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Metabolites
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The Thermodynamic Regulation of Microbial Metabolisms by Environmental Factors
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The Thermodynamic Regulation of Microbial Metabolisms by Environmental Factors

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Microbiology and Ecological Metabolomics".

Deadline for manuscript submissions: closed (15 May 2022) | Viewed by 5504

Special Issue Editors

Dr. Emily B. Graham

E-Mail Website
Guest Editor
1. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
2. School of Biological Sciences, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA
Interests: environmental science; microbial ecology; biogeochemistry; metabolomics; wildfire science
Special Issues, Collections and Topics in MDPI journals
Dr. Hyun-Seob Song

E-Mail Website
Guest Editor
Department of Biological Systems Engineering, Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska, 1400 R St, Lincoln, NE 68588, USA
Interests: microbial community modeling; metabolic modeling; metabolic network analysis; system optimization
Special Issues, Collections and Topics in MDPI journals
Dr. Jianqiu Zheng

E-Mail Website
Guest Editor
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
Interests: ecosystem science

Special Issue Information

Dear Colleagues,

Bioenergetics is a central tenet governing metabolic processes and underlies many model-based predictions of microbially-mediated biogeochemical cycling. New high-resolution techniques have allowed for greater insight into the thermodynamic drivers of microbial activity and the complexity of their interactions in natural environments, as well as their variation across environmental gradients. Such an understanding is important for constraining process-based models to improve predictions of microbial and biogeochemical responses to a changing climate. We seek submissions from scientists working in diverse disciplines who strive to understand microbial activity and biogeochemistry using bioenergetic tools at various spatio-temporal scales. Both experimental (lab and field) and modelling (empirical, numerical, and conceptual) approaches are welcome. Submissions that integrate experiments and models are especially encouraged, as well as submissions presenting results in the context of environmental change.

Dr. Emily B. Graham
Dr. Hyun-Seob Song
Dr. Jianqiu Zheng
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolic modeling
  • thermodynamics
  • microbial metabolism
  • genomics
  • metabolomics
  • climate change
  • environmental bioenergetics

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Published Papers (2 papers)

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Research

14 pages, 2635 KiB  
Article
Site-Differentiated Iron–Sulfur Cluster Ligation Affects Flavin-Based Electron Bifurcation Activity
by Courtney E. Wise, Anastasia E. Ledinina and Carolyn E. Lubner
Metabolites 2022, 12(9), 823; https://doi.org/10.3390/metabo12090823 - 1 Sep 2022
Cited by 3 | Viewed by 2323
Abstract
Electron bifurcation is an elegant mechanism of biological energy conversion that effectively couples three different physiologically relevant substrates. As such, enzymes that perform this function often play critical roles in modulating cellular redox metabolism. One such enzyme is NADH-dependent reduced-ferredoxin: NADP+ oxidoreductase [...] Read more.
Electron bifurcation is an elegant mechanism of biological energy conversion that effectively couples three different physiologically relevant substrates. As such, enzymes that perform this function often play critical roles in modulating cellular redox metabolism. One such enzyme is NADH-dependent reduced-ferredoxin: NADP+ oxidoreductase (NfnSL), which couples the thermodynamically favorable reduction of NAD+ to drive the unfavorable reduction of ferredoxin from NADPH. The interaction of NfnSL with its substrates is constrained to strict stoichiometric conditions, which ensures minimal energy losses from non-productive intramolecular electron transfer reactions. However, the determinants for this are not well understood. One curious feature of NfnSL is that both initial acceptors of bifurcated electrons are unique iron–sulfur (FeS) clusters containing one non-cysteinyl ligand each. The biochemical impact and mechanistic roles of site-differentiated FeS ligands are enigmatic, despite their incidence in many redox active enzymes. Herein, we describe the biochemical study of wild-type NfnSL and a variant in which one of the site-differentiated ligands has been replaced with a cysteine. Results of dye-based steady-state kinetics experiments, substrate-binding measurements, biochemical activity assays, and assessments of electron distribution across the enzyme indicate that this site-differentiated ligand in NfnSL plays a role in maintaining fidelity of the coordinated reactions performed by the two electron transfer pathways. Given the commonality of these cofactors, our findings have broad implications beyond electron bifurcation and mechanistic biochemistry and may inform on means of modulating the redox balance of the cell for targeted metabolic engineering approaches. Full article
(This article belongs to the Special Issue The Thermodynamic Regulation of Microbial Metabolisms by Environmental Factors)
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16 pages, 1872 KiB  
Article
iNovo479: Metabolic Modeling Provides a Roadmap to Optimize Bioproduct Yield from Deconstructed Lignin Aromatics by Novosphingobium aromaticivorans
by Alexandra M. Linz, Yanjun Ma, Samuel Scholz, Daniel R. Noguera and Timothy J. Donohue
Metabolites 2022, 12(4), 366; https://doi.org/10.3390/metabo12040366 - 18 Apr 2022
Cited by 4 | Viewed by 2273
Abstract
Lignin is an abundant renewable source of aromatics and precursors for the production of other organic chemicals. However, lignin is a heterogeneous polymer, so the mixture of aromatics released during its depolymerization can make its conversion to chemicals challenging. Microbes are a potential [...] Read more.
Lignin is an abundant renewable source of aromatics and precursors for the production of other organic chemicals. However, lignin is a heterogeneous polymer, so the mixture of aromatics released during its depolymerization can make its conversion to chemicals challenging. Microbes are a potential solution to this challenge, as some can catabolize multiple aromatic substrates into one product. Novosphingobium aromaticivorans has this ability, and its use as a bacterial chassis for lignin valorization could be improved by the ability to predict product yields based on thermodynamic and metabolic inputs. In this work, we built a genome-scale metabolic model of N. aromaticivorans, iNovo479, to guide the engineering of strains for aromatic conversion into products. iNovo479 predicted product yields from single or multiple aromatics, and the impact of combinations of aromatic and non-aromatic substrates on product yields. We show that enzyme reactions from other organisms can be added to iNovo479 to predict the feasibility and profitability of producing additional products by engineered strains. Thus, we conclude that iNovo479 can help guide the design of bacteria to convert lignin aromatics into valuable chemicals. Full article
(This article belongs to the Special Issue The Thermodynamic Regulation of Microbial Metabolisms by Environmental Factors)
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