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1. Aromatic acid metabolism in Methylobacterium extorquens reveals interplay between methylotrophic and heterotrophic pathways

   https://doi.org/10.1128/aem.00761-25  

   Govindaraju, Alekhya M; Martinez-Gomez, Norma Cecilia (September 2025, Applied and Environmental Microbiology)

   Bose, Arpita (Ed.)

   ABSTRACT Efforts toward microbial conversion of lignin to value-added products face many challenges because lignin’s methoxylated aromatic monomers release toxic C₁byproducts such as formaldehyde. The ability to grow on methoxylated aromatic acids (e.g., vanillic acid) has been identified in certain clades of methylotrophs, bacteria characterized by their unique ability to tolerate and metabolize high concentrations of formaldehyde. Here, we use a phyllosphere methylotroph isolate,Methylobacterium extorquensSLI 505, as a model to identify the fate of formaldehyde during methylotrophic growth on vanillic acid.M. extorquensSLI 505 displays concentration-dependent growth phenotypes on vanillic acid without concomitant formaldehyde accumulation. We conclude thatM. extorquensSLI 505 overcomes metabolic bottlenecks from simultaneous assimilation of multicarbon and C₁intermediates by allocating formaldehyde toward dissimilation and assimilating the ring carbons of vanillic acid heterotrophically. We correlate this strategy with maximization of bioenergetic yields and demonstrate that formaldehyde dissimilation for energy generation rather than formaldehyde detoxification is advantageous for growth on aromatic acids.M. extorquensSLI 505 also exhibits catabolite repression during growth on methanol and low concentrations of vanillic acid, but no diauxic patterns during growth on methanol and high concentrations of vanillic acid. Results from this study outline metabolic strategies employed byM. extorquensSLI 505 for growth on a complex single substrate that generates both C₁and multicarbon intermediates and emphasizes the robustness ofM. extorquensfor biotechnological applications for lignin valorization.IMPORTANCELignin, one of the most abundant and renewable carbon sources on Earth, is a promising alternative to non-renewable fossil fuels used to produce petrochemicals. Degradation of lignin releases toxic C₁byproducts such as formaldehyde, and thus most microorganisms are not suitable for biorefining lignin. By contrast,Methylobacterium extorquensSLI 505 is capable of growth on high concentrations of aromatic acids without concomitant formaldehyde accumulation. In addition, we show that the growth ofM. extorquensSLI 505 on aromatic acids is coupled to the production of the bioplastic, polyhydroxybutyrate. Aromatic acids serve as a model by which to understand howM. extorquensSLI 505 balances methylotrophic and heterotrophic pathways during growth to provide strategies for growth optimization when using complex substrates in both ecological and industrial fermentation applications. 

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2. Hyperaccumulation of Gadolinium by Methylorubrum extorquens AM1 Reveals Impacts of Lanthanides on Cellular Processes Beyond Methylotrophy

   https://doi.org/10.3389/fmicb.2022.820327  

   Good, Nathan M.; Lee, Harvey D.; Hawker, Emily R.; Su, Morgan Z.; Gilad, Assaf A.; Martinez-Gomez, N. Cecilia (March 2022, Frontiers in Microbiology)

   Lanthanides (Ln) are a new group of life metals, and many questions remain regarding how they are acquired and used in biology. Methylotrophic bacteria can acquire, transport, biomineralize, and use Ln as part of a cofactor complex with pyrroloquinoline quinone (PQQ) in alcohol dehydrogenases. For most methylotrophic bacteria use is restricted to the light Ln, which range from lanthanum to samarium (atomic numbers 57–62). Understanding how the cell differentiates between light and heavy Ln, and the impacts of these metals on the metabolic network, will advance the field of Ln biochemistry and give insights into enzyme catalysis, stress homeostasis, and metal biomineralization and compartmentalization. We report robust methanol growth with the heavy Ln gadolinium by a genetic variant of the model methylotrophic bacterium Methylorubrum extorquens AM1, named evo -HLn, for “ evo lved for H eavy L antha n ides.” A non-synonymous single nucleotide polymorphism in a cytosolic hybrid histidine kinase/response regulator allowed for sweeping transcriptional alterations to heavy metal stress response, methanol oxidation, and central metabolism. Increased expression of genes for Ln acquisition and uptake, production of the Ln-chelating lanthanophore, PQQ biosynthesis, and phosphate transport and metabolism resulted in gadolinium hyperaccumulation of 36-fold with a trade-off for light Ln accumulation. Gadolinium was hyperaccumulated in an enlarged acidocalcisome-like compartment. This is the first evidence of a bacterial intracellular Ln-containing compartment that we name the “lanthasome.” Carotenoid and toblerol biosynthesis were also upregulated. Due to its unique capabilities, evo -HLn can be used to further magnetic resonance imaging (MRI) and bioremediation technologies. In this regard, we show that gadolinium hyperaccumulation was sufficient to produce MRI contrast in whole cells, and that evo -HLn was able to readily acquire the metal from the MRI contrast agent gadopentetic acid. Finally, hyperaccumulation of gadolinium, differential uptake of light and heavy Ln, increased PQQ levels, and phosphate transport provide new insights into strategies for Ln recovery. 

