Publications

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List of Publications (Niehaus lab members in bold font):

2024

Zmuda AJ, Kang XJ, Wissbroecker KB, Freund-Saxhaug K, Costa KC, Hegeman AD, Niehaus TD (2024) A universal metabolite repair enzyme removes a strong inhibitor of the TCA cycle. Nature Communications (provisionally accepted)

2023

Abdul Halim MF, Fonseca DR, Niehaus TD, Costa KC. (2023) Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis. J Biol Chem. 300: 105550.

Zmuda AJ and Niehaus TD (2023) Systems and strategies for plant protein expression. Methods in Enzymology 680: 3-34 

2022

Hillmann KB, Goethel ME, Erickson NA, Niehaus TD (2022) Identification of a S-(2-succino)cysteine breakdown pathway that uses a novel S-(2-succino) lyase. J Biol Chem. 298:102639

Hillmann KB and Niehaus TD (2022) Genome Sequences of Two Pseudomonas Isolates That Can Use Metformin as the Sole Nitrogen Source. Microbiol Resour Announc 18: e0063922

Haas NW, Jain A, Hying Z, Arif SJ, Niehaus TD, Gralnick JA, Fixen KR (2022) PioABC-Dependent Fe(II) Oxidation during Photoheterotrophic Growth on an Oxidized Carbon Substrate Increases Growth Yield. Appl Environ Microbiol 88: e0097422

Jeffryes JG, Lerma-Ortiz C, Liu F, Golubev A, Niehaus TD, Elbadawi-Sidhu M, Fiehn O, Hanson AD, Tyo KE, Henry CS (2022) Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions. Metab Eng. 69: 302-312

2021

Niehaus TD (2021) Phosphatases are involved in modulating the TCA cycle in plants. Molecular Plant 14: 1036-1037

2020

Niehaus TD and Hillmann KB (2020) Enzyme promiscuity, metabolite damage, and metabolite damage control systems of the tricarboxylic acid cycle. FEBS J 287: 1343-1358

2019

Niehaus TD, Patterson JA, Alexander DC, Folz JS, Pyc M, MacTavish BS, Bruner SD, Mullen RT, Fiehn O, Hanson AD (2019) The metabolite repair enzyme Nit1 is a dual-targeted amidase that disposes of damaged glutathione in Arabidopsis. Biochem J 476: 683-697

2018

Hanson AD, Amthor JS, Sun J, Niehaus TD, Gregory JF 3rd, Bruner SD, Ding Y (2018) Redesigning thiamin synthesis: Prospects and potential payoffs. Plant Sci 273: 92-99

Paerl RW, Bertrand EM, Rowland E, Schatt P, Mehiri M, Niehaus TD, Hanson AD, Riemann L, Yves-Bouget F (2018) Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis. Sci Rep 8: 5940

Niehaus TD, Elbadawi-Sidhu M, Huang L, Prunetti L, Gregory JF, de Crécy-Lagard V, Fiehn O, Hanson AD (2018) Evidence that the metabolite repair enzyme NAD(P)HX epimerase has a moonlighting function. Biosci Rep 38: pii: BSR20180223

Niehaus TD, Folz J, McCarty DR, Cooper AJL, Moraga D, Fiehn O, Hanson AD (2018) Identification of a metabolic disposal route for the oncometabolite S-(2-succino)cysteine in Bacillus subtilis. J Biol Chem 293: 8255-8263

2017

Niehaus TD, Elbadawi-Sidhu, M, de Crécy-Lagard V, Fiehn O, Hanson AD (2017) Discovery of a widespread prokaryotic 5-oxoprolinase that was hiding in plain sight. J Biol Chem 292: 16360-16367

Browne DR, Jenkins J, Schmutz J, Shu S, Barry K, Grimwood J, Chiniquy J, Sharma A, Niehaus TD, Weiss TL, Koppisch AT, Fox DT, Dhungana S, Okada S, Chappell J, Devarenne TP (2017) Draft Nuclear Genome Sequence of the Liquid Hydrocarbon-Accumulating Green Microalga Botryococcus braunii Race B (Showa). Genome Announc doi: 10.1128/genomeA.00215-17.

