Molybdoproteomes and evolution of molybdenum utilization

Abstract

The trace element molybdenum (Mo) is utilized in many life forms, and it is a key component of several enzymes involved in nitrogen, sulfur, and carbon metabolism. With the exception of nitrogenase, Mo is bound in proteins to a pterin, thus forming the molybdenum cofactor (Moco) at the catalytic sites of molybdoenzymes. Although a number of molybdoenzymes are well characterized structurally and functionally, evolutionary analyses of Mo utilization are limited. Here, we carried out comparative genomic and phylogenetic analyses to examine the occurrence and evolution of Mo utilization in bacteria, archaea and eukaryotes at the level of (i) Mo transport and Moco utilization trait, and (ii) Mo-dependent enzymes. Our results revealed that most prokaryotes and all higher eukaryotes utilize Mo whereas many unicellular eukaryotes including parasites and most yeasts lost the ability to use this metal. In addition, eukaryotes have fewer molybdoenzyme families than prokaryotes. Dimethylsulfoxide reductase (DMSOR) and sulfite oxidase (SO) families were the most widespread molybdoenzymes in prokaryotes and eukaryotes, respectively. A distant group of the ModABC transport system, was predicted in the hyperthermophilic archaeon Pyrobaculum. ModE-type regulation of Mo uptake occurred in less than 30% of Moco-utilizing organisms. A link between Mo and selenocysteine utilization in prokaryotes was also identified wherein the selenocysteine trait was largely a subset of the Mo trait, presumably due to formate dehydrogenase, a Mo- and selenium-containing protein. Finally, analysis of environmental conditions and organisms that do or do not depend on Mo revealed that host-associated organisms and organisms with low G+C content tend to reduce their Mo utilization. Overall, our data provide new insights into Mo utilization and show its wide occurrence, yet limited use of this metal in individual organisms in all three domains of life.

Fig. 1. Occurrence of Moco biosynthesis pathway and molybdoenzymes in bacteria

The tree is based on the bacterial part of a highly resolved phylogenetic tree of life (39). Moco, molybdopterin cofactor biosynthesis pathway; SO, sulfite oxidase; XO, xanthine oxidase; DMSOR, dimethylsulfoxide reductase; AOR, aldehyde:ferredoxin oxidoreductase. Phyla in which none of the organisms possess the Moco biosynthesis pathway are shown in blue (if containing at least three organisms, shown in bold and blue). Phyla in which all organisms possess the Moco biosynthesis pathway are shown in red (if containing at least three organisms, shown in bold and red).

Fig. 2. Occurrence of Mo utilization and Moco-containing proteins in archaea

Moco, molybdopterin cofactor biosynthesis pathway; SO, sulfite oxidase; XO, xanthine oxidase; DMSOR, dimethylsulfoxide reductase; AOR, aldehyde:ferredoxin oxidoreductase. Phyla in which none of the organisms possess the Moco biosynthesis pathway are shown in blue (if containing at least 3 organisms, shown in bold and blue). Phyla in which all organisms possess Moco biosynthesis pathway are shown in red (if containing at least 3 organisms, shown in bold and red).

Fig. 3. Occurrence of Mo utilization and Moco-containing proteins in eukaryotes

Moco, molybdopterin cofactor biosynthesis pathway; SO, sulfite oxidase; XO, xanthine oxidase. Phyla in which none of the organisms possess the Moco biosynthesis pathway are shown in blue (if containing at least 3 organisms, shown in bold and blue). Phyla in which all organisms possess the Moco biosynthesis pathway are shown in red (if containing at least 3 organisms, shown in bold and red).

Fig. 4. Phylogenetic tree of periplasmic components of Mo/W transporters in prokaryotes

ModA-like proteins are shown in red and bold, TupA in purple, WtpA in green and ModA in blue. Representative sequences were selected from a large number of orthologous proteins based on sequence similarities. The sulfate and Fe³⁺ ABC transporter branches were compressed and represented by family names. The measurement of distance for the branch lengths (shown by a bar) is indicated.

Fig. 5. Genomic organization of ModABC, ModE, and different ModE variants in Moco-utilizing organisms

Different genes in representative genomes are shown by the indicated color schemes. (A). Full-length ModE (E. coli-type); (B). ModE_N + Mop/Di-Mop; (C). Orphan ModE_N; (D). MerR-Mop fusion; (E). Unknown1-Mop fusion; (F). Cyanobacteria-specific unknown2-Mop fusion; (G). Epsilonproteobacteria-specific Unknown3-ModE_N fusion; (H). ModE_N-COG1910 fusion.

Fig. 6. Genomic organization of ModE, ModE_N and secondary Mo/W transporters in some Moco-utilizing organisms

Different genes in representative genomes are shown by indicated color schemes.

Fig. 7. Distribution of Moco utilization and Sec utilization in the three domains of life

Relationships between Moco utilization and Sec utilization in archaea, bacteria and eukarya are shown by a Venn diagram.

Fig. 8. Relationship between environmental factors, properties of organisms and the Mo utilization trait

All organisms were classified into two groups: Moco (+), i.e., containing Moco utilization trait; Moco (−), i.e., lacking Moco utilization. (A) Habitat. (B) G+C content. (C) A different representation of the influence of GC content.

Fig. 9. Relationship between environmental factors, properties of organisms and different molybdoenzymes

(A) Oxygen requirement for AOR and SO. (B) Oxygen requirement and optimal temperature for nitrogenase.