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3. Laboratory Performance Evaluation of a Low-Cost Electrochemical Formaldehyde Sensor

   https://doi.org/10.3390/s23177444  

   Pei, Zheyuan; Balitskiy, Maxim; Thalman, Ryan; Kelly, Kerry E. (September 2023, Sensors)

   Formaldehyde is a known human carcinogen and an important indoor and outdoor air pollutant. However, current strategies for formaldehyde measurement, such as chromatographic and optical techniques, are expensive and labor intensive. Low-cost gas sensors have been emerging to provide effective measurement of air pollutants. In this study, we evaluated eight low-cost electrochemical formaldehyde sensors (SFA30, Sensirion®, Staefa, Switzerland) in the laboratory with a broadband cavity-enhanced absorption spectroscopy as the reference instrument. As a group, the sensors exhibited good linearity of response (R2 > 0.95), low limit of detection (11.3 ± 2.07 ppb), good accuracy (3.96 ± 0.33 ppb and 6.2 ± 0.3% N), acceptable repeatability (3.46% averaged coefficient of variation), reasonably fast response (131–439 s) and moderate inter-sensor variability (0.551 intraclass correlation coefficient) over the formaldehyde concentration range of 0–76 ppb. We also systematically investigated the effects of temperature and relative humidity on sensor response, and the results showed that formaldehyde concentration was the most important contributor to sensor response, followed by temperature, and relative humidity. The results suggest the feasibility of using this low-cost electrochemical sensor to measure formaldehyde concentrations at relevant concentration ranges in indoor and outdoor environments. 

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4. An enzymatic activation of formaldehyde for nucleotide methylation

   https://doi.org/10.1038/s41467-021-24756-8  

   Bou-Nader, Charles; Stull, Frederick W.; Pecqueur, Ludovic; Simon, Philippe; Guérineau, Vincent; Royant, Antoine; Fontecave, Marc; Lombard, Murielle; Palfey, Bruce A.; Hamdane, Djemel (December 2021, Nature Communications)

   Abstract Folate enzyme cofactors and their derivatives have the unique ability to provide a single carbon unit at different oxidation levels for the de novo synthesis of amino-acids, purines, or thymidylate, an essential DNA nucleotide. How these cofactors mediate methylene transfer is not fully settled yet, particularly with regard to how the methylene is transferred to the methylene acceptor. Here, we uncovered that the bacterial thymidylate synthase ThyX, which relies on both folate and flavin for activity, can also use a formaldehyde-shunt to directly synthesize thymidylate. Combining biochemical, spectroscopic and anaerobic crystallographic analyses, we showed that formaldehyde reacts with the reduced flavin coenzyme to form a carbinolamine intermediate used by ThyX for dUMP methylation. The crystallographic structure of this intermediate reveals how ThyX activates formaldehyde and uses it, with the assistance of active site residues, to methylate dUMP. Our results reveal that carbinolamine species promote methylene transfer and suggest that the use of a CH 2 O-shunt may be relevant in several other important folate-dependent reactions. 

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5. Tight Regulation of Extracellular Superoxide Points to Its Vital Role in the Physiology of the Globally Relevant Roseobacter Clade

   https://doi.org/10.1128/mBio.02668-18  

   Hansel, Colleen M.; Diaz, Julia M.; Plummer, Sydney; Giovannoni, Stephen J. (April 2019, mBio)

   ABSTRACT There is a growing appreciation within animal and plant physiology that the reactive oxygen species (ROS) superoxide is not only detrimental but also essential for life. Yet, despite widespread production of extracellular superoxide by healthy bacteria and phytoplankton, this molecule remains associated with stress and death. Here, we quantify extracellular superoxide production by seven ecologically diverse bacteria within the Roseobacter clade and specifically target the link between extracellular superoxide and physiology for two species. We reveal for all species a strong inverse relationship between cell-normalized superoxide production rates and cell number. For exponentially growing cells of Ruegeria pomeroyi DSS-3 and Roseobacter sp. strain AzwK-3b, we show that superoxide levels are regulated in response to cell density through rapid modulation of gross production and not decay. Over a life cycle of batch cultures, extracellular superoxide levels are tightly regulated through a balance of both production and decay processes allowing for nearly constant levels of superoxide during active growth and minimal levels upon entering stationary phase. Further, removal of superoxide through the addition of exogenous superoxide dismutase during growth leads to significant growth inhibition. Overall, these results point to tight regulation of extracellular superoxide in representative members of the Roseobacter clade, consistent with a role for superoxide in growth regulation as widely acknowledged in fungal, animal, and plant physiology. IMPORTANCE Formation of reactive oxygen species (ROS) through partial reduction of molecular oxygen is widely associated with stress within microbial and marine systems. Nevertheless, widespread observations of the production of the ROS superoxide by healthy and actively growing marine bacteria and phytoplankton call into question the role of superoxide in the health and physiology of marine microbes. Here, we show that superoxide is produced by several marine bacteria within the widespread and abundant Roseobacter clade. Superoxide levels outside the cell are controlled via a tightly regulated balance of production and decay processes in response to cell density and life stage in batch culture. Removal of extracellular superoxide leads to substantial growth inhibition. These findings point to an essential role for superoxide in the health and growth of this ubiquitous group of microbes, and likely beyond. 

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