Publications by authors named "Timothy Berry"

6 Publications

  • Page 1 of 1

Rhodoxanthin synthase from honeysuckle; a membrane diiron enzyme catalyzes the multistep conversation of β-carotene to rhodoxanthin.

Sci Adv 2020 Apr 22;6(17):eaay9226. Epub 2020 Apr 22.

DSM Nutritional Products, 60 Westview St, Lexington, MA 02421, USA.

Rhodoxanthin is a vibrant red carotenoid found across the plant kingdom and in certain birds and fish. It is a member of the atypical retro class of carotenoids, which contain an additional double bond and a concerted shift of the conjugated double bonds relative to the more widely occurring carotenoid pigments, and whose biosynthetic origins have long remained elusive. Here, we identify LHRS ( hydroxylase rhodoxanthin synthase), a variant β-carotene hydroxylase (BCH)-type integral membrane diiron enzyme that mediates the conversion of β-carotene into rhodoxanthin. We identify residues that are critical to rhodoxanthin formation by LHRS. Substitution of only three residues converts a typical BCH into a multifunctional enzyme that mediates a multistep pathway from β-carotene to rhodoxanthin via a series of distinct oxidation steps in which the product of each step becomes the substrate for the next catalytic cycle. We propose a biosynthetic pathway from β-carotene to rhodoxanthin.
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http://dx.doi.org/10.1126/sciadv.aay9226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176425PMC
April 2020

Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle.

Nat Microbiol 2019 05 11;4(5):864-875. Epub 2019 Mar 11.

Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Beneficial microbial associations enhance the fitness of most living organisms, and wood-feeding insects offer some of the most striking examples of this. Odontotaenius disjunctus is a wood-feeding beetle that possesses a digestive tract with four main compartments, each of which contains well-differentiated microbial populations, suggesting that anatomical properties and separation of these compartments may enhance energy extraction from woody biomass. Here, using integrated chemical analyses, we demonstrate that lignocellulose deconstruction and fermentation occur sequentially across compartments, and that selection for microbial groups and their metabolic pathways is facilitated by gut anatomical features. Metaproteogenomics showed that higher oxygen concentration in the midgut drives lignocellulose depolymerization, while a thicker gut wall in the anterior hindgut reduces oxygen diffusion and favours hydrogen accumulation, facilitating fermentation, homoacetogenesis and nitrogen fixation. We demonstrate that depolymerization continues in the posterior hindgut, and that the beetle excretes an energy- and nutrient-rich product on which its offspring subsist and develop. Our results show that the establishment of beneficial microbial partners within a host requires both the acquisition of the microorganisms and the formation of specific habitats within the host to promote key microbial metabolic functions. Together, gut anatomical properties and microbial functional assembly enable lignocellulose deconstruction and colony subsistence on an extremely nutrient-poor diet.
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http://dx.doi.org/10.1038/s41564-019-0384-yDOI Listing
May 2019

Degradation and Microbial Uptake of C Fullerols in Contrasting Agricultural Soils.

Environ Sci Technol 2017 02 23;51(3):1387-1394. Epub 2017 Jan 23.

Department of Agronomy, Purdue University , West Lafayette, Indiana 47907, United States.

The environmental fate of functionalized carbon nanomaterials (CNM) remains poorly understood. Using C-labeled nanomaterial we present the results of a study investigating the mineralization and microbial uptake of surface-functionalized C (fullerols) in agricultural soils with contrasting properties. Soil microcosms rapidly mineralized fullerol C, as determined by C-content in the respired CO, with higher fullerol mineralization in an organic, clay-rich soil versus a silty, low C soil (∼56.3% vs ∼30.9% fullerol C mineralized over 65 days). By tracking the enriched C from fullerol into microbial phospholipid fatty acids (PLFA) we also report, for the first time, the incorporation of nanomaterial-derived C into soil microbial biomass, primarily by fungi and Gram-negative bacteria. While more fullerol C was incorporated into PLFA in the organic C-rich soil (0.77% vs 0.19% of PLFA C), this soil incorporated fullerol C into biomass less efficiently than the silty, low C soil (0.13% and 0.84% of assimilated fullerol C, respectively). These results demonstrate that, in contrast to pristine C, surface functionalized C are unlikely to accumulate in surface soils and are readily mineralized by a range of soil microorganisms.
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http://dx.doi.org/10.1021/acs.est.6b04637DOI Listing
February 2017

Weathering of pyrogenic organic matter induces fungal oxidative enzyme response in single culture inoculation experiments.