2016

Mimura M*, Zallot R*, Niehaus TD*, Hasnain G, Gidda SK, Nguyen TND, Anderson EM, Mullen RT, Brown G, Yakunin AF, de Crécy-Lagard V, Gregory JF, McCarty DR, Hanson AD (2016) Arabidopsis TH2 Encodes the Orphan Enzyme Thiamin Monophosphate Phosphatase. Plant Cell 28: 2683-2696

Linscott KB*, Niehaus TD*, Zhaung X, Bell SA, Chappell J (2016) Mapping a Kingdom-Specific Functional Domain of Squalene Synthase. Biochim Biophys Acta 1861: 1049-1057

Henry CS, Lerma-Ortiz C, Gerdes SY, Mullen JD, Colasanti R, Zhukov A, Frelin O, Thiaville JJ, Zallot R, Niehaus TD, Hasnain G, Conrad N, Hanson AD, de Crécy-Lagard V (2016) Systematic identification and analysis of frequent gene fusion events in metabolic pathways. BMC Genomics 17: 473

Lerma-Ortiz C, Jeffryes JG, Cooper AJ, Niehaus TD, Thamm AM, Frelin O, Aunins T, Fiehn O, de Crécy-Lagard V, Henry CS, Hanson AD (2016) 'Nothing of chemistry disappears in biology': the Top 30 damage-prone endogenous metabolites. Biochem Soc Trans 44: 961-971

2015

Niehaus TD, Thamm AM, de Crécy-Lagard V, Hanson AD (2015) Proteins of unknown biochemical function - A persistent problem and a roadmap to help overcome it. Plant Physiol 169:1436-1442

Jeffryes JG, Colastani RL, Elbadawi-Sidhu M, Kind T, Niehaus TD, Broadbelt LJ, Hanson AD, Fiehn O, Tyo KE, Henry CS (2015) MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. J Cheminform 7: 44

Niehaus TD, Gerdes S, Hodge-Hanson K, Zhukov A, Cooper AJ, ElBadawi-Sidhu M, Fiehn O, Downs DM, Hanson AD (2015) Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family. BMC Genomics 16: 382

2014

Bell SA, Niehaus TD, Nybo SE, Chappell J (2014) Structure-function mapping of key determinants for hydrocarbon biosynthesis by squalene and squalene synthase-like enzymes from the green alga Botryococcus braunii race B. Biochemistry 53: 7570-7581

Niehaus TD, Nguyen TN, Gidda SK, ElBadawi-Sidhu M, Lambrecht JA, McCarty DR, Downs DM, Cooper AJ, Fiehn O, Mullen RT, Hanson AD (2014) Arabidopsis and maize RidA proteins preempt reactive enamine/imine damage to branched-chain amino acid biosynthesis in plastids. Plant Cell 26: 3010-3022

Seaver SM, Gerdes S, Frelin O, Lerma-Ortiz C, Bradbury LM, Zallot R, Hasnain G, Niehaus TD, El Yacoubi B, Pasternak S, Olson R, Pusch G, Overbeek R, Stevens R, de Crécy-Lagard V, Ware D, Hanson AD, Henry CS (2014) High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proc Natl Acad Sci USA 111: 9645-9650

Marbaix AY, Tyteca D, Niehaus TD, Hanson AD, Linster CL, Van Schaftingen E (2014) Occurrence and subcellular distribution of the NADPHX repair system in mammals. Biochem J 460: 49-58

Niehaus TD, Richardson LG, Gidda SK, ElBadawi-Sidhu M, Meissen JK, Mullen RT, Fiehn O, Hanson AD (2014) Plants utilize a highly conserved system for repair of NADH and NADPH hydrates. Plant Physiol 165: 52-61

Khatri W, Hendrix R, Niehaus TD, Chappell J, Curtis WR (2014) Hydrocarbon production in high density Botryococcus braunii race B continuous culture. Biotechnol Bioeng 111: 493-503

2013

Bradbury LMT*, Niehaus TD*, Hanson AD (2013) Comparative genomics approaches to understanding and manipulating plant metabolism. Curr Opin Biotech 24: 278-284

2012

Niehaus TD, Kinison S, Okada S, Devarenne TP, Chappell J (2012) Functional Identification of triterpene methyltransferases from Botryococcus braunii Race B.  J Biol Chem 11: 8163-8173

2011

Niehaus TD, Okada S, Devarenne TP, Watt DS, Sviripa V, Chappell J (2011) Identification of unique mechanisms for triterpene biosynthesis in Botryococcus braunii.  Proc Natl Acad Sci USA 108: 12260-12265