About

Robert M Kelly is the Alcoa Professor of Chemical and Biomolecular Engineering at NC State University. His research focuses on the genomics, physiology, enzymology, and biotechnological potential of microorganisms that thrive in extreme environments, such as geothermal sites and volcanic regions. These microorganisms, primarily extremely thermophilic bacteria and archaea, have optimal growth temperatures above 70°C and produce highly thermostable enzymes that hold promise as biocatalysts. Kelly's work involves understanding the bioenergetics, biochemistry, physiology, and genomics of these organisms, with applications in biotransformations, biofuels, metal recovery, and industrial biocatalysis. His research has contributed to technological developments related to bioenergy, biometallurgy, and synthetic biology, addressing fundamental issues at the interface of biology and engineering.

Research topics

• Biology
• Computational biology
• Genetics
• Evolutionary biology
• Computer Science
• Ecology
• Astronomy
• Zoology
• Pulp and paper industry
• Physics
• Botany
• Library science
• Data science
• Engineering
• World Wide Web
• Biochemistry
• Biotechnology

Selected publications

• pH Threshold Impacts Chalcopyrite Bioleaching Dynamics for the Extreme Thermoacidophile <i>Sulfurisphaera ohwakuensis</i>

  Biotechnology and Bioengineering · 2025-01-31 · 3 citations

  articleOpen accessSenior authorCorresponding

  ABSTRACT The extremely thermoacidophilic archaeon Sulfurisphaera ohwakuensis served as the basis for probing how initial pH (pH initial ) affects copper mobilization from chalcopyrite. Screening of small‐scale cultures (75 mL) at 75°C revealed that ~pH 3.0 was a maximal threshold for bioleaching onset. Subsequently, chalcopyrite at 10 g/L in 750 mL culture media, containing small amounts of ferric ion, adjusted to pH 2.5 with sulfuric acid and incubated for 24 h at 75°C before inoculation, brought the pH to approximately 3.0 through abiotic chemical reactions. However, the resulting subtle differences in pH initial (3.0 ± 0.15) in bioleaching cultures, while not affecting microbial growth, were critical to bioleaching onset and progress. Initial iron levels were less important than pH initial in starting the bioleaching process. X‐Ray Diffraction (XRD) surface analysis informed bioleaching trajectories over 21 days and reinforced the impact of pH initial . The subtle differences in pH initial markedly affected S. ohwakuensis onset and outcomes, as it presumably would for other bioleaching thermoacidophilic archaea. Furthermore, the findings here highlight the challenges faced in replicating bioleaching experiments across, and even within, laboratories as well as in achieving consistent results in bioleaching processes.

  PublisherOA PDFDOI

• 1542P IOS-1002, a first-in-class multi-checkpoint inhibitor, shows encouraging clinical activity in combination with pembrolizumab in advanced solid tumors

  Annals of Oncology · 2025-09-01

  article
  PublisherDOI

• Structural and kinetic characterization of an acetoacetyl-Coenzyme A: acetate Coenzyme A transferase from the extreme thermophile <i>Thermosipho melanesiensis</i>

  Biochemical Journal · 2025-01-27 · 1 citations

  articleOpen accessSenior author

  Family 1 Coenzyme A transferases (CtfAB) from the extremely thermophilic bacterium, Thermosipho melanesiensis, has been used for in vivo acetone production up to 70°C. This enzyme has tentatively been identified as the rate-limiting step, due to its relatively low-binding affinity for acetate. However, existing kinetic and mechanistic studies on this enzyme are insufficient to evaluate this hypothesis. Here, kinetic analysis of purified recombinant T. melanesiensis CtfAB showed that it has a ping-pong bi-bi mechanism typical of Coenzyme A (CoA) transferases with Km values for acetate and acetoacetyl-CoA of 85 mM and 135 μM, respectively. Product inhibition by acetyl-CoA was competitive with respect to acetoacetyl-CoA and non-competitive with respect to acetate. Crystal structures of wild-type and mutant T. melanesiensis CtfAB were solved in the presence of acetate and in the presence or absence of acetyl-CoA. These structures led to a proposed structural basis for the competitive and non-competitive inhibition of acetyl-CoA: acetate binds independently of acetyl-CoA in an apparent low-affinity binding pocket in CtfA that is directly adjacent to a catalytic glutamate in CtfB. Similar to other CoA transferases, acetyl-CoA is bound in an apparent high-affinity binding site in CtfB with most interactions occurring between the phospho-ADP of CoA and CtfB residues far from the acetate binding pocket. This structural-based mechanism also explains the organic acid promiscuity of CtfAB. High-affinity interactions are predominantly between the conserved phospho-ADP of CoA, and the variable organic acid binding site is a low-affinity binding site with few specific interactions.

