2020 – Current Publications
119
Cole, C.G.; Zhang, Z.J.; Dommaraju, S.R.; Dong, Q.; Pope, R.L.; Son, S.S.; McSpadden, E.J.; Woodson, C.K.; Lin, H.; Dylla, N.P.; Sidebottom, A.M.; Sundararajan, A.; Mitchell, D.A.; Pamer, E.G. “Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance.” Cell Host Microbe, 1931-3128 (2025). doi:10.1016/j.chom.2025.11.007
RODEO-assisted mining of clinical metagenomes shows that lanthipeptide-producing microbes can cause prolonged gut dysbiosis and susceptibility to post-antibiotic infections.
118
Bregman, M.H.; Cogan, D.P.; Shelton, K.E.; Rice, A.J.; Dommaraju, S.R.; Nair, S.K.; Mitchell, D.A. “Structure-based discovery and definition of RiPP recognition elements.” mSystems, 0: e01252-25 (2025). doi:10.1128/msystems.01252-25
Improvements to RRE-Finder expands RRE discovery to >90,000 high-confidence RREs. AlphaFold 3 modeling of >8,000 complexes revealed 13 recognition motifs and validated RRE–peptide interactions.
117
Nguyen, D.T.; Ramos-Figueroa, J.S.; Vinogradov, A.A.; Goto, Y.; Gadgil, M.G.; Splain, R.A.; Suga, H.; van der Donk, W.A.; Mitchell, D.A. “Aminoacyl-tRNA specificity of a ligase catalyzing non-ribosomal peptide extension.” J. Am. Chem. Soc., 147: 37893-37898 (2025). doi:10.1021/jacs.5c12610
The peptide aminoacyl-tRNA ligase BhaBCala was found to recognize both the amino acid and tRNA components of its substrate, revealing key determinants of specificity and guiding efforts to engineer PEARLs for expanded amino acid incorporation.
116
Mi, X.; Barrett, S.E.; Mitchell, D.A; Shukla, D. “LassoESM a tailored language model for enhanced lasso peptide property prediction.” Nat. Commun., 16: 8545 (2025). doi:10.1038/s41467-025-63412-3
LassoESM, a lasso peptide-tailored language model, enables accurate prediction of cyclase-substrate compatibility and RNA polymerase inhibitory activity, which empowers rational design and discovery of functional lasso peptides.
115
Dommaraju, S.R.; Kandy, S.K.; Ren, H.; Luciano, D.P.; Fujiki, S.; Sarlah, D.; Zhao, H.; Chekan, J.R.; Mitchell, D.A. “A versatile enzymatic pathway for modification of peptide C-termini.” ACS Cent. Sci., 11: 2143-2153 (2025). doi:10.1021/acscentsci.5c01243
Daptide biosynthetic enzymes convert peptide C-termini to aminoacetone, diaminopropane, dimethylimidazoline, etc. and can install these modifications onto a broad range of substrates.
114
Rice, A.J.; Gadgil, M.G.; Bisignano, P.; Stein, R.A.; Mchaourab, H.S.; Mitchell, D.A. “Peptidic tryptophan halogenation by a promiscuous flavin-dependent enzyme.” Angew. Chem. Int. Ed., e202509729 (2025). doi:10.1002/anie.202509729
The tryptophan halogenase ChlH was found to exhibit high selectivity on its native substrate, but modify a diverse array of linear peptides, macrocyclic peptides, and even some proteins in vitro.
113
Rice, A.J.; Sword, T.T.; Chengan, K.; Mitchell, D.A.; Mouncey, N.J.; Moore, S.J.; Bailey, C.B. “Cell-free synthetic biology for natural product biosynthesis and discovery.” Chem. Soc. Rev., 54: 4314-4352 (2025). doi:10.1039/D4CS01198H
A review article discussing cell-free biosynthesis and the multitude of ways in which it can be leveraged for natural product discovery, production, and engineering.
112
Zdouc, M.M.; et al. “MIBiG 4.0 advancing biosynthetic gene cluster curation through global collaboration.” Nucleic Acids Res., 53: D678-D690 (2025). doi:10.1093/nar/gkae1115
This latest release of MIBiG describes numerous enhancements to a premier natural products repository, such as expanded annotation, curation, classification, and strong cross-database integration.
