Article
Multidisciplinary Sciences
Agnieszka Winiarska, Fidel Ramirez-Amador, Dominik Hege, Yvonne Gemmecker, Simone Prinz, Georg Hochberg, Johann Heider, Maciej Szaleniec, Jan Michael Schuller
Summary: In this study, the cryo-electron microscopy technique was used to reveal that the aldehyde oxidoreductases (AORs) from Aromatoleum aromaticum form filaments consisting of repeating AorAB protomers capped by a single NAD-binding AorC subunit. The structure also reveals the binding mode of the native substrate benzoate and the electronconducting nanowire formed by the polyferredoxin-like subunit AorA. A hypothetical catalytic mechanism was proposed based on quantum mechanics:molecular mechanics (QM:MM) modeling, which provides insights for further engineering in synthetic biology and biotechnology applications.
Article
Ecology
Barbara Bayer, Mak A. Saito, Matthew R. McIlvin, Sebastian Lucker, Dawn M. Moran, Thomas S. Lankiewicz, Christopher L. Dupont, Alyson E. Santoro
Summary: The genome and proteome analysis of the marine Nitrospira isolate N. marina reveals its adaptations to thrive in the oxic ocean environment and its metabolic versatility to survive under low oxygen conditions while maintaining nitrite oxidation-driven autotrophy.
Article
Microbiology
Yijun Zhu, Mohammed Dwidar, Ina Nemet, Jennifer A. Buffa, Naseer Sangwan, Xinmin S. Li, James T. Anderson, Kymberleigh A. Romano, Xiaoming Fu, Masanori Funabashi, Zeneng Wang, Pooja Keranahalli, Shawna Battle, Aaron N. Tittle, Adeline M. Hajjar, Valentin Gogonea, Michael A. Fischbach, Joseph A. DiDonato, Stanley L. Hazen
Summary: Recent studies have shown the critical role of gut microbiota in metabolizing dietary phenylalanine into phenylacetic acid (PAA), which is important for the production of phenylacetylglutamine (PAGln) linked to atherosclerotic cardio-vascular disease (ASCVD). Researchers have identified two different microbial pathways, involving phenylpyruvate:ferre-doxin oxidoreductase (PPFOR) and phenylpyruvate decarboxylase (PPDC), for PAA formation in the gut. The abundance of these pathways is significantly higher in ASCVD patients compared to controls. These findings provide insights into the therapeutic targeting of PAGln formation in vivo.
CELL HOST & MICROBE
(2023)
Article
Multidisciplinary Sciences
Steffen Buessecker, Marike Palmer, Dengxun Lai, Joshua Dimapilis, Xavier Mayali, Damon Mosier, Jian-Yu Jiao, Daniel R. Colman, Lisa M. Keller, Emily St. John, Michelle Miranda, Cristina Gonzalez, Lizett Gonzalez, Christian Sam, Christopher Villa, Madeline Zhuo, Nicholas Bodman, Fernando Robles, Eric S. Boyd, Alysia D. Cox, Brian St. Clair, Zheng-Shuang Hua, Wen-Jun Li, Anna-Louise Reysenbach, Matthew B. Stott, Peter K. Weber, Jennifer Pett-Ridge, Anne E. Dekas, Brian P. Hedlund, Jeremy A. Dodsworth
Summary: Trace metals, specifically tungsten, play a crucial role in the growth and evolution of the archaeal lineage Caldarchaeales. The genome-guided cultivation of Wolframiiraptor gerlachensis revealed its dependence on tungsten and its ability to assimilate xylose. This study suggests that tungsten-associated enzymes were present in the common ancestor of Wolframiiraptoraceae and highlights the importance of tungsten-dependent metabolism in early anaerobic thermophiles.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Linta Reji, Emily L. Cardarelli, Kristin Boye, John R. Bargar, Christopher A. Francis
Summary: The subsurface microbiome contains a vast diversity of untapped phylogenetic and metabolic novelty, with major implications for global biogeochemical cycling. Through genome-resolved metagenomics, we found that hydrological variables strongly influence the ecophysiology of Thaumarchaeota in alluvial sediments, leading to shifts in population structure and metabolic features.
