1 Supplementary Information Purinyl-cobamide is a native prosthetic group of reductive dehalogenases Authors and affiliations: Jun Yan 1,2,3,4,5* , Meng Bi 1 , Allen K. Bourdon 6 , Abigail T. Farmer 6 , Po-Hsiang Wang 7 , Olivia Molenda 7 , Andrew Quaile 7 , Nannan Jiang 3,4,5,8 , Yi Yang 3,9 , Yongchao Yin 1 , Burcu Şimşir 3,9 , Shawn R. Campagna 6 , Elizabeth A. Edwards 7 , and Frank E. Löffler 1,3,4,5,8,9,10* 1 Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, USA; 2 Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, P.R.China; 3 Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, USA; 4 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA; 5 Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA; 6 Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA; 7 Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada; 8 Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA; 9 Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA; and 10 Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee 37996, USA. Corresponding authors: [email protected] and [email protected]Nature Chemical Biology: doi:10.1038/nchembio.2512
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PDF SI Purinyl cobamide NCB manuscript 9 25 17 Jun...4 Supplementary Table 2. Information about CobT and homologous proteins used for phylogenetic tree construction (Fig. 4b in main
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1
Supplementary Information
Purinyl-cobamide is a native prosthetic group of reductive dehalogenases
Authors and affiliations:
Jun Yan1,2,3,4,5*, Meng Bi1, Allen K. Bourdon6, Abigail T. Farmer6, Po-Hsiang Wang7,
Olivia Molenda7, Andrew Quaile7, Nannan Jiang3,4,5,8, Yi Yang3,9, Yongchao Yin1, Burcu
Şimşir3,9, Shawn R. Campagna6, Elizabeth A. Edwards7, and Frank E. Löffler1,3,4,5,8,9,10*
1Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996,
USA; 2Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of
Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016,
P.R.China; 3Center for Environmental Biotechnology, University of Tennessee,
Knoxville, Tennessee 37996, USA; 4Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, USA; 5Joint Institute for Biological Sciences
(JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA;
6Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA;
7Department of Chemical Engineering and Applied Chemistry, University of Toronto,
Toronto, Ontario, M5S 3E5, Canada; 8Bredesen Center for Interdisciplinary Research
and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA;
9Department of Civil and Environmental Engineering, University of Tennessee, Knoxville,
Tennessee 37996, USA; and 10Department of Biosystems Engineering & Soil Science,
University of Tennessee, Knoxville, Tennessee 37996, USA.
mean values ± standard deviation from three independent cultures.
cDC
E, v
inyl
chl
orid
e an
d et
hene
(µm
oles
/bot
tle)
Time (day)
Vitamin B12
Purinyl-Cba
No corrinoid
Nature Chemical Biology: doi:10.1038/nchembio.2512
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Supplementary Figure 9. Demonstration of the utility of 15N-labeling to obtain lower
base compositional information. Mass spectra of (a) unlabeled and (b) 15N-labeled 5-
OHBza-Cba (i.e., factor III) produced by Geobacter sulfurreducens strain PCA. The
15N-labeled 5-OHBza-Cba was purified from Geobacter sulfurreducens cells grown with
15N-NH4Cl as the sole nitrogen source. Mass shifts of 12.95 Dalton in the m/z values of
[M+H]+ and [M+Na]+ base peaks matched the predicted mass increase based on the
total number of two N atoms in the Bza lower base structure.
a
b
Rel
ativ
e ab
unda
nce
(%)
m/z
1343.54
1356.51
1365.53
1378.48
Unlabeled 5-OHBza-Cba R
elat
ive
abun
danc
e (%
)
N
N
OH 15N-labeled 5-OHBza-Cba
Nature Chemical Biology: doi:10.1038/nchembio.2512
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References
1. Hazra, A.B. et al. Anaerobic biosynthesis of the lower ligand of vitamin B12. Proc. Natl. Acad. Sci. USA 112, 10792-10797 (2015).
2. Cheong, C.-G., Escalante-Semerena, J.C. & Rayment, I. Structural investigation of the biosynthesis of alternative lower ligands for cobamides by nicotinate mononucleotide: 5,6-dimethylbenzimidazole phosphoribosyltransferase from Salmonella enterica. J. Biol. Chem. 276, 37612-37620 (2001).
3. Stupperich, E., Eisinger, H.-J. & Schurr, S. Corrinoids in anaerobic bacteria. FEMS Microbiol. Lett. 87, 355-360 (1990).
4. Crofts, T.S., Seth, E.C., Hazra, A.B. & Taga, M.E. Cobamide structure depends on both lower ligand availability and CobT substrate specificity. Chem. Biol. 20, 1265-1274 (2013).
5. Renz, P. in Chemistry and biochemistry of B12 (ed. Banerjee, R.) 558-572 (John Wiley & Sons, Inc., 1999).
6. Kräutler, B. et al. The cofactor of tetrachloroethene reductive dehalogenase of Dehalospirillum multivorans is norpseudo-B12, a new type of a natural corrinoid. Helv. Chim. Acta 86, 3698-3716 (2003).
7. Hoffmann, B. et al. Native corrinoids from Clostridium cochlearium are adeninylcobamides: spectroscopic analysis and identification of pseudovitamin B12 and factor A. J. Bacteriol. 182, 4773-4782 (2000).
8. Men, Y.J. et al. Sustainable growth of Dehalococcoides mccartyi 195 by corrinoid salvaging and remodeling in defined lactate-fermenting consortia. Appl. Environ. Microbiol. 80, 2133-2141 (2014).
9. Chan, C.H. & Escalante-Semerena, J.C. ArsAB, a novel enzyme from Sporomusa ovata activates phenolic bases for adenosylcobamide biosynthesis. Mol. Microbiol. 81, 952-967 (2011).
10. Guimarães, D.H., Weber, A., Klaiber, I., Vogler, B. & Renz, P. Guanylcobamide and hypoxanthylcobamide-corrinoids formed by Desulfovibrio vulgaris. Arch. Microbiol. 162, 272-276 (1994).
11. Datsenko, K.A. & Wanner, B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97, 6640-6645 (2000).
Nature Chemical Biology: doi:10.1038/nchembio.2512