Publications by authors named "Stephanie G Hays"

10 Publications

  • Page 1 of 1

Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts.

Science 2021 07;373(6554)

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

Bacteriophage predation selects for diverse antiphage systems that frequently cluster on mobilizable defense islands in bacterial genomes. However, molecular insight into the reciprocal dynamics of phage-bacterial adaptations in nature is lacking, particularly in clinical contexts where there is need to inform phage therapy efforts and to understand how phages drive pathogen evolution. Using time-shift experiments, we uncovered fluctuations in 's resistance to phages in clinical samples. We mapped phage resistance determinants to SXT integrative and conjugative elements (ICEs), which notoriously also confer antibiotic resistance. We found that SXT ICEs, which are widespread in γ-proteobacteria, invariably encode phage defense systems localized to a single hotspot of genetic exchange. We identified mechanisms that allow phage to counter SXT-mediated defense in clinical samples, and document the selection of a novel phage-encoded defense inhibitor. Phage infection stimulates high-frequency SXT ICE conjugation, leading to the concurrent dissemination of phage and antibiotic resistances.
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http://dx.doi.org/10.1126/science.abg2166DOI Listing
July 2021

Bacteriophage ICP1: A Persistent Predator of .

Annu Rev Virol 2021 Jul 27. Epub 2021 Jul 27.

Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA; email:

Bacteriophages or phages-viruses of bacteria-are abundant and considered to be highly diverse. Interestingly, a particular group of lytic -specific phages (vibriophages) of the International Centre for Diarrheal Disease Research, Bangladesh cholera phage 1 (ICP1) lineage show high levels of genome conservation over large spans of time and geography, despite a constant coevolutionary arms race with their host. From a collection of 67 sequenced ICP1 isolates, mostly from clinical samples, we find these phages have mosaic genomes consisting of large, conserved modules disrupted by variable sequences that likely evolve mostly through mobile endonuclease-mediated recombination during coinfection. Several variable regions have been associated with adaptations against antiphage elements in ; notably, this includes ICP1's CRISPR-Cas system. The ongoing association of ICP1 and in cholera-endemic regions makes this system a rich source for discovery of novel defense and counterdefense strategies in bacteria-phage conflicts in nature. Expected final online publication date for the , Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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http://dx.doi.org/10.1146/annurev-virology-091919-072020DOI Listing
July 2021

Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus.

PLoS One 2021 26;16(5):e0251296. Epub 2021 May 26.

University of California, Berkeley, California, United States of America.

Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to SARS-CoV-2 outbreak prevention on college and university campuses. Here we describe the voluntary saliva testing program instituted at the University of California, Berkeley during an early period of the SARS-CoV-2 pandemic in 2020. The program was administered as a research study ahead of clinical implementation, enabling us to launch surveillance testing while continuing to optimize the assay. Results of both the testing protocol itself and the study participants' experience show how the program succeeded in providing routine, robust testing capable of contributing to outbreak prevention within a campus community and offer strategies for encouraging participation and a sense of civic responsibility.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0251296PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8153421PMC
June 2021

Dominant phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite.

Elife 2020 04 24;9. Epub 2020 Apr 24.

Department of Plant and Microbial Biology, University of California, Berkeley, United States.

Bacteria, bacteriophages that prey upon them, and mobile genetic elements (MGEs) compete in dynamic environments, evolving strategies to sense the milieu. The first discovered environmental sensing by phages, lysis inhibition, has only been characterized and studied in the limited context of T-even coliphages. Here, we discover lysis inhibition in the etiological agent of the diarrheal disease cholera, infected by ICP1, a phage ubiquitous in clinical samples. This work identifies the ICP1-encoded holin, and antiholin, that mediate lysis inhibition. Further, we show that an MGE, the defensive phage satellite PLE, collapses lysis inhibition. Through ysis nhibition isruption a conserved PLE protein, LidI, is sufficient to limit the phage produced from infection, bottlenecking ICP1. These studies link a novel incarnation of the classic lysis inhibition phenomenon with conserved defensive function of a phage satellite in a disease context, highlighting the importance of lysis timing during infection and parasitization.
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http://dx.doi.org/10.7554/eLife.53200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182436PMC
April 2020

Viral Satellites Exploit Phage Proteins to Escape Degradation of the Bacterial Host Chromosome.

