Research

Phage non-canonical DNA

Glycyl Radical Enzymes (GREs)

Pyrimidine degradation pathways

Purine degradation pathways

Sulfonate metabolism

Synthetic Biology

Phage non-canonical DNA

Selected Papers

1. Science 2021, 372(6541):512-516.

DNA modifications vary in form and function but generally do not alter Watson-Crick base pairing. Diaminopurine (Z) is an exception because it completely replaces adenine and forms three hydrogen bonds with thymine in cyanophage S-2L genomic DNA. However, the biosynthesis, prevalence, and importance of Z genomes remain unexplored. Here, we report a multienzyme system that supports Zgenome synthesis. We identified dozens of globally widespread phages harboring such enzymes, and we further verified the Z genome in one of these phages, Acinetobacter phage SH-Ab 15497, by using liquid chromatography with ultraviolet and mass spectrometry. The Z genome endows phages with evolutionary advantages for evading the attack of host restriction enzymes, and the characterization of its biosynthetic pathway enables dZ-DNA production on a large scale for a diverse range of applications.

Z-genome biosynthetic pathway


Validation of Z incorporation in the genome of Acinetobacter phage SH-Ab 15497

2.Nat Microbiol 2023, Jun 12.

Many bacteriophages evade bacterial immune recognition by substituting adenine with 2,6-diaminopurine (Z) in their genomes. The Z-genome biosynthetic pathway involves PurZ that belongs to the PurA (adenylosuccinate synthetase) family and bears particular similarity to archaeal PurA. However, how the transition of PurA to PurZ occurred during evolution is not clear; recapturing this process may shed light on the origin of Z-containing phages. Here we describe the computer-guided identifcation and biochemical characterization of a naturally existing PurZ variant, PurZ0, which uses guanosine triphosphate as the phosphate donor rather than the ATP used by PurZ. The atomic resolution structure of PurZ0 reveals a guanine nucleotide binding pocket highly analogous to that of archaeal PurA. Phylogenetic analyses suggest PurZ0 as an intermediate during the evolution of archaeal PurA to phage PurZ. Maintaining the balance of diferent purines necessitates further evolvement of guanosine triphosphate-using PurZ0 to ATP-using PurZ in adaptation to Z-genome life.

SSN and substrate-binding site analysis of PurZ and its variants. a, SSN analysis of PurZ and its variant. The full network is displayed at an E-value of 10−37. The network forms two ‘clusters’, with the PurZ cluster in blue and the PurZ0 cluster in red. The diamond-labelled nodes are the representative sequences of the two clusters. The enlarged 1–5 nodes in the red cluster are A0A7L7SI10, A0A6M3T9C6, A0A4D6E427, A0A4P8N3X9 and A0A427UIJ1, respectively, and were verified for enzymatic activity in this study. The enlarged 1–5 nodes in the blue cluster are G3FFN6, A0A7U3TBV6, A0A2L0V130, A0A2H5BHJ6 and A0A5C7KHP9, respectively, and have been verified for enzymatic activity by us as well as others4,5,7 . b, Key residues and known or predicted substrates of PurA, PurZ and PurZ0. c, Key residues interacting with different substrates in PurA and PurZ.

Glycyl Radical Enzymes (GREs)

Selected Papers

1. Annual Rev Biochem 2021, 90:817-846.

Sulfonates include diverse natural products and anthropogenic chemicals and are widespread in the environment. Many bacteria can degrade sulfonates and obtain sulfur, carbon, and energy for growth, playing important roles in the biogeochemical sulfur cycle. Cleavage of the inert sulfonate C–S bond involves a variety of enzymes, cofactors, and oxygen-dependent and oxygen-independent catalytic mechanisms. Sulfonate degradation by strictly anaerobic bacteria was recently found to involve C–S bond cleavage through O2-sensitive free radical chemistry, catalyzed by glycyl radical enzymes (GREs). The associated discoveries of new enzymes and metabolic pathways for sulfonate metabolism in diverse anaerobic bacteria have enriched our understanding of sulfonate chemistry in the anaerobic biosphere. An anaerobic environment of particular interest is the human gut microbiome where sulfonate degradation by sulfate- and sulfite-reducing bacteria (SSRB) produces H2S, a process linked to certain chronic diseases and conditions.

