primarily of recalcitrant polymers that most metazoans are unable to deconstruct. Many herbivores gain access to nutrients in this material indirectly by associating with microbial symbionts, and leaf-cutter ants are a paradigmatic example. These ants use fresh foliar biomass as manure...

In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accur...

Computational prediction of protein function is frequently error-prone and incomplete. In Mycobacterium tuberculosis (Mtb), ∼25% of all genes have no predicted function and are annotated as hypothetical proteins, severely limiting our understanding of Mtb pathogenicity. Here, we utilize a high-throughput quantitative activity-based protein profilin...