Article
Multidisciplinary Sciences
Anuj Kumar, Florian Kremp, Jennifer Roth, Sven A. Freibert, Volker Mueller, Jan M. Schuller
Summary: This study reports the cryo-EM structure of the Stn class transhydrogenase from Sporomusa ovata and dissects its electron transfer pathway.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
Jia-Wei Zhang, Hong-Po Dong, Li-Jun Hou, Yang Liu, Ya-Fei Ou, Yan-Ling Zheng, Ping Han, Xia Liang, Guo-Yu Yin, Dian-Ming Wu, Min Liu, Meng Li
Summary: Asgard archaea, known for their potential in utilizing various organic substrates in sediment carbon cycling, have a new affiliate phylum called Hermodarchaeota which shows potential in anaerobic degradation of alkanes and aromatic compounds. Through screening metagenomic datasets, genes similar to Hermodarchaeota were identified in marine and freshwater sediments, suggesting widespread presence of Asgard archaea capable of degrading alkanes and aromatics.
Review
Biochemistry & Molecular Biology
Wilfred R. R. Hagen
Summary: The development of tungsten biochemistry is discussed, with a focus on personal involvement. A comprehensive catalog of genes, enzymes, and reactions related to tungsten has been compiled. EPR spectroscopy has played a significant role in understanding tungstopterin-based catalysis. However, the lack of pre-steady-state data remains a challenge. Tungstate transport systems and biosynthetic machinery for tungstopterin enzymes have been studied, revealing their specificity for tungsten and additional selectivity. Metallomics analysis of Pyrococcus furiosus has provided a comprehensive inventory of tungsten proteins.
Article
Biochemistry & Molecular Biology
Lu Xiao, Guoxia Liu, Fuyu Gong, Zhen Cai, Yin Li
Summary: This study investigated the reductive carboxylation activities of six heterotetrameric PFORs from hyperthermophilic archaea, revealing diversity in their functions. Among them, PFORpfm from Pyrolobus fumarii showed the highest reductive carboxylation activities and red/ox ratio, indicating the potential significance of PFOR in autotrophic CO2 fixation in high temperature environments.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biology
Laura Prioretti, Giulia D'Ermo, Pascale Infossi, Arlette Kpebe, Regine Lebrun, Marielle Bauzan, Elisabeth Lojou, Bruno Guigliarelli, Marie-Therese Giudici-Orticoni, Marianne Guiral
Summary: Aquifex aeolicus is a microaerophilic bacterium that oxidizes hydrogen and sulfur and assimilates CO2 via the reverse tricarboxylic acid cycle (rTCA). It possesses pentameric versions of key enzymes (PFOR and OGOR) involved in this pathway, which are highly abundant in the cell. Two low redox potential and oxygen-stable ferredoxins (Fd6 and Fd7) were identified in A. aeolicus and shown to interact with PFOR and OGOR, potentially serving as electron donors in vivo.
Article
Immunology
Kairuo Wang, Yixuan Guo, Yuanyuan Liu, Xiao Cui, Xiang Gu, Lixiang Li, Yanqing Li, Ming Li
Summary: This study found that the deficiency of F. prausnitzii in the gut is associated with elevated F. prausnitzii-reactive IgA in ulcerative colitis (UC) patients. Forced immunization of rabbits with F. prausnitzii led to intestinal inflammation. PFOR was identified as an IgA-binding antigen of F. prausnitzii and its immunoreactivity was validated in peripheral blood mononuclear cells (PBMCs), which showed elevated expression of inflammatory cytokines. Phylogenetic analysis revealed that PFOR is a common but conserved protein among gut bacteria.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Natalie Payne, Arlette Kpebe, Chloe Guendon, Carole Baffert, Julien Ros, Regine Lebrun, Yann Denis, Laetitia Shintu, Myriam Brugna
Summary: Through studying Desulfovibrio fructosovorans, we discovered that Hnd is involved in ethanol metabolism and oxidizes H-2 via its electron bifurcation mechanism, producing NADH and reduced ferredoxin.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biology
Faisal Alharbi, Thomas Knura, Bettina Siebers, Kesen Ma
Summary: This study investigates the thermostability and oxygen stability of pyruvate decarboxylase (PDC) from two thermoacidophile microorganisms, Saccharolobus solfataricus and Sulfolobus acidocaldarius. The results show that both enzymes are CoA-dependent and thermostable, with no loss of activity in the presence of oxygen.