Org Geochem 2016 Feb 12;92:32-41. Epub 2015 Dec 12.

Department of Earth, Atmospheric, and Planetary Sciences and the Purdue Climate Change Research Center, Purdue University, West Lafayette, IN 47907, USA.

The addition of pyrogenic organic matter (PyOM), the aromatic carbon-rich product of the incomplete combustion of plant biomass or fossil fuels, to soil can influence the rate of microbial metabolism of native soil carbon. The interaction of soil heterotrophs with PyOM may be governed by the surficial chemical and physical properties of PyOM that evolve with environmental exposure. We present results of a 36-day laboratory incubation investigating the interaction of a common white-rot fungus, with three forms of C-enriched (2.08 atom% C) PyOM derived from (450 °C): one freshly produced, and two artificially weathered (254 nm, UV light-water treatment and water-leaching alone). Analysis (FTIR, XPS) of the UV-weathered PyOM showed increased aliphatic C-H content and oxidation of aromatic carbon relative to both the original and water-leached PyOM. The addition of both weathered forms of PyOM stimulated (positively primed) fungal respiration of the growth media, while the unaltered PyOM mildly inhibited (negatively primed) respiration. Artificial weathering resulted in higher oxidative (laccase and peroxidase) enzyme activity than unaltered PyOM, possibly the result of a diminished capacity to bind reactive substrates and extracellular enzymes after weathering. However, and contrary to expectations, simple water-leached weathering resulted in a relatively higher enzyme activity and respiration than that of UV-weathering. The C content of respired CO indicated negligible fungal oxidation of PyOM for all treatments, demonstrating the overall low microbial reactivity of this high temperature PyOM. The increased enzymatic and positive priming response of to weathered PyOM highlights the importance of weathering-induced chemistry in controlling PyOM-microbe-soil carbon interactions.
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http://dx.doi.org/10.1016/j.orggeochem.2015.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5897110PMC
February 2016

Soil microbial response to photo-degraded C60 fullerenes.

Environ Pollut 2016 Apr 15;211:338-45. Epub 2016 Jan 15.

Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette 47907, IN, USA. Electronic address:

Recent studies indicate that while unfunctionalized carbon nanomaterials (CNMs) exhibit very low decomposition rates in soils, even minor surface functionalization (e.g., as a result of photochemical weathering) may accelerate microbial decay. We present results from a C60 fullerene-soil incubation study designed to investigate the potential links between photochemical and microbial degradation of photo-irradiated C60. Irradiating aqueous (13)C-labeled C60 with solar-wavelength light resulted in a complex mixture of intermediate products with decreased aromaticity. Although addition of irradiated C60 to soil microcosms had little effect on net soil respiration, excess (13)C in the respired CO2 demonstrates that photo-irradiating C60 enhanced its degradation in soil, with ∼ 0.78% of 60 day photo-irradiated C60 mineralized. Community analysis by DGGE found that soil microbial community structure was altered and depended on the photo-treatment duration. These findings demonstrate how abiotic and biotic transformation processes can couple to influence degradation of CNMs in the natural environment.
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http://dx.doi.org/10.1016/j.envpol.2015.12.025DOI Listing
April 2016

Oxidative enzymatic response of white-rot fungi to single-walled carbon nanotubes.

Environ Pollut 2014 Oct 21;193:197-204. Epub 2014 Jul 21.

Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States.

Although carbon nanomaterials such as single-walled carbon nanotubes (SWCNT) are becoming increasingly prevalent in manufacturing, there is little knowledge on the environmental fate of these materials. Environmental degradation of SWCNT is hindered by their highly condensed aromatic structure as well as the size and aspect ratio, which prevents intracellular degradation and limits microbial decomposition to extracellular processes such as those catalyzed by oxidative enzymes. This study investigates the peroxidase and laccase enzymatic response of the saprotrophic white-rot fungi Trametes versicolor and Phlebia tremellosa when exposed to SWCNTs of different purity and surface chemistry under different growth conditions. Both unpurified, metal catalyst-rich SWCNT and purified, carboxylated SWCNTs promoted significant changes in the oxidative enzyme activity of the fungi while pristine SWCNT did not. These results suggest that functionalization of purified SWCNT is essential to up regulate enzymes that may be capable of decomposing CNT in the environment.
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http://dx.doi.org/10.1016/j.envpol.2014.06.013DOI Listing
October 2014