Cell Host Microbe 2019 10;26(4):504-514.e4

Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address:

Phage defense systems are often found on mobile genetic elements (MGEs), where they constitutively defend against invaders or are induced to respond to new assaults. Phage satellites, one type of MGE, are induced during phage infection to promote their own transmission, reducing phage production and protecting their hosts in the process. One such satellite in Vibrio cholerae, phage-inducible chromosomal island-like element (PLE), sabotages the lytic phage ICP1, which triggers PLE excision from the bacterial chromosome, replication, and transduction to neighboring cells. Analysis of patient stool samples from different geographic regions revealed that ICP1 has evolved to possess one of two syntenic loci encoding an SF1B-type helicase, either of which PLE exploits to drive replication. Further, loss of PLE mobilization limits anti-phage activity because of phage-mediated degradation of the bacterial genome. Our work provides insight into the unique challenges facing parasites of lytic phages and underscores the adaptions of satellites to their ever-evolving target phage.
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http://dx.doi.org/10.1016/j.chom.2019.09.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6910227PMC
October 2019

Mimicking lichens: incorporation of yeast strains together with sucrose-secreting cyanobacteria improves survival, growth, ROS removal, and lipid production in a stable mutualistic co-culture production platform.

Biotechnol Biofuels 2017 21;10:55. Epub 2017 Mar 21.

Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218 USA.

Background: The feasibility of heterotrophic-phototrophic symbioses was tested via pairing of yeast strains , , or with a sucrose-secreting cyanobacterium .

Results: The phototroph showed no growth in standard BG-11 medium with yeast extract, but grew well in BG-11 medium alone or supplemented with yeast nitrogen base without amino acids (YNB w/o aa). Among three yeast species, and adapted well to the BG-11 medium supplemented with YNB w/o aa, sucrose, and various concentrations of NaCl needed to maintain sucrose secretion from , while growth of was highly dependent on sucrose levels. and grew efficiently and utilized sucrose produced by the partner in co-culture. Co-cultures of and were sustained over 1 month in both batch and in semi-continuous culture, with the final biomass and overall lipid yields in the batch co-culture 40 to 60% higher compared to batch mono-cultures of The co-cultures showed enhanced levels of palmitoleic and linoleic acids. Furthermore, cyanobacterial growth in co-culture with was significantly superior to axenic growth, as was unable to grow in the absence of the yeast partner when cultivated at lower densities in liquid medium. Accumulated reactive oxygen species was observed to severely inhibit axenic growth of cyanobacteria, which was efficiently alleviated through catalase supply and even more effectively with co-cultures of .

Conclusions: The pairing of a cyanobacterium and eukaryotic heterotroph in the artificial lichen of this study demonstrates the importance of mutual interactions between phototrophs and heterotrophs, e.g., phototrophs provide a carbon source to heterotrophs, and heterotrophs assist phototrophic growth and survival by removing/eliminating oxidative stress. Our results establish a potential stable production platform that combines the metabolic capability of photoautotrophs to capture inorganic carbon with the channeling of the resulting organic carbon directly to a robust heterotroph partner for producing biofuel and other chemical precursors.
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http://dx.doi.org/10.1186/s13068-017-0736-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5360037PMC
March 2017

Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction.

J Biol Eng 2017 23;11. Epub 2017 Jan 23.

MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI USA.

Background: Microbial consortia composed of autotrophic and heterotrophic species abound in nature, yet examples of synthetic communities with mixed metabolism are limited in the laboratory. We previously engineered a model cyanobacterium, PCC 7942, to secrete the bulk of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes. Here, we tested the capability of sucrose-secreting cyanobacteria to act as a flexible platform for the construction of synthetic, light-driven consortia by pairing them with three disparate heterotrophs: , or . The comparison of these different co-culture dyads reveals general design principles for the construction of robust autotroph/heterotroph consortia.

