Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium.

Nathan G Walworth,Michael D Lee,Fei-Xue Fu,Mak A Saito,Sergio A Sañudo-Wilhelmy,Eric A Webb,Pingping Qu,Christopher Suffridge,David A Hutchins

doi:10.3389/fmicb.2018.00189

Abstract

Only select prokaryotes can biosynthesize vitamin B12 (i.e., cobalamins), but these organic co-enzymes are required by all microbial life and can be vanishingly scarce across extensive ocean biomes. Although global ocean genome data suggest cyanobacteria to be a major euphotic source of cobalamins, recent studies have highlighted that >95% of cyanobacteria can only produce a cobalamin analog, pseudo-B12, due to the absence of the BluB protein that synthesizes the α ligand 5,6-dimethylbenzimidizole (DMB) required to biosynthesize cobalamins. Pseudo-B12 is substantially less bioavailable to eukaryotic algae, as only certain taxa can intracellularly remodel it to one of the cobalamins. Here we present phylogenetic, metagenomic, transcriptomic, proteomic, and chemical analyses providing multiple lines of evidence that the nitrogen-fixing cyanobacterium Trichodesmium transcribes and translates the biosynthetic, cobalamin-requiring BluB enzyme. Phylogenetic evidence suggests that the Trichodesmium DMB biosynthesis gene, bluB, is of ancient origin, which could have aided in its ecological differentiation from other nitrogen-fixing cyanobacteria. Additionally, orthologue analyses reveal two genes encoding iron-dependent B12 biosynthetic enzymes (cbiX and isiB), suggesting that iron availability may be linked not only to new nitrogen supplies from nitrogen fixation, but also to B12 inputs by Trichodesmium. These analyses suggest that Trichodesmium contains the genus-wide genomic potential for a previously unrecognized role as a source of cobalamins, which may prove to considerably impact marine biogeochemical cycles.

Highlights

Marine cyanobacteria and eukaryotic algae are estimated to be responsible for up to 50% of global carbon fixation, and can be limited by both macronutrients and micronutrients (Field et al, 1998; Arrigo, 2005; Hutchins et al, 2009; Hutchins and Boyd, 2016)
We provide multiple lines of evidence both in culture and in situ that suggest Trichodesmium can transcribe and translate the full genomic pathway to biosynthesize and/or metabolize cobalamins
Since the synthesis of pseudo-B12 is an oxygenindependent pathway, Trichodesmium may have originally relied on pseudo-B12 biosynthesis in conjunction with early nitrogen fixation

Summary

Introduction

Marine cyanobacteria and eukaryotic algae are estimated to be responsible for up to 50% of global carbon fixation, and can be limited by both macronutrients (e.g., nitrogen and phosphorus) and micronutrients (e.g., iron) (Field et al, 1998; Arrigo, 2005; Hutchins et al, 2009; Hutchins and Boyd, 2016). Trichodesmium Iron-Mediated Cobalamin Biosynthesis bind to enzymes to increase reaction rates and are required for essential cellular processes such as DNA repair, redox reactions, photosynthesis, and carbon fixation (Monteverde et al, 2016). Some chemical form of vitamin B12 is required by all microbial life for a range of functions, including methionine biosynthesis, ribonucleotide reduction, photoregulation, and various onecarbon metabolisms (Sañudo-Wilhelmy et al, 2014; Fang et al, 2017). A primary type of B12, cobalamin (CBL), is a complex coenzyme with an α ligand of 5,6-dimethylbenzimidizole (DMB), and a β ligand of either an adenosyl-, methyl-, cyanide-, or hydroxylgroup (Ado-, Me-, CN-, or OH-; Heal et al, 2016; Figure 1). Methylcobalamin (Me-CBL) has a methyl group as its β ligand and is involved in methylation reactions, whereas adenosylcobalamin (Ado-CBL, coenzyme B12) has an adenosyl group (5–deoxyadenosine) and is involved in radical-based rearrangements and reductions (Banerjee and Ragsdale, 2003)

Methods

Results

Conclusion