58. Glycyl Radical Enzymes Catalyzing the Dehydration of Two Isomers of N-Methyl-4-hydroxyproline
Jiang L#, Yang Y#, Huang L, Zhou Y, An J, Zheng Y, Chen Y, Liu Y, Huang J, Ang EL, Zhao S, Zhao H, Liao R*, Wei Y*, Zhang Y*
ACS Catal. 2024 DOI: 10.1021/acscatal.4c00216
https://doi.org/10.1021/acscatal.4c00216
57. 2,6-diaminopurine (Z)-containing toehold probes improve genotyping sensitivity
Kang S#, Liu Q#, Zhang J, Zhang Y*, Qi H*
Biotechnol. Bioeng. 2023 DOI: 10.1002/bit.28642
https://doi.org/10.1002/bit.28642
56. Mechanistic investigation of a D to N mutation in DAHP synthase that dictates carbon flux into the shikimate pathway in yeast
Liu H, Xiao Q, Wu X, Ma H, Li J, Guo X, Liu Z, Zhang Y, Luo Y*
Commun Chem. 2023 DOI: 10.1038/s42004-023-00946-x
http://doi.org/10.1038/s42004-023-00946-x
55. Oxygenolytic sulfoquinovose degradation by an iron-dependent alkanesulfonate dioxygenase
Ye Z#, Wei Y#, Jiang L, Zhang Y*
iScience. 2023 DOI: 10.1016/j.isci.2023.107803
https://doi.org/10.1016/j.isci.2023.107803
54. Isethionate is an intermediate in the utilization of sulfoacetate as a terminal electron acceptor by the human gut pathobiont Bilophila wadsworthia
Liu X#, Wei Y#, Zhang J, Zhou Y, Du Y, Zhang Y*
J Biol Chem. 2023 DOI: 10.1016/j.jbc.2023.105010
https://doi.org/10.1016/j.jbc.2023.105010
53. A variant of the sulfoglycolytic transketolase pathway for the degradation of sulfoquinovose into sulfoacetate
Chu R#, Wei Y#, Liu J, Li B, Zhang J, Zhou Y, Du Y, Zhang Y*
Appl Environ Microbiol. 2023 DOI: 10.1128/aem.00617-23
https://doi.org/10.1128/aem.00617-23
52. Anaerobic phloroglucinol degradation by Clostridium scatologenes
Zhou Y#, Wei Y, Jiang L, Jiao X*, Zhang Y*
mBio. 2023 DOI:10.1128/mbio.01099-23
https://doi.org/10.1128/mbio.01099-23
51. Alternative Z-genome biosynthesis pathway shows evolutionary progression from archaea to phage
Tong Y#, Wu X#, Liu Y#, Chen H, Zhou Y, Jiang L, Li M*, Zhao S*, Zhang Y*
Nat Microbiol. 2023 DOI:10.1038/s41564-023-01410-1
https://doi.org/10.1038/s41564-023-01410-1
50. A (S)-3-hydroxybutyrate dehydrogenase belonging to the 3-hydroxyacyl-CoA dehydrogenase family facilitates hydroxyacid degradation in anaerobic bacteria
Zhou Y#, Wei Y#, Jiang L, Zhang Y*, Jiao X*
Appl Environ Microbiol. 2023 DOI:10.1128/aem.00366-23
http://dx.doi.org/10.1128/aem.00366-23
49. Anaerobic purinolytic enzymes enable dietary purine clearance by engineered gut bacteria
Tong Y#, Wei Y#, Ju Y#, Li P, Zhang Y, Li L, Gao L, Liu S, Liu D, Hu Y, Li Z, Yu H, Luo Y, Wang J, Wang Y*, Zhang Y*
Cell Chem Biol. 2023 DOI: 10.1016/j.chembiol.2023.04.008
https://doi.org/10.1016/j.chembiol.2023.04.008
48. Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization
Zhou S#, Wu Y#, Zhao Y#, Zhang Z, Jiang L, Liu L, Zhang Y, Tang J, Yuan Y*
Natl Sci Rev. 2023 DOI: 10.1093/nsr/nwad073
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47. New mechanisms for bacterial degradation of sulfoquinovose
Wei Y#, Tong Y, Zhang Y*
Biosci Rep. 2022 DOI：10.1042/BSR20220314
https://doi.org/10.1042/BSR20220314