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• Engineering the hyperthermophilic archaeon <i>Pyrococcus furiosus</i> for 1-propanol production

  Applied and Environmental Microbiology · 2025-04-07 · 3 citations

  articleOpen access

  ABSTRACT Society relies heavily on chemicals traditionally produced through the refinement of fossil fuels. The conversion of renewable biomass to value-added chemicals by microbes, particularly hyperthermophiles (T opt ≥80°C), offers a renewable alternative to this traditional approach. Herein, we describe the engineering of the hyperthermophilic archaeon Pyrococcus furiosus , which grows optimally (T opt ) at 100°C, for the conversion of sugar to 1-propanol. This was accomplished by constructing a hybrid metabolic pathway consisting of two native and seven heterologously produced enzymes to convert acetyl-CoA from carbohydrate metabolism to 1-propanol. A total of eleven foreign genes from two other organisms were utilized, one from the thermophilic bacterium Thermoanaerobacter sp. strain X514 and 10 from the thermoacidophilic archaeon Metallosphaera sedula, both of which grow optimally near 70°C. The recombinant P. furiosus strain produced 1-propanol at similar concentrations (up to ~1 mM) when incubated at 75°C to activate the gene products of Thermoanaerobacter sp. strain X514 and M. sedula and by initially incubating at 95°C for P. furiosus growth and then subsequently returning to 75°C to promote 1-propanol formation. Note that 1-propanol was not produced if the culture was grown only at 95°C. This work has the potential for future optimization through harnessing the genome-scale metabolic model of P. furiosus that was used herein to identify engineering targets to increase 1-propanol titer. IMPORTANCE As petroleum reserves become increasingly strained, the development of renewable alternatives to traditional chemical synthesis becomes more important. In this work, a high-temperature biological system for sugar to 1-propanol conversion was demonstrated by metabolic engineering of the hyperthermophilic archaeon Pyrococcus furiosus (T opt 100°C). The engineered strain produced 1-propanol by temperature shifting from 75°C to 95°C and then back to 75°C to accommodate the temperature ranges for native and foreign proteins associated with 1-propanol biosynthesis. Genome-scale metabolic modeling informed the carbon and reductant flux in the system, identified potential factors limiting 1-propanol production, and revealed potential optimization targets.

  PublisherDOI

• Abstract 2371 Enhancing Molecular Biotechnology Laboratory Education for Diverse Institutions

  Journal of Biological Chemistry · 2025-05-01

  articleOpen accessSenior author

  The rapid pace of scientific discovery poses economic and time constraints on educators who wish to integrate the latest research in their teaching. Yet, educational strategies that rely on lecture alone or traditional, but outdated, laboratory experiences ineffectively prepare the current and future generations of students that will comprise the US biomedical workforce. Therefore, the higher education community would benefit from a flexible and dynamic paradigm that conveys up-to-date molecular biology laboratory training suitable for use at diverse institutions.

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• Xylanolytic metabolism is regulated by coordination of transcription factors XynR and XylR in extremely thermophilic <i>Caldicellulosiruptorales</i>

