Biology subjects

Rothschild, L. J.

Publications and source records attributed to Rothschild, L. J..

6 recordsLinked to original sources

bioRxiv2023

Bacillus subtilis engineered for aerospace medicine: a platform for off-planet production of pharmaceutical peptides

1.Biologics, such as pharmaceutical peptides, have notoriously short shelf lives, insufficient for long-duration space flight missions to the Moon or Mars. To enable the sustainable presence of humans on the Moon or Mars, we must develop methods for on-site production of pharmaceutical peptides in space, a concept we call Astropharmacy. Here, we present proof-of-concept for the first step needed: a low-mass system for pharmaceutical production designed to be stable in space. To demonstrate feasibility, we engineered strains of the space-hardy spore-forming bacterium, Bacillus subtilis, to secrete two pharmaceutical peptides important for astronaut health: teriparatide (an anabolic agent for combating osteoporosis) and filgrastim (an effective countermeasure for radiation-induced neutropenia). We found that the secretion peptides from the walM and yoqH genes of B. subtilis 168 worked well for secreting teriparatide and filgrastim, respectively. In consideration of the TRISH challenge to produce a dose equivalent in 24 hours, dried spores of our engineered strains were used to produce 1 dose equivalent of teriparatide from a 2 mL culture and 1 dose equivalent of filgrastim from 52 mL of culture in 24 hours. Further optimization of strain growth conditions, expression conditions, and promoter sequences should allow higher production rates to be achieved. These strains provide the template for future optimization efforts and address the first step in the Astropharmacy, capable of on-site production, purification, and processing of biopharmaceutical compounds in platforms amenable for use in space.

pharmacology and toxicology↗

bioRxiv2022

Assessing the intrageneric environmental boundaries of the extremophilic cyanobacterium Chroococcidiopsis (Pleurocapsales) and its implications for space exploration

The cyanobacterium Chroococcidiopsis contains species found in extreme environments, thus providing the opportunity to study adaptation to a range of environments within the confines of a single genus. Due to its extremophilic nature, it has attracted attention for space settlement as well as a model for life elsewhere. In this study, eight unialgal strains from diverse habitats, isolated in unialgal culture and grown in laboratory conditions, were characterized for their ability to survive a range of extreme environments including UVC (254 nm) radiation, oxidative damage, desiccation, and repeated freeze/thawing. The study revealed two previously uncharacterized saltwater isolates of Chroococcidiopsis that were more radiation resistant than most of the other isolates. Isolate CCMP 1991 from Hawaii survived up to 1750 J{middle dot}m-2, and isolate CCMP 3184 from Samoa survived up to 1000 J{middle dot}m-2 (254 nm UVR) compared with 250 J{middle dot}m-2 for most other isolates tested. These two UV radiation-resistant isolates are closely related phylogenetically, but inhabit different environments. Each was further characterized for its ability to repair DNA damage as assessed by the repair of UV- induced thymine dimers and for oxidative damage tolerance via resistance to H2O2-induced (oxidative) damage. Both isolates repaired thymine dimers faster in the light than in the dark with the Hawaiian isolate repairing faster than the Samoan isolate in the light, suggesting repair by photoreactivation. The Hawaiian isolate was more tolerant to H2O2 exposure than the Samoan isolate, indicating a possible role for antioxidants in the protection of the cell. Both isolates were more tolerant than the other isolates tested to freeze/thawing in liquid nitrogen, which is also known to cause DNA damage. Spectral absorbance scans were performed to detect pigments in each isolate. While all showed peaks likely to be chlorophyll a, carotenoids, phycocyanin, scytonemin and MAAs, the Hawaiian isolate contained a pigment that absorbed at around 325 nm that none of the other isolates contained. Although this pigment is outside the range of UVC absorbance, it is hypothesized that it may play a role in DNA protection as a UV sunscreen or as an antioxidant. The phenotypic similarities in radiation resistance and freeze/thawing resistance among the Hawaiian, Somoan and Negev isolates appear to be the result of environmental adaptation rather than phylogenetic markers as the first of these have been previously shown to be part of a saltwater clade, while the Negev strain falls within a freshwater clade. As pigmentation, and likely resistance to other environmental conditions, can be induced, these data provide a baseline study of strains in an uninduced state. Thus, the true environmental limits to Chroococcidiopsis likely go beyond our current knowledge. The implications of this is discussed in relation to space exploration

microbiology↗

bioRxiv2022

Universal functions of prion candidates across all three domains of life suggest a primeval role of protein self-templating.