46. Enzymatic synthesis of the unnatural nucleotide 2′-deoxyisoguanosine 5′-monophosphate
Zhao F#, Wei Y#, Wang Y, Zhou Y,Tong Y, Ang EL, Liu S*, Zhao H*, Zhang Y*
45. Anaerobic hydroxyproline degradation involving C-N cleavage by a glycyl radical enzyme
Duan Y#, Wei Y#, Xing M, Liu J, Jiang L, Lu Q, Liu X, Ang EL, Liao RZ, Yuchi Z*, Zhao H*, Zhang Y*
J Am Chem Soc. 2022 DOI:10.1021/jacs.2c01673
https://doi.org/10.1021/jacs.2c01673
44. Rapid antigen diagnostics as frontline testing in the COVID-19 pandemic
Xu J*, Kerr L, Jiang Y, Suo W, Zhang L, Lao T, Chen Y*, Zhang Y*
Small Science 2022 Jul 5 : 2200009
43. (S)-3-aminopiperidine-2,6-dione is a biosynthetic intermediate of microbial blue pigment indigoidine
Zhang Z, Li P, Wang M, Zhang Y, Wu B, Tao Y, Pan G, Chen Y*
mLife 2022 DOI: 10.1002/mlf2.12023
https://doi.org/10.1002/mlf2.12023
42. Genetic suppressors of Δgrx3 Δgrx4, lacking redundant multi-domain monothiol yeast glutaredoxins, rescue growth and iron homeostasis
Li G#, Nanjaraj A#, Dancis A* and Zhang Y*
Biosci Rep. 2022 DOI: 10.1042/bsr20212665
https://doi.org/10.1042/BSR20212665
41. Identification and characterization of the biosynthetic pathway of the sulfonolipid capnine
Liu Y#, Wei Y#, Teh TM, Liu D, Zhou Y, Zhao S, Ang EL, Zhao H*, Zhang Y*
Biochemistry 2022 DOI: 10.1021/acs.biochem.2c00102
https://pubs.acs.org/doi/10.1021/acs.biochem.2c00102
40. Structures of PKA-phospholamban complexes reveal a mechanism of familial dilated cardiomyopathy
Qin J, Zhang J, Lin L, Haji-Ghassemi O, Lin Z, Woycechowsky KJ, Petegem FV, Zhang Y*, Yuchi Z*
eLife 2022;11:e75346
https://elifesciences.org/articles/75346
39. Handheld microfluidic filtration platform enables rapid, low-cost and robust self-testing of SARS-CoV-2 virus
Xu J, Jiang J-C, Sun L, Liam Kerr, Paulsson, J, Zhang Y*, Lao T*
Small 2021 17(52):e2104009
https://doi.org/10.1002/smll.202104009
38. Mechanistically diverse pathways for sulfoquinovose degradation in Bacteria
Liu J#, Wei Y#, Ma K#, An J#, Liu X, Liu Y, Ang EL, Zhao H*, Zhang Y*
ACS Catal. 2021, 11: 14740-14750
https://pubs.acs.org/doi/10.1021/acscatal.1c04321
37. Biochemical investigation of 3-sulfopropionaldehyde reductase HpfD
An J#, Wei Y#, Liu J, Ang EL, Zhao H*, Zhang Y*
ChemBioChem. 2021, 22(19), 2862-2866
https://doi.org/10.1002/cbic.202100316
36. Structural and biochemical investigation of UTP cyclohydrolase
Zhang H#, Wei Y#, Lin L, Liu J, Chu R, Cao P, Ang EL, Zhao H*, Yuchi Z*, Zhang Y*
ACS Catal. 2021, 11(14), 8895–8901
https://pubs.acs.org/doi/10.1021/acscatal.1c02252
35. A widespread pathway for substitution of adenine by diaminopurine in phage genomes
Zhou Y#, Xu X#, Wei Y#, Cheng Y, Guo Y, Khudyakov I, Liu F, He P, Song Z, Li Z, Gao Y, Ang EL, Zhao H*, Zhang Y*, Zhao S*
Science 2021, 372(6541):512-516
https://www.science.org/doi/10.1126/science.abe4882
34. Structural Insights into the Diamide Modulation of Ryanodine Receptor.
Ma R#, Ghassemi OH#, Ma D, Jiang H, Lin L, Yao L, Samurkas A, Li Y, Wang Y, Wu S, Zhang Y, Murayama T, Moussian B, Petegem FV*, Yuchi Z*
Biophysical Journal. 2021, 120(3), 149a.