111
Clark, J.D.; Mi, X.; Mitchell, D.A.; Shukla, D. “Substrate prediction for RiPP biosynthetic enzymes via masked language modeling and transfer learning.” Digit. Discov., 4: 343-354 (2025). doi:10.1039/D4DD00170B
110
Barrett, S.E.; Yin, S.; Jordan, P.; Brunson, J.K.; Gordon-Nunez, J.; Costa Machado da Cruz, G.; Rosario, C.; Okada, B.K.; Anderson, K.; Pires, T.A.; Wang, R.; Shukla, D.; Burk, M.J.; Mitchell, D.A. “Substrate interactions guide cyclase engineering and lasso peptide diversification.” Nat. Chem. Biol., 21: 412-419 (2025). doi:10.1038/s41589-024-01727-w
Identifies key interactions between lasso cyclases and their core peptides which provides insights on substrate selectivity and cyclase engineering for lasso peptide diversification.
109
Barrett, S.E.; Mitchell, D.A. “Advances in lasso peptide discovery, biosynthesis and function.” Trends Genet., 40: 950-968 (2024). doi:10.1016/j.tig.2024.08.002
A review discussing the latest advances for lasso peptide discovery and new insights on lasso peptide biosynthesis and biological function.
108
Woodard, A.M.; Peccati, F.; Navo, C.D.; Jiménez-Osés, G.; Mitchell, D.A. “Darobactin substrate engineering and computation show radical stability governs ether versus C-C bond formation.” J. Am. Chem. Soc., 146: 14328-14340 (2024). doi:10.1021/jacs.4c03994
Investigation of the radical SAM enzyme involved in darobactin biosynthesis. Computational and experimental work provides new insight into darobactin and rSAM catalysis.
107
Lee, A.R.; Carter R.S.; Imani, A.S.; Dommaraju, S.R.; Hudson, G.A.; Mitchell, D.A.; Freeman, M.F. “Discovery of borosin catalytic strategies and function through bioinformatic profiling.” ACS Chem. Biol., 19: 1116-1124 (2024). doi:10.1021/acschembio.4c00066
RODEO was expanded to analyze borosins, facilitating a large-scale analysis of borosins. This analysis led to the discovery of several new aspects of borosin biosynthesis.
106
Shi, C.; Patel, V.D.; Mitchell, D.A.; Zhao, H. “Polythiazole-containing hemolytic peptide from Enterococcus caccae.” ChemBioChem, 25: e202400212 (2024). doi:10.1002/cbic.202400212
A streptolysin S-like cytolysin was discovered in Enterococcus allowing for a more detailed structural characterization of an elusive virulence factor.
105
Nguyen, D.T.; Zhu, L.; Gray, D.L.; Woods, T.J.; Padhi, C.; Flatt, K.M.; Mitchell, D.A.; van der Donk, W.A. “Biosynthesis of macrocyclic peptides with C-terminal β-amino-α-keto acid groups by three different metalloenzymes.” ACS Cent. Sci., 10: 1022-1032 (2024). doi:10.1021/acscentsci.4c00088
Bioinformatics was utilized to discover a novel RiPP class biosynthesized by distinct metalloenzyme families including MNIO, B12-rSAM, and cytochrome P450.
104
Ren, H.; Huang, C.; Pan, Y.; Dommaraju, S.R.; Cui, H.; Li, M.; Gadgil, M.G.; Mitchell, D.A.; Zhao, H. “Non-modular fatty acid synthases yield distinct N-terminal acylation in ribosomomal peptides.” Nat. Chem., 16: 1320-1329 (2024). doi:10.1038/s41557-024-01491-3
Identified a new compound, “lipoavitide,” that is a fatty acid/RiPP hybrid. Using structural characterization and in vitro reconstitution, a putative biosynthetic pathway was suggested.
103
Harris, L.A.; Saad, H.; Shelton, K.E.; Zhu, L.; Guo, X.; Mitchell, D.A. “Tryptophan-centric bioinformatics identifies new lasso peptide modifications.” Biochem., 63: 865-879 (2024). doi:10.1021/acs.biochem.4c00035
Bioinformatic strategy to discover lasso peptides with new modifications to tryptophan was used to identify and characterize two news groups of lasso peptides.