Article
Multidisciplinary Sciences
Michael P. Andreas, Tobias W. Giessen
Summary: Researchers conducted a large-scale computational analysis to discover over 6,000 encapsulin-like systems, and proposed hypotheses about their potential biological functions, indicating that encapsulins likely evolved from HK97-type bacteriophages.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Wenzhe Hu, Jie Pan, Bin Wang, Jun Guo, Meng Li, Meiying Xu
Summary: This study obtained four archaeal metagenome-assembled genomes (MAGs) from black-odorous aquatic sediments in Foshan, Guangdong, China, revealing the taxonomic and potential metabolic diversity of a new order Ca. Gimiplasmatales. The MAGs showed biosynthesis capabilities for isoprenoids and nucleotides, a mixotrophic lifestyle, and sulfur, hydrogen, and arsenic transformation potentials. Comparative genomics suggested that the H4F Wood-Ljungdahl pathway in Ca. Gimiplasmatales and Methanomassiliicoccales may have been acquired through interdomain lateral gene transfer from Firmicutes.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Christopher T. Straub, Ryan G. Bing, Jack P. Wang, Vincent L. Chiang, Michael W. W. Adams, Robert M. Kelly
BIOTECHNOLOGY FOR BIOFUELS
(2020)
Article
Biochemistry & Molecular Biology
Christopher T. Straub, Gerritt Schut, Jonathan K. Otten, Lisa M. Keller, Michael W. W. Adams, Robert M. Kelly
Article
Nanoscience & Nanotechnology
Wenxing Yang, Gregory E. Vansuch, Yawei Liu, Tao Jin, Qiliang Liu, Aimin Ge, Monica L. K. Sanchez, Dominik K. Haja, Michael W. W. Adams, R. Brian Dyer, Tianquan Lian
ACS APPLIED MATERIALS & INTERFACES
(2020)
Article
Biotechnology & Applied Microbiology
Gabriel M. Rubinstein, Gina L. Lipscomb, Amanda M. Williams-Rhaesa, Gerrit J. Schut, Robert M. Kelly, Michael W. W. Adams
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2020)
Article
Environmental Sciences
Ji-Won Moon, Charles J. Paradis, Dominique C. Joyner, Frederick von Netzer, Erica L. Majumder, Emma R. Dixon, Mircea Podar, Xiaoxuan Ge, Peter J. Walian, Heidi J. Smith, Xiaoqin Wu, Grant M. Zane, Kathleen F. Walker, Michael P. Thorgersen, Farris L. Poole, Lauren M. Lui, Benjamin G. Adams, Kara B. De Leon, Sheridan S. Brewer, Daniel E. Williams, Kenneth A. Lowe, Miguel Rodriguez, Tonia L. Mehlhorn, Susan M. Pfiffner, Romy Chakraborty, Adam P. Arkin, Judy D. Wall, Matthew W. Fields, Michael W. W. Adams, David A. Stahl, Dwayne A. Elias, Terry C. Hazen
Article
Multidisciplinary Sciences
Regina L. Wilpiszeski, Caitlin M. Gionfriddo, Ann M. Wymore, Ji-Won Moon, Kenneth A. Lowe, Mircea Podar, Sa'ad Rafie, Matthew W. Fields, Terry C. Hazen, Xiaoxuan Ge, Farris Poole, Michael W. W. Adams, Romy Chakraborty, Yupeng Fan, Joy D. Van Nostrand, Jizhong Zhou, Adam P. Arkin, Dwayne A. Elias
Article
Multidisciplinary Sciences
Xiang Feng, Gerrit J. Schut, Gina L. Lipscomb, Huilin Li, Michael W. W. Adams
Summary: EtfABCX is a flavin-based electron bifurcation complex that enables reduction of ferredoxin by coupling the reaction to the reduction of menaquinone. The structure reveals that low-potential electrons are transferred directly to ferredoxin, while high-potential electrons reduce the quinone via [4Fe-4S] clusters in EtfX, suggesting an evolutionary link between bifurcating and nonbifurcating systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Sonya M. Clarkson, Dominik K. Haja, Michael W. W. Adams
Summary: Iron is an essential nutrient that can exist in different forms in various environments. The archaeon Pyrococcus furiosus can directly assimilate iron from dissolved iron sulfide cluster complexes, providing new insights into the utilization of iron sulfide and proposing a model for iron sulfide assimilation from an insoluble mineral.