https://doi.org/10.1016/j.bpj.2020.11.1090
33. The glycyl radical enzyme arylacetate decarboxylase from Olsenella scatoligenes
Lu Q#, Wei Y#, Lin L, Liu L, Duan Y, Li Y, Zhai W, Liu Y, Ang EL, Zhao H*, Yuchi Z*, Zhang Y*
ACS Catal. 2021, 11(9) 5789–5794
https://pubs.acs.org/doi/10.1021/acscatal.1c01253
32. Glycyl Radical Enzymes and Sulfonate Metabolism in the Microbiome
Wei Y, Zhang Y*
Annual Rev Biochem. 2021, 90:817-846
https://doi.org/10.1146/annurev-biochem-080120-024103
31. Serological antibody testing in the COVID-19 pandemic: their molecular basis and applications
Jiang J-C, Zhang Y*
Biochem Soc Trans. 2020 48 (6): 2851–2863
https://doi.org/10.1042/BST20200744
30. A transaldolase-dependent sulfoglycolysis pathway in Bacillus megaterium DSM 1804
Liu Y#, Wei Y#, Zhou Y, Ang EL, Zhao H*, Zhang Y*
Biochem Biophys Res Comm. 2020 Dec 17, 533(4), 1109-1114
https://doi.org/10.1016/j.bbrc.2020.09.124
29. Structural basis for diamide modulation of ryanodine receptor
Ma R#, Ghassemi OH#, Ma D#, Jiang H, Lin L, Yao L, Samurkas A, Li Y, Wang Y, Cao P, Wu S, Zhang Y, Murayama T, Moussian B, Petegem FV*, Yuchi Z*
Nat Chem Biol. 2020 Nov;16(11):1246-1254
https://www.nature.com/articles/s41589-020-0627-5
28. A ferredoxin-dependent dihydropyrimidine dehydrogenase in Clostridium chromiireducens
Wang F#,Wei Y#, Lu Q, Ang EL, Zhao H*, Zhang Y*
Biosci Rep. 2020 Jul 31;40(7):BSR20201642
https://doi.org/10.1042/BSR20201642
27. Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate
Liu J#, Wei Y#, Lin L, Teng L, Yin J, Lu Q, Chen J, Zheng Y, Li Y, Xu R, Zhai W, Liu Y, Liu Y, Cao P, Ang EL, Zhao H*, Yuchi Z*, Zhang Y*
Proc Natl Acad Sci U S A. 2020 Jul 7;117(27):15599-15608
https://doi.org/10.1073/pnas.2003434117
26. A pathway for degradation of uracil to acetyl coenzyme A in Bacillus megaterium
Zhu D#, Wei Y #, Yin J, Liu D, Ang EL, Zhao H*, Zhang Y*
Appl & Environ Microbiol. 2020 Mar 18;86(7):e02837-19
https://doi.org/10.1128/AEM.02837-19
25. An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine
Yin J#, Wei Y#, Liu D, Hu Y, Lu Q, Ang EL, Zhao H*, Zhang Y*
J Biol Chem. 2019 Oct 25; 294(43): 15662-15671
https://doi.org/10.1074/jbc.RA119.010406
24. A gene cluster for taurine sulfur assimilation in an anaerobic human gut bacteria
Xing M#, Wei Y#, Hua G, Li M, Nanjaraj Urs AN, Wang F, Hu Y, Zhai W, Liu Y, Ang EL, Zhao H*, Zhang Y*
Biochem J. 2019 Aug 15;476(15):2271-2279
23. Identification and characterization of a new sulfoacetaldehyde reductase from the human gut bacterium Bifidobacterium kashiwanohense
Zhou Y#, Wei Y#, Nanjaraj A, Lin L, Xu T, Hu Y, Ang EL, Zhao H*, Yuchi Z*, Zhang Y*
Biosci Rep. 2019 Jun 20;39(6)
https://doi.org/10.1042/BSR20190715
22. A pathway for isethionate dissimilation in Bacillus krulwichiae
Tong Y#, Wei Y#, Hu Y, Ang EL, Zhao H*, Zhang Y*
Appl & Environ Microbiol. 2019 Jul 18;85(15)
https://doi.org/10.1128/AEM.00793-19
21. Biochemical and structural investigation of taurine:2-oxoglutarate aminotransferase from Bifidobacterium kashiwanohense
Li M#, Wei Y#, Yin J, Lin L, Zhou Y, Hua G, Cao P, Ang EL, Zhao H*, Yuchi Z*, Zhang Y*