  Applied and Environmental Microbiology · 2025-06-04

  articleOpen accessSenior author

  ABSTRACT Global transcription factors (TFs) control metabolic processes in bacteria to efficiently utilize available carbon. The order Caldicellulosiruptorales has drawn interest due to the ability of its members to degrade components of lignocellulosic biomass. Regulatory reconstruction of Anaerocellum (f. Caldicellulosiruptor) bescii identified two major global transcription factors for xylan utilization, XynR and XylR, and the corresponding putative transcription factor binding sites. Recombinant versions of XynR (LacI family) and XylR (ROK family) were subjected to fluorescence polarization (FP) and biolayer interferometry (BLI) analysis to confirm the predicted binding sites. Four XynR sites and two XylR sites were validated, accounting for 20 of 26 genes regulated by XynR and six of seven genes regulated by XylR. Bioinformatic analysis of the individual genes controlled by the two regulators showed an inter-dependent scheme for xylan conversion; the transport of xylooligosaccharides (XOS) is dependent on XylR, while enzymes responsible for hydrolysis are controlled by both regulators. For xylose catabolism by the xylose isomerase-xylulose kinase pathway, regulation is also split, with XylR controlling xylose isomerase and XynR controlling xylokinase. The XynR/XylR regulator pair within A. bescii is conserved in all sequenced species of Caldicellulosiruptorales , suggesting similarities in regulating linear xylan conversion. In other xylanolytic thermophiles, XylR homologs control xylan degradation, compared to just 6 out of 26 genes for A. bescii . These results show that two separate regulatory schemes (dual repression) are coordinated by A. bescii to effectively regulate the hemicellulose inventory and xylan catabolism. IMPORTANCE To take full advantage of extreme thermophiles as platform metabolic engineering microorganisms, the tools for genetic manipulation must be further developed, and strategies that exploit a better understanding of metabolic regulation need to be discerned. Anaerocellum bescii , the most studied of the extremely thermophilic fermentative anaerobic bacteria that can utilize microcrystalline cellulose, can degrade microcrystalline cellulose and hemicellulose and has been metabolically engineered to convert the resulting sugars to products such as ethanol and acetone. For xylan, in particular, two major global transcription factors (TFs), XynR and XylR, play a role in sugar metabolism, although their predicted regulatory interdependence from bioinformatics analysis has not been elucidated experimentally. Here, fluorescence polarization (FP) and biolayer interferometry (BLI) were used to explore this issue to support metabolic engineering efforts aimed at improving carbohydrate processing to industrial chemicals.

  PublisherDOI

• Anaerocellum (f. Caldicellulosiruptor) bescii

  Trends in Microbiology · 2025-02-27 · 1 citations

  articleSenior author
  PublisherDOI

• Metabolic engineering in Hot Acid: Strategies enabling chemolithotrophy in thermoacidophilic archaea

  Metabolic Engineering · 2025-06-10 · 1 citations

  articleSenior authorCorresponding
  PublisherDOI

• Engineering ethanologenicity into the extremely thermophilic bacterium Anaerocellum (f. Caldicellulosiriuptor) bescii

  Metabolic Engineering · 2024-09-19 · 8 citations

  articleOpen accessSenior authorCorresponding
  PublisherOA PDFDOI

• Suitability of tunable diode laser absorption spectroscopy experiments for low density flows

  AIP conference proceedings · 2024-01-01

  articleOpen access1st authorCorresponding

  In this report we investigate the suitability of different gases for TDLAS of low density hypersonic nozzle-exit flows, but tunnel results are not be presented yet. Oxygen (for an Earth atmosphere), carbon dioxide (for a Martian atmosphere) and seeded rubidium are the considered candidates for TDLAS measurements. We demonstrate the design of a simple, minimum-path-length TDLAS system that can be used to measure the temperature and velocity of a hypersonic nozzle flow. This system is tested in laboratory air, and the absorption signals are then scaled using an in-house code to predict absorption in rarefied flows in the shock tunnel, comparing between different candidate optical configurations. A design for TDLAS measurements inside a hypersonic facility is discussed, along with the challenges associated with hypersonic ground test facilities.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01GM090209

  NIH · $530k · 2012

• Leveraging Extreme Thermoacidophily for Bio-based Chemicals

  NSF · $301k · 2018–2023

• Collaborative Research: Biotransformations Near and Above 100°C: Hyperthermophilic Microorganisms and Enzymes for Bioenergy Conversion

  NSF · $420k · 2006–2010

• Molecular Biotechnology Training at North Carolina State University

  NIH · $222k · 2000–2015

• COLLABORATIVE RESEARCH: Exploiting microbial hyperthermophilicity to produce an industrial chemical

  NSF · $257k · 2013–2018

Frequent coauthors

• Michael W. W. Adams

  University of Georgia

  106 shared

• Sara E. Blumer‐Schuette

  Oakland University

  36 shared

• Gina L. Lipscomb

  University of Georgia

  27 shared

• Jonathan M. Conway

  Princeton University

  25 shared

• Ryan G. Bing

  North Carolina State University

  25 shared

• Donald A. Comfort

  University of Dayton

  24 shared

• Shannon B. Conners

  SAS Institute (United States)

  22 shared

• Farris L. Poole

  University of Georgia

  22 shared