102
Nguyen, D.T.; Mitchell, D.A.; van der Donk, W.A. “Genome mining for new enzyme chemistry.” ACS Catal., 14: 4536-4553 (2024). doi:10.1021/acscatal.3c06322
A review describing the advances in mining genome for new chemical transformations.
101
Fernandez, H.; Kretsch, A.; Kunakom, S.; Kadjo, A.; Mitchell, D.; Eustaquio, A. “High-yield lasso peptide production in a Burkholderia bacterial host by plasmid copy number engineering.” ACS Synth. Biol., 13: 337-350 (2024). doi:10.1021/acssynbio.3c00597
Tuning of plasmid copy number in a Burkholderia isolate was leveraged to produce two new lasso peptides, mycetolassins, in high titers.
100
Saad, H.; Majer, T.; Bhattarai, K.; Lampe, S.; Nguyen, D.T.; Kramer, M.; Straetenger, J.; Oesterbelt, H.B.; Mitchell, D.A.; Gross, H. “Bioinformatic-guided discovery of biaryl-linked lasso peptides.” Chem. Sci., 14: 13176-13183 (2023). doi:10.1039/D3SC02380J
Dscovery and structural characterization of two new (C-N) biaryl-tailored lasso peptides modified by P450 enzymes.
99
Chadwick, G.L.; Joiner A.M.N.; Ramesh, S.; Mitchell, D.A.; Nayak, D.D. “McrD binds asymmetrically to methyl-coenzyme M reductase improving active-site accessibility during assembly.” Proc. Natl. Acad. Sci. U.S.A., 120: e2302815120 (2023). doi:10.1073/pnas.2302815120
CryoEM reveals the role of McrD in the assembly of methyl-coenzyme M reductase, a ubiquitous enzyme in methanogens and key player in the global carbon cycle.
98
Ren, H.; Dommaraju, S.R.; Huang, C.; Cui, H.; Pan, Y.; Nesic, M.; Zhu, L.; Sarlah, D.; Mitchell, D.A.; Zhao, H. “Genome mining unveils a class of ribosomal peptides with two amino termini.” Nat. Commun., 14: 1624 (2023). doi:10.1038/s41467-023-37287-1.
RRE-Finder was used to bioinformatically discover the daptides, new RiPP class featuring two amino termini.
97
Precord, T.W.; Ramesh, S.; Dommaraju, S.R.; Harris, L.A.; Kille, B.L.; Mitchell, D.A. “Catalytic site proximity profiling for functional unification of sequence-diverse radical S-adenosylmethionine enzymes.” ACS Bio. Med. Chem. Au, 3: 240-251 (2023). doi:10.1021/acsbiomedchemau.2c00085.
Identification of paraphyletic sactisynthases by profiling of catalytic site proximity residues. A new sactisynthase from S. sparsogenes is reported using this method.
96
Kretsch, A.M.; Gadgil, M.G.; DiCaprio, A.J.; Barrett, S.E.; Kille, B.L.; Si, Y.; Zhu, L.; Mitchell, D.A. “Peptidase activation by a leader peptide-bound RiPP recognition element.” Biochem., 62: 956-967 (2023). doi:10.1021/acs.biochem.2c00700
Bioinformatic and biochemical techniques unraveled the function of RRE domains in lasso peptide biosynthesis.
95
Shelton, K.E.; Mitchell, D.A. “Bioinformatic prediction and experimental validation of RiPP recognition elements.” Meth. Enzymol., 679: 191-233 (2023). doi:10.1016/bs.mie.2022.08.050
A review covering bioinformatic methods to predict RiPP recognition elements (RREs) and experimental methods to confirm the role of RREs as leader peptide binders.
94
Rice, A.J.; Pelton, J.M.; Kramer, N.J.; Catlin, D.S.; Nair, S.K.; Pogorelov, T.V.; Mitchell, D.A.; Bowers, A.A. “Enzymatic pyridine aromatization during thiopeptide biosynthesis.” J. Am. Chem. Soc., 144: 21116-21124 (2022). doi:10.1021/jacs.2c07377
An in-depth mechanistic investigation of the class-defining [4+2] enzyme in thiopeptide and pyritide biosynthesis.