Article
Biochemical Research Methods
Vishwanath S. Khadye, Sneha Sawant, Kurshedaktar Shaikh, Ritika Srivastava, Sanjeev Chandrayan, Annamma A. Odaneth
Summary: This study aimed to optimize the expression and secretion of a thermostable BGL from Pyrococcus furiosus in B. subtilis, resulting in a significant improvement in the yield of PfuBGL. The research demonstrated the high potential of utilizing B. subtilis as a host organism for industrial production of various proteins/enzymes.
PROTEIN EXPRESSION AND PURIFICATION
(2021)
Article
Microbiology
Dominik K. Haja, Michael W. W. Adams
Summary: Multiple Resistance and pH (Mrp) antiporters are complexes that transport ions across membranes in response to a proton motive force. In Pyrococcus furiosus, three copies of Mrp encoding genes are found, with one using sodium as the coupling ion to maintain cytoplasmic pH. Deletion of the Mrp gene makes the bacterium more sensitive to acidification during growth, but does not significantly affect optimal pH or sodium ion concentration for growth.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Xiang Feng, Gerrit J. Schut, Dominik K. Haja, Michael W. W. Adams, Huilin Li
Summary: Electron bifurcation allows energetically unfavorable biochemical reactions to occur. This study reports a new bifurcating flavoenzyme structure that couples hydrogen oxidation with NAD reduction through electron transfer. By elucidating its structure and function, we gain a deeper understanding of the electron transfer pathways in hydrogenases.
Article
Microbiology
Francesco Smedile, Dionysis Foustoukos, Sushmita Patwardhan, Kelli Mullane, Ian Schlegel, Michael W. Adams, Gerrit J. Schut, Donato Giovannelli, Costantino Vetriani
Summary: Physiological and gene expression studies of deep-sea bacteria under pressure conditions similar to their natural habitat are important for understanding their growth kinetics and metabolic adaptations. This study focused on Campylobacterium Nautilia sp. strain PV-1, a piezophilic bacterium that displays unique protein expression patterns in response to different hydrostatic pressure regimes. The findings suggest that pressure adaptation extends to enzymes involved in central metabolic pathways.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Jennifer L. Goff, Yan Chen, Michael P. Thorgersen, Linh T. Hoang, Farris L. Poole II, Elizabeth G. Szink, Gary Siuzdak, Christopher J. Petzold, Michael W. W. Adams
Summary: Multiple heavy metal contamination is a common global problem that can disrupt microbial biogeochemical cycling. However, there is a lack of studies on the effects of combinations of heavy metals on bacteria. In this study, we assessed the impact of eight metal contaminants on cell processes using a multiomics approach. The combination of metals had unexpected effects on cell physiology, including a disruption of iron homeostasis and decreased activity of important enzymes. This research highlights the need for multi-metal studies to understand the impacts of complex contaminants on microbial systems.
Article
Environmental Sciences
Michael P. Thorgersen, Jennifer L. Goff, Farris L. Poole, Kathleen F. Walker, Andrew D. Putt, Lauren M. Lui, Terry C. Hazen, Adam P. Arkin, Michael W. W. Adams
Summary: Environmental contamination affects microbial communities by limiting diversity and total metabolic activity. The study investigates metal contamination in sediment and finds that the operational speciation of certain elements changes due to contamination. Furthermore, the availability of essential elements also changes. The decreased operational speciation of phosphorus in contaminated sediment may increase the dependence of microbial communities on other phosphorus sources.
ENVIRONMENTAL POLLUTION
(2023)
Article
Multidisciplinary Sciences
Pragya Prakash, Sanjeev Chandrayan, Purnima Tiwari, Hare Ram Singh, Santosh Kumar Jha
Summary: In this study, multiple bacterial strains were isolated from soil and water, screened for glutaminase-free L-asparaginase activity, and purified for further characterization. The optimal working pH for purification was found to be 8.6, resulting in a purity level of 99.2% for the L-asparaginase enzyme. This developed purification process and characterization could be instrumental for naturally occurring enzymes, as most current processes focus on recombinant enzymes.
JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE
(2021)