Results: We observed heterotrophic growth dependent upon cyanobacterial photosynthate in each co-culture pair. Furthermore, these synthetic consortia could be stabilized over the long-term (weeks to months) and both species could persist when challenged with specific perturbations. Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph sucrose utilization, as well as other species-independent interactions that we observed across all dyads. One destabilizing interaction we observed was that non-sucrose byproducts of oxygenic photosynthesis negatively impacted heterotroph growth. Conversely, inoculation of each heterotrophic species enhanced cyanobacterial growth in comparison to axenic cultures. Finally, these consortia can be flexibly programmed for photoproduction of target compounds and proteins; by changing the heterotroph in co-culture to specialized strains of or we demonstrate production of alpha-amylase and polyhydroxybutyrate respectively.

Conclusions: Enabled by the unprecedented flexibility of this consortia design, we uncover species-independent design principles that influence cyanobacteria/heterotroph consortia robustness. The modular nature of these communities and their unusual robustness exhibits promise as a platform for highly-versatile photoproduction strategies that capitalize on multi-species interactions and could be utilized as a tool for the study of nascent symbioses. Further consortia improvements via engineered interventions beyond those we show here (i.e., increased efficiency growing on sucrose) could improve these communities as production platforms.
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http://dx.doi.org/10.1186/s13036-017-0048-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259876PMC
January 2017

Building Spatial Synthetic Biology with Compartments, Scaffolds, and Communities.

Cold Spring Harb Perspect Biol 2016 08 1;8(8). Epub 2016 Aug 1.

Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115.

Traditional views of synthetic biology often treat the cell as an unstructured container in which biological reactions proceed uniformly. In reality, the organization of biological molecules has profound effects on cellular function: not only metabolic, but also physical and mechanical. Here, we discuss a variety of perturbations available to biologists in controlling protein, nucleotide, and membrane localization. These range from simple tags, fusions, and scaffolds to heterologous expression of compartments and other structures that confer unique physical properties to cells. Next, we relate these principles to those guiding the spatial environments outside of cells such as the extracellular matrix. Finally, we discuss new directions in building intercellular organizations to create novel symbioses.
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http://dx.doi.org/10.1101/cshperspect.a024018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968161PMC
August 2016

Better together: engineering and application of microbial symbioses.

Curr Opin Biotechnol 2015 Dec 28;36:40-9. Epub 2015 Aug 28.

Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, WAB 563, Boston, MA 02115, USA. Electronic address:

Symbioses provide a way to surpass the limitations of individual microbes. Natural communities exemplify this in symbioses like lichens and biofilms that are robust to perturbations, an essential feature in fluctuating environments. Metabolic capabilities also expand in consortia enabling the division of labor across organisms as seen in photosynthetic and methanogenic communities. In engineered consortia, the external environment provides levers of control for microbes repurposed from nature or engineered to interact through synthetic biology. Consortia have successfully been applied to real-world problems including remediation and energy, however there are still fundamental questions to be answered. It is clear that continued study is necessary for the understanding and engineering of microbial systems that are more than the sum of their parts.
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http://dx.doi.org/10.1016/j.copbio.2015.08.008DOI Listing
December 2015

Engineering cyanobacteria as photosynthetic feedstock factories.

Photosynth Res 2015 Mar 14;123(3):285-95. Epub 2014 Feb 14.

Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.

Carbohydrate feedstocks are at the root of bioindustrial production and are needed in greater quantities than ever due to increased prioritization of renewable fuels with reduced carbon footprints. Cyanobacteria possess a number of features that make them well suited as an alternative feedstock crop in comparison to traditional terrestrial plant species. Recent advances in genetic engineering, as well as promising preliminary investigations of cyanobacteria in a number of distinct production regimes have illustrated the potential of these aquatic phototrophs as biosynthetic chassis. Further improvements in strain productivities and design, along with enhanced understanding of photosynthetic metabolism in cyanobacteria may pave the way to translate cyanobacterial theoretical potential into realized application.
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http://dx.doi.org/10.1007/s11120-014-9980-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5851442PMC
March 2015
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