93
Ayikpoe, R.S.; Shi, C.; Battiste, A.J.; Eslami, S.M.; Ramesh, S.; Simon, M.A.; Bothwell, I.R.; Lee, H.; Rice, A.J.; Ren, H.; Tian, Q.; Harris, L.A.; Sarksian, R.; Zhu, L.; Frerk, A.M.; Precord, T.W.; van der Donk, W.A.; Mitchell, D.A.; Zhao, H. “A scalable platform to discover antimicrobials of ribosomal origin.” Nat. Commun., 13: 6135 (2022). doi:10.1038/s41467-022-33890-w
A robotic system was developed to rapidly refactor RiPP BGCs, which were then expressed in E. coli. Using this method, three antibacterial RiPPs were discovered.
92
Ongpipattanakul, C.; Desormeaux, E.K.; DiCaprio, A.J.; van der Donk, W.A.; Mitchell, D.A.; Nair, S.K. “Mechanism of action of ribosomally synthesized and post-translationally modified peptides.” Chem. Rev., 122: 14722-14814 (2022). doi:10.1021/acs.chemrev.2c00210
Comprehensive review of the modes of action of bacterial RiPPs.
91
Nguyen, D.T.; Le, T.T.; Rice, A.J.; Hudson, G.A.; van der Donk, W.A.; Mitchell, D.A. “Accessing diverse pyridine-based macrocyclic peptides by a two-site recognition pathway.” J. Am. Chem. Soc., 144: 11263-11269 (2022). doi:10.1021/jacs.2c02824
Characterization of a versatile biosynthetic pathway to generate 14- to 68-membered pyridine-based macrocyclic peptides with diverse structures.
90
Harris, L.A.; Mitchell, D.A. “Reactivity-based screening for natural product discovery.” Meth. Enzymol., 665: 177-208 (2022). doi:10.1016/bs.mie.2021.11.018
A review detailing the use of reactivity-based screening to discover natural products with specific functional groups.
89
Oberg, N.; Precord, T.W.; Mitchell, D.A.; Gerlt, J.A. “RadicalSAM.org: a resource to interpret sequence-function space and discover new radical SAM enzyme chemistry.” ACS Bio. Med. Chem. Au, 2: 22-35 (2022). doi:10.1021/acsbiomedchemau.1c00048
RadicalSAM.org, a new web-based genomic enzymology resource, is described, which aims to accelerate the characterization of the rSAM superfamily.
88
Ramesh, S.; Guo, X.; DiCaprio, A.J.; De Lio, A.M.; Harris, L.A.; Kille, B.L.; Pogorelov, T.V.; Mitchell, D.A. “Bioinformatics-guided expansion and discovery of graspetides.” ACS Chem. Biol., 16: 2787-2797 (2021). doi:10.1021/acschembio.1c00672
RODEO’s utility was expanded to cover graspetides, facilitating the most comprehensive bioinformatic analysis of graspetides to date and the discovery of conformational isomers thatisin and iso-thatisin.
87
Liu, A.; Krushnamurthy, P.H.; Subramanya, K.S.; Mitchell, D.A.; Mahanta, N. “Enzymatic thioamidation of peptide backbones.” Meth. Enzymol., 656: 459-494 (2021). doi:10.1016/bs.mie.2021.04.010
A detailed review of methods and precise experimental protocols for investigating peptide backbone thioamidation by YcaO enzymes.
86
Guo, X.R.; Zhang, J.; Li, X.; Xiao, E.; Lange, J.; Rienstra, C.; Burke, M.D.; Mitchell, D.A. “Sterol sponge mechanism is conserved for glycosylated polyene macrolides.” ACS Cent. Sci., 7: 781-791 (2021). doi:10.1021/acscentsci.1c00148
Bioinformatics and a tetrazine-based probe were used to expand the glycosylated polyene macrolide natural product class, allowing the confirmation of a generalized sterol sponge mechanism of action.
85
Si, Y.; Kretsch, A.M.; Daigh, L.M.; Burk, M.J.; Mitchell, D.A. “Cell-Free biosynthesis to evaluate lasso peptide formation and enzyme-substrate tolerance.” J. Am. Chem. Soc., 143: 5917-5927 (2021). doi:10.1021/jacs.1c01452
Cell-free biosynthesis was used to produce known and novel lasso peptides, and to evaluate enzyme-substrate tolerance.