Mechanistic model for G• cofactor formation

2. Nat. Comm. 2018 Oct 11;9(1):4224.

Here we report the use of comparative genomics for the discovery of indoleacetate decarboxylase, an O2-sensitive glycyl radical enzyme catalysing the decarboxylation of indoleacetate to form skatole as the terminal step of tryptophan fermentation in certain anaerobic bacteria. We describe its biochemical characterization and compare it to other glycyl radical decarboxylases. Indoleacetate decarboxylase may serve as a genetic marker for the identification of skatole-producing environmental and human-associated bacteria, with impacts on human health and the livestock industry.

Why does shit stink?
Pathways for fermentation of Tryptophan (Trp). Trp is converted into skatole. IAD, indoleacetate decarboxylase


3. Nat. Comm. 2019 Apr 8;10(1):1609.

Here, we describe the structural and biochemical characterization of an oxygen- sensitive enzyme that catalyzes the radical-mediated C-S bond cleavage of isethionate to form sulfite and acetaldehyde. We demonstrate its involvement in pathways that enables C2 sulfonates to be used as terminal electron acceptors for anaerobic respiration in sulfate- and sulfite-reducing bacteria. Furthermore, it plays a key role in converting bile salt-derived taurine into H2S in the disease-associated gut bacterium Bilophila wadsworthia.

C2 sulfonate induced IseG-dependent pathway in SSRB


4. Proc Natl Acad Sci U S A. 2020 Jul 7;117(27):15599-15608.

Here, we report the discovery and charac- terization of two O2-sensitive glycyl radical enzymes that use distinct mechanisms for DHPS degradation. DHPS-sulfolyase (HpsG) in sulfate- and sulfite-reducing bacteria catalyzes C–S cleavage to release sulfite for use as a terminal electron acceptor in respiration, producing H2S. DHPS-dehydratase (HpfG), in fermenting bacteria, catalyzes C–O cleavage to generate 3-sulfopropionaldehyde, subsequently reduced by the NADH-dependent sulfopropionaldehyde reductase (HpfD).

Radical-dependent (S)-DHPS degradation pathways involving the sulfolyase HpsG and dehydratase HpfG.


5. ACS Catalysis 2021, 11(9) 5789–5794.

Here, we report the discovery and structural and biochemical investigation of a fourth GRE arylacetate decarboxylase (AAD) from Olsenella scatoligenes that catalyzes HPA decarboxylation. AAD also catalyzes the decarboxylation of p-aminophenylacetate, which is not a substrate of HPAD, and lacks the Fe−S cluster containing small subunit.

The structure of AAD in complex with p-hydroxyphenylacetate
was determined by X-ray crystallography. The differing substrate ranges and active site structures of AAD and HPAD suggest distinct catalytic mechanisms, underscoring the diversity of radicalmediated decarboxylation reactions.


6. J. Am. Chem. Soc. 2022, 144, 22, 9715–9722

Here, we report a pathway for anaerobic hydroxyproline degradation that involves a new GRE, trans-4-hydroxy-D-proline (t4D-HP) C−N-lyase (HplG). In this pathway, cis-4-hydroxy-L-proline (c4L HP)isfirstisomerized to t4D-HP, followed by radical-mediated ring opening by HplG to give 2-amino-4-ketopentanoate (AKP), the first example of a ring opening reaction catalyzed by a GRE 1,2-eliminase. Subsequent cleavage by AKP thiolase (OrtAB) yields acetyl-CoA and D-alanine.

Proposed pathway for trans-4-hydroxy-D- proline degradation by the CbHplG-containing C. bacterium. c4L-HP, cis-4-hydroxy-L-proline; t4D-HP, trans-4-hydroxy-D-proline; AKP, 2-amino-4- ketopentanoate; PLP, pyridoxal phosphate; HplF, c4L-HP epimerase; HplG, GRE t4D-HP lyase; OrtAB, AKP thiolase; ALR, alanine racemase; and ALD, L-alanine dehydrogenase.