Biochem J. 2019 Jun 11;476(11):1605-1619
https://doi.org/10.1042/BCJ20190206
20. Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria
Xing M#, Wei Y#, Zhou Y, Zhang J, Lin L, Hu Y, Hua G, Nanjaraj A, Liu D, Wang F, Guo C, Tong Y, Li M, Liu Y, Ang E, Zhao H*, Yuchi Z*, Zhang Y*
Nat Comm. 2019 Apr 8;10(1):1609
https://www.nature.com/articles/s41467-019-09618-8
19. Structure of glycerol dehydrogenase (GldA) from Escherichia coli
Zhang J#, Nanjaraj A#, Lin L, Zhou Y, Hu Y, Hua G, Gao Q, Yuchi Z*, Zhang Y*
Acta Crystallogr F. 2019 Mar 1;75(Pt 3):176-183
https://doi.org/10.1107/S2053230X19000037
18. Biochemical and structural investigation of sulfoacetaldehyde reductase from Klebsiella oxytoca
Zhou Y#, Wei Y#, Lin L, Xu T, Ang E, Zhao H*, Yuchi Z*, Zhang Y*
Biochem J. 2019 Feb 28;476(4):733-746
https://doi.org/10.1042/BCJ20190005
17. Cloning and expression of a non-ribosomal peptide synthetase to generate blue rose
Nanjaraj A, Hu Y, Li P, Yuchi Z, Chen Y*, Zhang Y*
ACS Synth Biol. 2019 Aug 16;8(8):1698-1704
https://pubs.acs.org/doi/10.1021/acssynbio.8b00187
16. Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole
Liu D#, Wei Y#, Liu X, Zhou Y, Jiang L, Yin J, Wang F, Hu Y, Nanjaraj A, Liu Y, Ang E, Zhao S*, Zhao H*, Zhang Y*
Nat Comm. 2018 Oct 11;9(1):4224
https://www.nature.com/articles/s41467-018-06627-x
15. Developing a colorimetric assay for Fe(II)/2-oxoglutarate-dependent dioxygenase
Guo C#, Hu Y#, Yang C, Nanjaraj A, Zhang Y*
Anal Biochem. 2018, May 1; 548: 109-114
https://doi.org/10.1016/j.ab.2018.02.013
14. Characterization of santalene synthases using an inorganic pyrophosphatase coupled colorimetric assay
Hua G#, Hu Y#, Yang C, Liu D, Mao Z, Zhang L, Zhang Y*
Anal Biochem. 2018, Apr 15; 547: 26-36
https://doi.org/10.1016/j.ab.2018.02.002
13. EPR studies of wild type and mutant Dre2 identify essential [2Fe–2S] and [4Fe–4S] clusters and their cysteine ligands
Zhang Y, Yang C, Dancis A, Nakamaru-Ogiso E
J Biochem. 2017, Jan; 161(1): 67-78
https://doi.org/10.1093/jb/mvw054
12. Conserved electron donor complex Dre2-Tah18 Is required for ribonucleotide reductase metallocofactor assembly and DNA synthesis
Zhang Y#, Li H#, Zhang C, An X, Liu L, Stubbe J, Huang M
Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17): E1695-704
https://doi.org/10.1073/pnas.140520411
11. Frataxin-bypassing Isu1: characterization of the bypass activity in cells and mitochondria
Yoon H, Knight SA, Pandey A, Pain J, Zhang Y, Pain D, Dancis A
Biochem J. 2014, Apr 1; 459(1): 71-81
https://doi.org/10.1042/BJ20131273
10. Investigation of in vivo roles of the carboxyl terminal tails of the small subunit (ββ’) of S. cerevisiae ribonucleotide reductase: contribution to cofactor formation and inter-subunit association within the active holoenzyme
Zhang Y, Liu L, Stubbe J. Huang M
J Biol Chem. 2013 May 17; 288(20): 13951-9
https://doi.org/10.1074/jbc.M113.467001
Selected as the “Papers of The Week”, highlighted at http://www.jbc.org/content/288/20/13960/suppl/DCAuthor_profile
9. Investigation of in vivo diferric tyrosyl radical formation in Saccharomyces cerevisiae Rnr2 protein requirement of Rnr4 and contribution of Grx3/4 and Dre2
