Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics

Abstract

20 21The vitamin B 12 family of cofactors known as cobamides are essential for a variety of microbial 22 metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent 23 . CC-BY-NC 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/342006 doi: bioRxiv preprint first posted online Jun. 8, 2018; 2 and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in 24 this data set have at least one of 15 cobamide-dependent enzyme families, yet only 37% are 25 predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis varies at 26 the phylum level, with 57% of Actinobacteria, 45% of Proteobacteria, and 30% of Firmicutes, 27and less than 1% of Bacteroidetes containing the complete biosynthetic pathway. Cobamide 28 structure could be predicted for 58% of cobamide-producing species, based on the presence of 29 signature lower ligand biosynthesis and attachment genes. Our predictions also revealed that 30 was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/342006 doi: bioRxiv preprint first posted online Jun. 8, 2018; 3 Introduction 41Microorganisms almost universally reside in complex communities where individual 42 members interact with each other through physical and chemical networks. A major type of 43 chemical interaction is nutrient crossfeeding, in which microbes that lack the ability to synthesize 44 particular required nutrients (termed auxotrophs) obtain these nutrients from other organisms in 45 their community (Seth and Taga, 2014). By understanding which organisms require nutrients and 46 which can produce them, we can predict specific metabolic interactions between members of a 47 microbial community (Abreu and Taga, 2016). With the development of next-generation 48 sequencing, the genome sequences of tens of thousands of bacteria from diverse environments 49 are now available, leading to the possibility of predicting community interactions based on the 50 genomes of individual members. However, the power to predict the metabolism of an organism 51 by analyzing its genome remains limited. 52The critical roles of cobamides (the vitamin B 12 family of enzyme cofactors) in the 53 metabolism of humans and diverse microbes has long been appreciated. Only recently, however, 54 has cobamide-dependent metabolism been recognized as a potential mediator of microbial 55 interactions (Degnan et al., 2014b;Seth and Taga, 2014). Cobamides are used in a variety of 56 enzymes in prokaryotes, including those involved in central metabolic processes such as carbon 57 metabolism and the biosynthesis of methionine and deoxynucleotides (Fig. 1). Some of the 58 functions carried out by cobamide-depend...

The diversity and ecological significance of microbial traits potentially involved in B12biosynthesis in the global ocean

“…This agrees with previous studies suggesting that cobalamin in the surface ocean may be primarily the result of de novo synthesis by heterotrophic bacteria or via modification of cyanobacteriallyproduced pseudocobalamin, while Thaumarchaeota may be a major cobalamin producer at depth (14). Despite the high abundance of Bacteroidetes in the MES, studies have shown that only 0.6% of Bacteroidetes have complete B12 synthesis pathways (15). Gene families (e.g.…”

“…Second, consistent with our current knowledge (14), only a few microbial genera in the ocean were found to carry de novo B12 biosynthesis potential by judging the gene families linked to the microbial taxa. However, comparative genomics of currently sequenced microbial genomes from NCBI RefSeq suggest that 37% of prokaryotic microbial species have the potential to biosynthesize cobamides de novo, though complete pathways are not always detected (15). Among these, 57% of Actinobacteria are predicted to biosynthesize cobamides, whereas only 0.6% of Bacteroidetes have the complete pathway (15).…”

“…B12 can be fully synthesized only by a small fraction of prokaryotes (7,15) due to the multiple enzymatic steps involved (Supplementary Figure 1). By applying VB12Path (29) to the TARA Oceans shotgun metagenome data, an average of 0.2% reads per sample were identified to encode gene families potentially involved in B12 biosynthesis pathways.…”

“…Two distinct pools of B12 analogs were found in the ocean, including the cobalamin pool produced by a few prokaryotes such as Thaumarchaeota and alpha-/gamma-proteobacterial lineages (e.g. Rhodobacterales, Rhizobiales and most of Rickettsiales) (7,11,14,15), and the pseudocobalamin pool produced by Cyanobacteria as representatives (11,14). Over the past years, the importance of B12 has been widely noticed, including influencing the growth rate of phytoplankton in the ocean (16), impacting the size and diversity of microbial community in terrestrial ecosystems (17), and altering the health status of hosts in the human intestinal system (18,19).…”

pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms

“…The copyright holder for this preprint this version posted November 29, 2023. ; https://doi.org/10.1101/2023.11.29.569236 doi: bioRxiv preprint inhibitory constants for corrinoid-dependent enzymes about 100-fold, suggesting the disruption of metabolic pathways directly or indirectly impacted N2O-consuming populations. Only a subset of bacteria and archaea synthesize corrinoids [86], and corrinoid prototrophs supply this essential nutrient to corrinoid auxotrophs [87,88]. The addition of N2O disrupts these interactions, an effect influenced by the concentration of N2O.…”