Pyrimidine degradation pathways

Selected Papers

1. J Biol Chem. 2019 Oct 25; 294(43): 15662-15671.

Here, we report the biochemical characterization of a β-alanine:2-oxoglutarate aminotransferase (PydD) and a NAD(P)H-dependent malonic semialdehyde reductase (PydE) from a pyrimidine degradation gene cluster in the bacterium Lysinibacillus massiliensis.

Association of PydD and PydE with reductive pyrimidine catabolism. 
A) Genome neighborhoods of close homologs of PydA and PydB in different bacteria with some containing PydD and PydE. B) Proposed pathway for β-alanine degradation by PydDE.


2. Appl & Environ Microbiol. 2020 Mar 18;86(7):e02837-19.

Here we report the characterization of a β-alanine:pyruvate aminotransferase (PydD2), and a NAD+-dependent malonic semialdehyde dehydrogenase (MSDH), from a reductive pyrimidine catabolism gene cluster in Bacillus megaterium.

Variants of the extended reductive pyrimidine catabolism (Pyd) pathway. A) Representative extended Pyd pathway gene clusters in Firmicutes bacteria. B) Comparison of the two extended reductive pyrimidine degradation pathways, involving either PydD1 and PydE as previously reported (8),or PydD2 and MSDH as described in this study.


3. Biosci Rep. 2020 Jul 31;40(7):BSR20201642.

Here, we report the biochemical characterization of a Clostridial PydA homolog (PydAc) from a Pyd gene cluster in the strict anaerobic bacterium Clostridium chromiireducens.

Pyd gene clusters in bacteria. PydA, dihydropyrimidine dehydrogenase; PydB, di- hydropyrimidinase; PydC, ureidopropionase; PydD, β-alanine aminotransferase; PydE, malonic semialdehyde reductase; MSDH, malonic semialdehyde dehydrogenase; PydA1, dihydropyrimidine dehydrogenase Fdx1 and FAD / NADPH domains; PydA2, dihy- dropyrimidine dehydrogenase FMN and Fdx2 domains; PydAc, Clostridial dihydropyrimidine dehydrogenase homolog.


4. ACS Catalysis 2021, 11(14), 8895–8901.

The URC (uracil catabolism) pathway, present in fungi and bacteria, enables pyrimidines to be used as nitrogen sources for growth. Although its mechanistic details are unclear, uracil is thought to be first converted into a uridine nucleotide, followed by pyrimidine ring cleavage catalyzed by Urc1p, a distant homologue of GTP cyclohydrolase II (RibA). Here we report a biochemical investigation of Urc1p from Pichia pastoris (Komagataella phaffii) (PpUrc1p) and its bacterial homologue from Rhodococcus wratislaviensis (RwUrcA). Like RibA, the substrate of recombinant PpUrc1p was found to be a nucleoside triphosphate (UTP), and turnover was accompanied by the release of pyrophosphate. The products phosphoribosylurea and malonic semialdehyde were confirmed by mass spectrometry. We also determined a 1.60 Å crystal structure of RwUrcA, which included a C-terminal segment that is not resolved in RibA structures reported to date, containing a conserved Lys residue positioned to interact with the UTP α-phosphate. Further mutagenesis studies revealed roles of active site residues in substrate binding and catalysis, providing insights into the mechanism by which Urc1p catalyzes two sequential hydrolyses at C6 and C4 for the uracil ring.

Crystal structure of Rhodococcus wratislaviensis UrcA. (A) Crystal structure of dUTP bound RwUrcA showing a dimer in asymmetric unit. (B) Enlarged view of the active site of RwUrcA crystal structure. 2Fo − Fc electron densities for dUTP are shown at 1.0σ, and the best-fit model for dUTP into the electron density is shown. The electron density in the pyrophosphate region is well-defined, while that in the UMP region is fragmented, possibly corresponding to a mixture of reaction products and intermediates. (C) Structural model of UTP-bound RwUrcA, predicted by induced-fit-docking.