84
Liu, A.; Si, Y.; Dong, S.; Mahanta, N.; Penkala, H.N.; Nair, S.K.; Mitchell, D.A. “Functional elucidation of TfuA in peptide backbone thioamidation.” Nat. Chem. Biol., 17: 585-592 (2021). doi:10.1038/s41589-021-00771-0
Functional revelation of the TfuA protein family and the proteinaceous sulfur donor involved in peptide backbone thioamidation.
83
Harris, L.A.; Saint-Vincent, P.M.B.; Guo, X.R.; Hudson, G.A.; DiCaprio, A.J.; Zhu, L.; Mitchell, D.A. “Reactivity-based screening for citrulline-containing natural products reveals a family of bacterial peptidyl arginine deiminases.” ACS Chem. Biol., 15: 3167-3175 (2020). doi:10.1021/acschembio.0c00685
A combination of a citrulline specific probe and other methods was used to discover the family of bacterial PADs responsible for converting arginine to citrulline in citrulassin biosynthesis.
82
Georgiou, M.A.; Dommaraju, S.R.; Guo, X.R.; Mast, D.H.; Mitchell, D.A. “Bioinformatic and reactivity-based discovery of linaridins.” ACS Chem. Biol., 15: 2976-2985 (2020). doi:10.1021/acschembio.0c00620
RODEO’s utility was expanded to cover all linaridins, this showed a wide diversity in the subclass and lead to the discovery of pegvadin A and B.
81
Montalbán-López, M. et al. “New developments in RiPP discovery, enzymology and engineering.” Nat. Prod. Rep., 38: 130-239 (2021). doi:10.1039/D0NP00027B
An update to Arnison et al. 2013, this review focuses on the advances in the RiPP field from 2013-2020.
80
Kloosterman, A.M.; Shelton, K.E.; van Wezel, G.P.; Medema, M.H.; Mitchell, D.A. “RRE-Finder: A genome-mining tool for class-independent RiPP discovery.” mSystems, 5: e00267-20 (2020). doi:10.1128/mSystems.00267-20
The RRE-Finder tool rapidly identifies RiPP recognition elements in gene clusters, facilitating discovery of novel natural products.
79
Hudson, G.A.; Hooper, A.R.; DiCaprio, A.J.; Sarlah, D.; Mitchell, D.A. “Structure prediction and synthesis of pyridine-based macrocyclic peptide natural products.” Org. Lett., 23: 253–256 (2021). doi:10.1021/acs.orglett.0c02699
The product of a biosynthetic gene cluster was structurally predicted, synthesized, and verified by enzyme reconstitution, requiring a reclassification of thiopeptides as a subclass of the pyritides.
78
Walker, M.C.; Eslami, S.M.; Hetrick, K.J.; Ackenhusen, S.E.; Mitchell, D.A.; van der Donk, W.A. “Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family.” BMC Genomics, 21: 387-403 (2020). doi:10.1186/s12864-020-06785-7
RODEO’s utility was expanded to covered all lanthipeptides, revealing the hidden size an diversity of this molecular class while also facilitating the discovery of birimositide.
77
Nayak, D.D.; Liu, A.; Agrawal, N.; Rodriguez-Carerro, R.; Dong, S.H.; Mitchell, D.A.; Nair, S.K.; Metcalf, W.W. “Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans.” PLoS Biol., 18: e3000507 (2020). doi:10.1371/journal.pbio.3000507
Characterization of three posttranslational modifications on methyl-coenzyme M reductase reveals their complex interaction, serving to fine-tune the enzyme activity.
76
Sieber, S.; Grendelmeier, S.M.; Harris, L.A.; Mitchell, D.A.; Gademann, K. “Microviridin 1777: A toxic chymotrypsin inhibitor discovered by a metabolomic approach.” J. Nat. Prod., 83: 438-446 (2020). doi:10.1021/acs.jnatprod.9b00986
A novel chymotrypsin inhibitor, microviridin 1777, was structurally characterized and found to be cytotoxic towards the grazer Thamnocephalus platyurus.