@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{wheaton_vitko_counts_dulkis_podolsky_mukherjee_kelly_2019, title={Extremely Thermoacidophilic Metallosphaera Species Mediate Mobilization and Oxidation of Vanadium and Molybdenum Oxides}, volume={85}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.02805-18}, abstractNote={
            In order to effectively leverage extremely thermoacidophilic archaea for the microbially based solubilization of solid-phase metal substrates (e.g., sulfides and oxides), understanding the mechanisms by which these archaea solubilize metals is important. Physiological analysis of
            Metallosphaera
            species growth in the presence of molybdenum and vanadium oxides revealed an indirect mode of metal mobilization, catalyzed by iron cycling. However, since the mobilized metals exist in more than one oxidation state, they could potentially serve directly as energetic substrates. Transcriptomic response to molybdenum and vanadium oxides provided evidence for new biomolecules participating in direct metal biooxidation. The findings expand the knowledge on the physiological versatility of these extremely thermoacidophilic archaea.
          }, number={5}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Wheaton, Garrett H. and Vitko, Nicholas P. and Counts, James A. and Dulkis, Jessica A. and Podolsky, Igor and Mukherjee, Arpan and Kelly, Robert M.}, year={2019}, month={Mar} }
 @article{mukherjee_wheaton_counts_ijeomah_desai_kelly_2017, title={VapC toxins drive cellular dormancy under uranium stress for the extreme thermoacidophile Metallosphaera prunae}, volume={19}, ISSN={["1462-2920"]}, DOI={10.1111/1462-2920.13808}, abstractNote={SummaryWhen abruptly exposed to toxic levels of hexavalent uranium, the extremely thermoacidophilic archaeon Metallosphaera prunae, originally isolated from an abandoned uranium mine, ceased to grow, and concomitantly exhibited heightened levels of cytosolic ribonuclease activity that corresponded to substantial degradation of cellular RNA. The M. prunae transcriptome during ‘uranium‐shock’ implicated VapC toxins as possible causative agents of the observed RNA degradation. Identifiable VapC toxins and PIN‐domain proteins encoded in the M. prunae genome were produced and characterized, three of which (VapC4, VapC7, VapC8) substantially degraded M. prunae rRNA in vitro. RNA cleavage specificity for these VapCs mapped to motifs within M. prunae rRNA. Furthermore, based on frequency of cleavage sequences, putative target mRNAs for these VapCs were identified; these were closely associated with translation, transcription, and replication. It is interesting to note that Metallosphaera sedula, a member of the same genus and which has a nearly identical genome sequence but not isolated from a uranium‐rich biotope, showed no evidence of dormancy when exposed to this metal. M. prunae utilizes VapC toxins for post‐transcriptional regulation under uranium stress to enter a cellular dormant state, thereby providing an adaptive response to what would otherwise be a deleterious environmental perturbation.}, number={7}, journal={ENVIRONMENTAL MICROBIOLOGY}, author={Mukherjee, Arpan and Wheaton, Garrett H. and Counts, James A. and Ijeomah, Brenda and Desai, Jigar and Kelly, Robert M.}, year={2017}, month={Jul}, pages={2831–2842} }
 @article{wheaton_mukherjee_kelly_2016, title={Transcriptomes of the Extremely Thermoacidophilic Archaeon Metallosphaera sedula Exposed to Metal "Shock" Reveal Generic and Specific Metal Responses}, volume={82}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01176-16}, abstractNote={ABSTRACT
          
            The extremely thermoacidophilic archaeon
            Metallosphaera sedula
            mobilizes metals by novel membrane-associated oxidase clusters and, consequently, requires metal resistance strategies. This issue was examined by “shocking”}, number={15}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Wheaton, Garrett H. and Mukherjee, Arpan and Kelly, Robert M.}, year={2016}, month={Aug}, pages={4613–4627} }
 @misc{wheaton_counts_mukherjee_kruh_kelly_2015, title={The Confluence of Heavy Metal Biooxidation and Heavy Metal Resistance: Implications for Bioleaching by Extreme Thermoacidophiles}, volume={5}, ISSN={["2075-163X"]}, DOI={10.3390/min5030397}, abstractNote={Abstract: Extreme thermoacidophiles ( T opt > 65 °C, pH opt < 3.5) inhabit unique environments fraught with challenges, including extremely high temperatures, low pH, as well as high levels of soluble metal species. In fact, certain members of this group thrive by metabolizing heavy metals, creating a dynamic equilibrium between biooxidation to meet bioenergetic needs and mechanisms for tolerating and resisting the toxic effects of solubilized metals. Extremely thermoacidophilic archaea dominate bioleaching operations at elevated temperatures and have been considered for processing certain mineral types (e.g., chalcopyrite), some of which are recalcitrant to their mesophilic counterparts. A key issue to consider, in addition to temperature and pH, is the extent to which solid phase heavy metals are solubilized and the concomitant impact of these mobilized metals on the microorganism’s growth physiology. Here, extreme thermoacidophiles are examined from the perspectives of biodiversity, heavy metal biooxidation, metal resistance mechanisms, microbe-solid interactions, and application of these archaea in biomining operations.}, number={3}, journal={MINERALS}, author={Wheaton, Garrett and Counts, James and Mukherjee, Arpan and Kruh, Jessica and Kelly, Robert}, year={2015}, month={Sep}, pages={397–451} }
 @article{mukherjee_wheaton_blum_kelly_2012, title={Uranium extremophily is an adaptive, rather than intrinsic, feature for extremely thermoacidophilic Metallosphaera species}, volume={109}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1210904109}, abstractNote={
            Thermoacidophilic archaea are found in heavy metal-rich environments, and, in some cases, these microorganisms are causative agents of metal mobilization through cellular processes related to their bioenergetics. Given the nature of their habitats, these microorganisms must deal with the potentially toxic effect of heavy metals. Here, we show that two thermoacidophilic
            Metallosphaera
            species with nearly identical (99.99%) genomes differed significantly in their sensitivity and reactivity to uranium (U).
            Metallosphaera prunae
            , isolated from a smoldering heap on a uranium mine in Thüringen, Germany, could be viewed as a “spontaneous mutant” of
            Metallosphaera sedula
            , an isolate from Pisciarelli Solfatara near Naples.
            Metallosphaera prunae
            tolerated triuranium octaoxide (U
            3
            O
            8
            ) and soluble uranium [U(VI)] to a much greater extent than
            M. sedula
            . Within 15 min following exposure to “U(VI) shock,”}, number={41}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Mukherjee, Arpan and Wheaton, Garrett H. and Blum, Paul H. and Kelly, Robert M.}, year={2012}, month={Oct}, pages={16702–16707} }