Purine degradation pathways

Selected Works

1. Cell Chemical Biology. 2023 July 20; 30: 1–11.

Here we report the identification and characterization of these enzymes, which include four hydrolases belonging to different enzyme families, and a prenyl-flavin mononucleotide-dependent decarboxylase. Introduction of the first two hydrolases to Escherichia coli Nissle 1917 enabled its anaerobic growth on xanthine as the sole nitrogen source. Oral supplementation of these engineered probiotics ameliorated hyperuricemia in a Drosophila melanogaster model, including the formation of renal uric acid stones and a shortened lifespan, providing a route toward the development of purinolytic probiotics.




Sulfonate metabolism


A series of papers by the Zhang lab taken together describe the interspecies taurine degradation network in the human gut microbiome.

Selected Papers

1. Biochem J. 2019 Feb 28;476(4):733-746.

Sulfoacetaldehyde reductase (IsfD) is a member of the short-chain dehydrogenase/reduc- tase (SDR) family, involved in nitrogen assimilation from aminoethylsulfonate (taurine) in certain environmental and human commensal bacteria.

IsfD-dependent metabolic pathway and genome neighborhood of IsfD.
(A) Schematic diagram showing the taurine nitrogen assimilatory pathway in bacteria. (B) Genome neighborhood of IsfD in Klebsiella oxytoca and Chromohalobacter salexigens


2. Biochem J. 2019 Jun 11;476(11):1605-1619.

Here we report the biochemical and structural characterization of a new taurine:2-oxoglutarate aminotransferase from the human gut bacterium Bifidobacterium kashiwanohense (BkToa).

Proposed taurine nitrogen assimilation pathway and related gene clusters.  A) Proposed taurine nitrogen assimilation pathway in Klebsiella oxytoca TauN1, and Chromohalobacter salexigens. B) Comparison of the BkToa, KoToa and CsToa genome neighbourhoods.


3. Biosci Rep. 2019 Jun 20;39(6).

Here we report the structural and biochemical characterization of a sulfoacetaldehyde reductase from the human gut fermenting bacterium Bifidobacterium kashiwanohense (BkTauF). 

Gene clusters and metabolic pathways involving different sulfoacetaldehyde reductases isozymes
(A) Gene clusters containing the sulfoacetaldehyde reductases IsfD (in Chromohalobacter salexigens), TauF (in Bifidobacterium kashiwanohense) and SarD (in Bilophila wadsworthia).
(B) Schematic diagram showing two bacterial taurine nitrogen assimilation pathways relying on different sulfoacetaldehyde reductase isozymes. The pathway in C. salexigens relies on IsfD (red), while the putative pathway in B. kashiwanohense relies on TauF (green). (C) Schematic diagram showing the taurine dissimilation pathway inB. wadsworthia.


4. Biochem J. 2019 Aug 15;476(15):2271-2279.

Here we report the biochemical characterization of an anaerobic pathway for taurine sulfur assimilation in a strain of Clostridium butyricum from the human gut. In this pathway, taurine is first converted to hydroxyethylsulfonate (isethionate), followed by C–S cleavage by the O2-sensitive isethionate sulfolyase IseG, recently identified in sulfate- and sulfite-reducing bacteria.

Figure 1. Occurrence of IseG in fermenting bacteria.
(A) Representative IseG-containing gene clusters in fermenting bacteria, putatively involved in taurine sulfur assimilation.
(B) Schematic diagram showing the proposed pathway for taurine sulfur assimilation by the IseG-containing gut bacterium Clostridium butyricum.


5. Nat. Comm. 2019 Apr 8;10(1):1609.

Here, we describe the structural and biochemical characterization of an oxygen- sensitive enzyme that catalyzes the radical-mediated C-S bond cleavage of isethionate to form sulfite and acetaldehyde. We demonstrate its involvement in pathways that enables C2 sulfonates to be used as terminal electron acceptors for anaerobic respiration in sulfate- and sulfite-reducing bacteria. Furthermore, it plays a key role in converting bile salt-derived taurine into H2S in the disease-associated gut bacterium Bilophila wadsworthia.