Zhang Y, Liu L, Wu X, An X, Stubbe J, Huang M
https://doi.org/10.1074/jbc.M111.294074
J Biol Chem. 2011. Dec 2; 286(48): 41499-509
Selected as the “Papers of The Week”, highlighted at http://www.jbc.org/content/286/48/41499/suppl/DCAuthor_profile
http://www.asbmb.org/asbmbtoday/asbmbtoday_article.aspx?id=14939
8. Bacillus subtilis class Ib ribonucleotide reductase is a dimanganese(III)-tyrosyl radical enzyme
Zhang Y, Stubbe J
Biochemistry. 2011 Jun 28; 50(25): 5615-23
http://hdl.handle.net/1721.1/72129
7. Cytosolic monothiol glutaredoxins function in intracellular iron sensing and trafficking via their bound iron-sulfur cluster
Mühlenhoff U, Molik S, Godoy JR, Uzarska MA, Richter N, Seubert A, Zhang Y, Stubbe J, Pierrel F, Herrero E, Lillig CH, Lill R
Cell Metab. 2010 Oct 6; 12(4): 373-85
https://doi.org/10.1016/j.cmet.2010.08.001
6. Rim2, pyrimidine nucleotide exchanger, is needed for iron utilization in mitochondria
Yoon H, Zhang Y, Pain J, Lyver ER, Lesuisse E, Pain D, Dancis A
Biochem J. 2011 Nov 15; 440(1): 137-46
https://doi.org/10.1042/BJ20111036
5. Dre2, a conserved eukaryotic protein with both [2Fe-2S] and [4Fe-4S] clusters, functions in cytosolic iron-sulfur protein biogenesis
Zhang Y, Lyver, ER, Amutha B, Ohnishi, T, Pain, D, and Dancis, A
Mol Cell Biol. 2008 Sept; 28(18): 5569-82
https://doi.org/10.1128/MCB.00642-08
4. Mrs3p, Mrs4p, and frataxin provide iron for Fe-S cluster synthesis in mitochondria
Zhang Y, Lyver, ER, Knight, SAB, Pain, D, Lesuisse, E, and Dancis, A
J Biol Chem. 2006 Aug 11; 281(32): 22493-502
https://doi.org/10.1074/jbc.M604246200
3. Frataxin and mitochondrial carrier proteins, Mrs3p and Mrs4p, cooperate in providing iron for heme synthesis
Zhang Y, Lyver, ER, Knight, SAB, Lesuisse, E, and Dancis, A
J Biol Chem. 2005 May 20; 280(20): 19794-807
https://doi.org/10.1074/jbc.M500397200
2. Yeast frataxin solution structure, iron binding, and ferrochelatase interaction
He Y, Alam SL, Proteasa SV, Zhang Y, Lesuisse E, Dancis A, and Stemmler TL
Biochemistry. 2004 Dec 28; 43(51): 16254-62
https://pubs.acs.org/doi/full/10.1021/bi0488193
1. Overexpression of ccl1-2 can bypass the need for the putative apocytochrome chaperone CycH during the biogenesis of c-type cytochromes
Deshmukh M, May M, Zhang Y, Gabbert KK, Karberg KA, Kranz RG, and Daldal F
Mol Microbiol. 2002 Nov; 46(4)1069-1080
https://doi.org/10.1046/j.1365-2958.2002.03212.x
Patents
- 铁和α酮戊二酸依赖性双加氧酶的酶活检测体系和方法（A generally applicable iron and α-oxoglutarate dependent dioxygenase enzyme assay system and assay kit）. ZL 2015 1 0897467.5
- 催化谷氨酰胺合成靛蓝获得蓝色花卉的转基因方法 (A method to obtain transgenic blue rose by introducing non-ribosomal peptide synthetase catalyzing the formation of indigoidine from glutamine). pending
- 一种高产檀香油的重组酵母菌及其构建方法与应用( A genetically engineered baker yeast strain and its application in santalol oil production). Pending
- 半乳糖凝集素-3检测试剂盒（Galectin-3 quantitation kit）ZL 2017 10589093.x
- 波形蛋白的体外重折叠方法（A new methodology for Vimentin recombinant protein refolding）ZL 2017 10565618.6