Gunhild Layer's research while affiliated with University of Freiburg and other places

... For the cofactor S-adenosyl-Lmethionine (SAM), several salvage pathways for L-methionine and SAM byproducts are known, and two novel oxygen-independent salvage pathways for the SAM byproducts 5 -deoxyadenosine and 5 -methylthioadenosine have been discovered (see Figure 4) in Rhodospirillum rubrum and pathogenic Escherichia coli [117]. Salvage pathways leading back to SAM, either from nature or by design, can provide important tools for advancing and broadening the synthetic applications of different classes of SAM-dependent enzymes [118]. ...

... It is shown that cob(II)alamin forms a relatively stable six-coordinated complex with sulfur dioxide anion radical SO 2 À having strong reducing properties. Indeed, dithionite (sulfur dioxide anion radical) produces the catalytically incompetent cob(II)alamin (Allen and Wang, 2014;Gagsteiger et al., 2022). Insights on the importance of the upper axial ligand in cobalamin structure and reactivity can be derived from a comparison of the structure of cob(II)alamin-SO 2 À with the other important complex -nitrosylcobalamin NOCbl (Hannibal et al., 2007;Hassanin et al., 2009b), which is readily formed when cob(II)alamin reacts with nitric oxide. ...

... Subsequently, these 441 homologs underwent filtering with sequence similarity networks (SSNs) 20 to identify isofunctional groups of radical SAM enzymes, leading to the identification of 413 Gms homologs based on an alignment score of 90. These 413 homologs are classified within the mega-1-1-24 subgroup and can be distinguished from other identified radical SAM enzymes, such as Tes 3,4 and Grs 5 involved in GDGTs biosynthesis (Supplementary Fig. 9), and AhbC/AhbD 21,22 involved in the anaerobic biosynthesis of heme b in methanogens and sulfate-reducing bacteria ( Supplementary Fig. 10). Phylogenetic analysis indicates these 413 Gms homologs are distributed widely in all three archaeal superphyla (Asgard, Tack, and DPANN) and Euryarchaeota ( Fig. 3a and Supplementary Fig. 11). ...

... Coproporphyrin (CP), specifically CP-III, is a critical porphyrin intermediate and precursor for heme biosynthesis via the CPD pathway [13]. Beyond its significance in Figure 1. ...

... We therefore hypothesized that acquiring a sufficient amount of methyl donors is an important housekeeping trait of the bacteria, affecting global and local methylation. SAM is thought to be provided to the bacteria through conversion of methylogenic amino acids (such as methionine), or, in some bacteria, regenerated using SAH recycling towards methionine via homocysteine, using MetH or MetE enzymes [36,37]. H. pylori was reported to lack MetH and MetE enzymes [38][39][40][41], leaving amino acid/methionine uptake as the most likely and dominant source of methyl donors. ...

... . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made Previous studies have linked production of metal chelating metabolites to pathological processes, and iron limitation has been shown to lead to expression of virulence factors 19, [65][66][67][68][69][70] . With the wide range of biological repercussions of siderophore production, and numerous studies that have described the ability of siderophores to coordinate the trace metals inside iron, it is difficult to generalize the biological roles of these molecules to different environments. ...

... Recombinant production and purification of carnitine monooxygenase from E. coli 37 The genome of the gut microbial strain E. coli KO11FL (25) (21). As also described for other Rieske-type proteins, components YeaX and YeaW were purified under 1 aerobic conditions. ...

... It can be further converted into chlorophylls (Chls) and bacteriochlorophylls (BChls) in the cells of photoautotrophs; heme, a porphyrin prosthetic group of many proteins, plays a role in many fundamental metabolic processes, including aerobic and anaerobic respiration and photosynthesis. (Fan et al. 2019). In addition, porphyrins are fundamental structures for many essential metabolites involved in the formation of cobalamin (vitamin B 12 ) and enzymes such as catalases, peroxidases, or cytochromes P450 (Layer et al., 2010). ...

... Denitrification is a multistep process involving nitrate reduction to ultimate nitrogen gas formation [49]. Heme d 1 is an isobacteriochlorin co-factor of the nitrite reductase, NirS, which catalyses the reduction of nitrite to nitric oxide [50]. Synthesis of heme d 1 requires enzymes encoded by the nir genes [51][52][53], several of which (and their protein products) were decreased: nirD (siroheme decarboxylase NirD subunit, −10.1-fold), nirE (uroporphyrinogen-III C-methyltransferase, −11.7-fold), nirG (siroheme decarboxylase NirG subunit, −7.8-fold), nirL (siroheme decarboxylase NirL subunit, −3-fold), nirN (dihydro-heme d1 dehydrogenase, −4.1-fold), nirQ (denitrification regulatory protein NirQ, −13.8-fold) and nirS (nitrite reductase, −5.9-fold). ...

... Then, a second reduction step catalyzed by the chlorophyllide oxidoreductase (COR; BchY, BchZ, and BchX) leads to the chlorophyllide chlorin into a bacteriochlorin ring structure to form bacteriochlorophyllide and give rise to the synthesis of Bchl (Wätzlich et al., 2009). Due to the significant amino acid sequence homology to the corresponding subunits NifD, NifK and NifH of nitrogenase, DPOR and COR complexes have been designated as "nitrogenase-like" (Fujita & Bauer, 2000;Moser & Layer, 2019). Regarding the UROD, this enzyme serves as a pivotal point in the tetrapyrrole biosynthesis pathway, facilitating the decarboxylation of uroporphyrinogen III into coproporphyrinogen III, essential for heme and chlorophyll synthesis (Fan et al., 2007). ...