C2 sulfonate induced IseG-dependent pathway in SSRB


6. ACS Catalysis 2021, 11: 14740-14750.

Here, we report the discovery of three additional sulfoglycolysis pathways, the first involving a transketolase (sulfo-TK) related to that in the pentose phosphate pathway, the second involving oxygenolytic C−S cleavage of SQ by a flavin-dependent alkanesulfonate monooxygenase (sulfo-ASMO), and the third being a variant of the sulfo-EMP pathway in Gram-positive bacteria (sulfo-EMP2). Our findings underscore the diversity of mechanisms through which bacteria degrade and utilize this ubiquitous organosulfur compound as a nutrient source.

Gene clusters and reaction schemes for the proposed sulfoquinovose degradation pathways. (A) Clostridium sp. MSTE9 sulfo-TK pathway, (B) N. aromaticivorans sulfo-ASMO pathway, and (C) B. urumqiensis sulfo-EMP2 pathway.


7. Biochemistry 2022 DOI: 10.1021/acs.biochem.2c00102.

Here we report the identification and biochemical characterization of the capnine biosynthetic enzymes cysteate synthase (CapA) and cysteate-C-fatty acyltransferase (CapB) from the pathogenic gliding bacterium Capnocytophaga ochracea and NAD(P)H-dependent dehydrocapnine reductase CapC from the avian pathogen Ornithobacterium rhinotracheale.

Biosynthetic pathways of capnine and sphingolipid. (A) Proposed capnine biosynthetic pathway: CapA, cysteate synthase; CapB, cysteate-C-fatty-acyltrasferase. (B) Sphingolipid biosynthetic pathway: CapC, 3-dehydrocapnine reductase; SPT, serine-C-fatty acyltransferase; KDSR, 3-ketodihydrosphingosine reductase. (C) Arrangement of CapA, CapB, and CapC genes in C. ochracea, O. rhinotracheale, and F. johnsoniae, respectively.


Synthetic Biology

Selected Works

1. ACS Synth. Biol. 2019 Aug 16;8(8):1698-1704.

Rose has been entwined with human culture and history. “Blue rose” in English signifies unattainable hope or an impossible mission as it does not exist naturally and is not breedable regardless of centuries of effort by gardeners. With the knowledge of genes and enzymes involved in flower pigmentation and modern genetic technologies, synthetic biologists have undertaken the challenge of producing blue rose by engineering the complicated vacuolar flavonoid pigmentation pathway and resulted in a mauve-colored rose. A completely different strategy presented in this study employs a dual expression plasmid containing bacterial idgS and sfp genes. The holoIdgS, activated by Sfp from its apo-form, is a functional nonribosomal
peptide synthetase that converts L-glutamine into the blue pigment indigoidine. Expression of these genes upon petal injection with agroinfiltration solution generates blue-hued rose flowers. We envision that implementing this proof-of-concept with obligatory modifications may have tremendous impact in floriculture to achieve a historic milestone in rose breeding.

Transformation of Reconstructed Dual Expression Plasmid into GV3101 Agrobacterium Strain and Petal Injection with Agro-Infiltration Solution for the Expression of Indigoidine in Rose Petals


2. ChemBioChem 2022 DOI：10.1002/cbic.202200295

Here we report the enzymatic conversion of 2’-deoxyxanthosine 5’-monophosphate (dXMP) intoACS Catalysis 2021, 11(9) 5789–5794.deoxyisoguanosine monophosphate (dBMP), a precursor of the unnatural isoguanine-isocytosine base pair. The reaction is catalyzed by the bacteriophage enzyme PurZ and bacterial PurB, and is a key addition to the toolbox for de novo biosynthesis of unnatural DNA.

The enzymatic conversion of 2’-deoxyxanthosine 5’-monophosphate (dXMP) into deoxyisoguanosine monophosphate (dBMP), a precursor of the unnatural isoguanine-isocytosine base pair is reported. The reaction is catalyzed by the bacteriophage enzyme PurZ and bacterial PurB, and is a key addition to the toolbox for de novo biosynthesis of unnatural DNA.