Amyloid-based prions have simple structures, a wide phylogenetic distribution, and a plethora of functions in contemporary organisms, suggesting they may be an ancient phenomenon. However, this hypothesis has yet to be addressed with a systematic, computational, and experimental approach. Here we present a framework to help guide future experimental verification of candidate prions with conserved functions in order to understand their role in the early stages of evolution and potentially in the origins of life. We identified candidate prions in all high-quality proteomes available in UniProt computationally, assessed their phylogenomic distributions, and analyzed candidate-prion functional annotations. Of the 27,980,560 proteins scanned, 228,561 were identified as candidate prions ([~]0.82%). Among these candidates, there were 84 Gene Ontology (GO) terms conserved across the 3 domains of life. We found that candidate prions with a possible role in adaptation were particularly well-represented within this group. We discuss unifying features of candidate prions to elucidate the primeval roles of prions and their associated functions. Candidate prions annotated as transcription factors, DNA binding, and kinases are particularly well suited to generating diverse responses to changes in their environment and could allow for adaptation and population expansion into more diverse environments. We hypothesized that these functions could be evolutionarily ancient, even if individual prion domains themselves are not evolutionarily conserved. Candidate prions annotated with these universally-occurring functions potentially represent the oldest extant prions on Earth and are therefore excellent experimental targets.

bioinformatics↗

bioRxiv2020

The hunt for ancient prions: Archaeal prion-like domains form amyloids and substitute for yeast prion domains

Prions are proteins capable of acquiring an alternate conformation that can then induce additional copies to adopt this same alternate conformation. Although initially discovered in relation to mammalian disease, subsequent studies have revealed the presence of prions in Bacteria and Viruses, suggesting an ancient evolutionary origin. Here we explore whether prions exist in Archaea - the last domain of life left unexplored with regard to prions. After searching for potential prion-forming protein sequences computationally, we tested candidates in vitro and in organisms from the two other domains of life: Escherichia coli and Saccharomyces cerevisiae. Out of the 16 candidate prion-forming domains tested, 8 bound to amyloid-specific dye, and six acted as protein-based elements of information transfer, driving non-Mendelian patterns of inheritance. We additionally identified short peptides from archaeal prion candidates that can form amyloid fibrils independently. Candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, suggesting that the presence of these amino acids may help distinguish functional prion domains from nonfunctional ones. Our data establish the presence of amyloid-forming prion-like domains in Archaea. Their discovery in all three domains of life further suggests the possibility that they were present at the time of the last universal common ancestor (LUCA). Significance StatementThis work establishes that amyloid-forming, prion-like domains exist in Archaea and are capable of vertically transmitting their prion phenotype - allowing them to function as protein-based elements of inheritance. These observations, coupled with prior discoveries in Eukarya and Bacteria, suggest that prion-based self-assembly was likely present in lifes last universal common ancestor (LUCA), and therefore may be one of the most ancient epigenetic mechanisms.

evolutionary biology↗

bioRxiv2018

Getting there and staying there: supporting and enabling persistent human life on Mars using synthetic natural rubber, self-healing materials, and biological batteries.

Planetary exploration requires a balance between preemptive planning and financial feasibility. The risk of mid-mission equipment failure, power shortages, or supply depletion incentivizes precautionary measures, but the financial strain of sending unnecessary mass into space limits this practice.\n\nTo balance the two, our team explored the advantages of biological solutions, namely the self-sustaining abilities of low-mass organisms, to make planetary exploration more self-sufficient and economical. Prioritizing repair over replacement, we are developing self-healing materials embedded with Bacillus subtilis. For longer-lasting energy, we are designing a \"biobactery\" using linearly oriented Escherichia coli to generate power. For renewable materials, we are engineering bacteria to synthesize and degrade rubber. Individually, these projects offer sustainable alternatives for repair, power, and materials. But when combined, these consolidated insights can provide us with the power to get to Mars and resources to sustain us while were there.

synthetic biology↗

bioRxiv2016

Ribo-attenuators: novel elements for reliable and modular riboswitch engineering

Riboswitches are structural genetic regulatory elements that directly couple the sensing of small molecules to gene expression. They have considerable potential for applications throughout synthetic biology and bio-manufacturing as they are able to sense a wide range of small molecules and regulate gene expression in response. Despite over a decade of research they have yet to reach this considerable potential as they cannot yet be treated as modular components. This is due to several limitations including sensitivity to changes in genetic context, low tunability, and variability in performance. To overcome the associated difficulties with riboswitches, we have designed and introduced a novel genetic element called a Ribo-attenuator in Bacteria. This genetic element allows for predictable tuning, insulation from contextual changes, and a reduction in expression variation. Ribo-attenuators allow riboswitches to be treated as truly modular and tunable components, and thus increases their reliability for a wide range of applications.

synthetic biology↗