@misc{manesh_willard_lewis_kelly_2024, title={Extremely thermoacidophilic archaea for metal bioleaching:<i> What</i><i> do</i><i> their</i> genomes tell Us?}, volume={391}, ISSN={["1873-2976"]}, DOI={10.1016/j.biortech.2023.129988}, abstractNote={Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.}, journal={BIORESOURCE TECHNOLOGY}, author={Manesh, Mohamad J. H. and Willard, Daniel J. and Lewis, April M. and Kelly, Robert M.}, year={2024}, month={Jan} }
 @article{cooper_lewis_notey_mukherjee_willard_blum_kelly_2023, title={Interplay between transcriptional regulators and VapBC toxin-antitoxin loci during thermal stress response in extremely thermoacidophilic archaea}, volume={2}, ISSN={["1462-2920"]}, DOI={10.1111/1462-2920.16350}, abstractNote={AbstractThermoacidophilic archaea lack sigma factors and the large inventory of heat shock proteins (HSPs) widespread in bacterial genomes, suggesting other strategies for handling thermal stress are involved. Heat shock transcriptomes for the thermoacidophilic archaeon Saccharolobus (f. Sulfolobus) solfataricus 98/2 revealed genes that were highly responsive to thermal stress, including transcriptional regulators YtrASs (Ssol_2420) and FadRSs (Ssol_0314), as well as type II toxin–antitoxin (TA) loci VapBC6 (Ssol_2337, Ssol_2338) and VapBC22 (Ssol_0819, Ssol_0818). The role, if any, of type II TA loci during stress response in microorganisms, such as Escherichia coli, is controversial. But, when genes encoding YtrASs, FadRSs, VapC22, VapB6, and VapC6 were systematically mutated in Sa. solfataricus 98/2, significant up‐regulation of the other genes within this set was observed, implicating an interconnected regulatory network during thermal stress response. VapBC6 and VapBC22 have close homologues in other Sulfolobales, as well as in other archaea (e.g. Pyrococcus furiosus and Archaeoglobus fulgidus), and their corresponding genes were also heat shock responsive. The interplay between VapBC TA loci and heat shock regulators in Sa solfataricus 98/2 not only indicates a cellular mechanism for heat shock response that differs from bacteria but one that could have common features within the thermophilic archaea.}, journal={ENVIRONMENTAL MICROBIOLOGY}, author={Cooper, Charlotte R. and Lewis, April M. and Notey, Jaspreet S. and Mukherjee, Arpan and Willard, Daniel J. and Blum, Paul H. and Kelly, Robert M.}, year={2023}, month={Feb} }
 @article{lewis_willard_manesh_sivabalasarma_albers_kelly_2023, title={Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin}, volume={4}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.00053-23}, abstractNote={Biofilms allow microbes to resist a multitude of stresses and stay proximate to vital nutrients. The mechanisms of entering and leaving a biofilm are highly regulated to ensure microbial survival, but are not yet well described in archaea.}, journal={MBIO}, author={Lewis, April M. and Willard, Daniel J. and Manesh, Mohamad J. H. J. and Sivabalasarma, Shamphavi and Albers, Sonja-Verena and Kelly, Robert M.}, year={2023}, month={Apr} }
 @article{lewis_recalde_bräsen_counts_nussbaum_bost_schocke_shen_willard_quax_et al._2021, title={The biology of thermoacidophilic archaea from the order Sulfolobales}, volume={45}, ISSN={1574-6976}, url={http://dx.doi.org/10.1093/femsre/fuaa063}, DOI={10.1093/femsre/fuaa063}, abstractNote={ABSTRACT
               Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.}, number={4}, journal={FEMS Microbiology Reviews}, publisher={Oxford University Press (OUP)}, author={Lewis, April M and Recalde, Alejandra and Bräsen, Christopher and Counts, James A and Nussbaum, Phillip and Bost, Jan and Schocke, Larissa and Shen, Lu and Willard, Daniel J and Quax, Tessa E F and et al.}, year={2021}, month={Jan} }
 @article{crosby_laemthong_lewis_straub_adams_kelly_2019, title={Extreme thermophiles as emerging metabolic engineering platforms}, volume={59}, ISSN={0958-1669}, url={http://dx.doi.org/10.1016/j.copbio.2019.02.006}, DOI={10.1016/j.copbio.2019.02.006}, abstractNote={Going forward, industrial biotechnology must consider non-model metabolic engineering platforms if it is to have maximal impact. This will include microorganisms that natively possess strategic physiological and metabolic features but lack either molecular genetic tools or such tools are rudimentary, requiring further development. If non-model platforms are successfully deployed, new avenues for production of fuels and chemicals from renewable feedstocks or waste materials will emerge. Here, the challenges and opportunities for extreme thermophiles as metabolic engineering platforms are discussed.}, journal={Current Opinion in Biotechnology}, publisher={Elsevier BV}, author={Crosby, James R and Laemthong, Tunyaboon and Lewis, April M and Straub, Christopher T and Adams, Michael WW and Kelly, Robert M}, year={2019}, month={Oct}, pages={55–64} }