Speciomics as a concept involving chemical speciation and omics.

The study of chemical speciation and the refinement and expansion of omics-based methods are both consolidated and highly active research fields. Although well established, such fields are extremely dynamic and are driven by the emergence of new strategies and improvements in instrumentation. In the case of omics-based studies, subareas including lipidomics, proteomics, metallomics, metabolomics and foodomics have emerged. Here, speciomics is being proposed as an "umbrella" term, that incorporates all of these subareas, to capture studies where the evaluation of chemical species is carried out using omics approaches. This paper contextualizes both speciomics and the speciome, and reviews omics applications used for species identification through examination of proteins, metalloproteins, metabolites, and nucleic acids. In addition, some implications from such studies and a perspective for future development of this area are provided. SIGNIFICANCE: The synergic effect between chemical speciation and omics is highlighted in this work, demonstrating an emerging area of research with a multitude of possibilities in terms of applications and further developments. This work not only defines and contextualizes speciomics and individual speciomes, but also demonstrates with some examples the great potential of this new interdisciplinary area of research.

Identification of major zinc-binding proteins from a marine cyanobacterium: insight into metal uptake in oligotrophic environments.

Marine cyanobacteria make a significant contribution to primary production whilst occupying some of the most nutrient poor regions of the world's oceans. The low bioavailability of trace metals can limit the growth of phytoplankton in ocean waters, but only scarce data are available on the requirements of marine microbes for zinc. Recent genome mining studies suggest that marine cyanobacteria have both uptake systems for zinc and proteins that utilize zinc as a cofactor. In this study, the oligotrophic strain Synechococcus sp. WH8102 was grown at different zinc concentrations. Using metalloproteomics approaches, we demonstrate that even though this organism's growth was not affected by extremely low zinc levels, cells accumulated significant quantities of zinc, which was shown to be protein-associated by 2D liquid chromatography and ICP-MS. This indicates that the mechanisms for zinc uptake in Synechococcus sp. WH8102 are extremely efficient. Significantly, expression of SYNW2224, a putative porin, was up-regulated during growth in zinc-depleted conditions. Furthermore, along with 30 other proteins, SYNW2224 was captured by immobilised zinc affinity chromatography, indicating the presence of surface-exposed site(s) with metal-binding capacity. It is proposed that this porin plays a role in high-affinity zinc uptake in this and other cyanobacteria.

Mining genomes of marine cyanobacteria for elements of zinc homeostasis.

Zinc is a recognized essential element for the majority of organisms, and is indispensable for the correct function of hundreds of enzymes and thousands of regulatory proteins. In aquatic photoautotrophs including cyanobacteria, zinc is thought to be required for carbonic anhydrase and alkaline phosphatase, although there is evidence that at least some carbonic anhydrases can be cambialistic, i.e., are able to acquire in vivo and function with different metal cofactors such as Co(2+) and Cd(2+). Given the global importance of marine phytoplankton, zinc availability in the oceans is likely to have an impact on both carbon and phosphorus cycles. Zinc concentrations in seawater vary over several orders of magnitude, and in the open oceans adopt a nutrient-like profile. Most studies on zinc handling by cyanobacteria have focused on freshwater strains and zinc toxicity; much less information is available on marine strains and zinc limitation. Several systems for zinc homeostasis have been characterized in the freshwater species Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803, but little is known about zinc requirements or zinc handling by marine species. Comparative metallo-genomics has begun to explore not only the putative zinc proteome, but also specific protein families predicted to have an involvement in zinc homeostasis, including sensors for excess and limitation (SmtB and its homologs as well as Zur), uptake systems (ZnuABC), putative intracellular zinc chaperones (COG0523) and metallothioneins (BmtA), and efflux pumps (ZiaA and its homologs).

The isolated Cys2His2 site in EC metallothionein mediates metal-specific protein folding.

The selectivity of proteins involved in metal ion homeostasis is an important part of the puzzle to understand how cells allocate the correct metal ions to the correct proteins. Due to their similar ligand-binding properties, and their frequent co-existence in soils, essential zinc and toxic cadmium are a particularly challenging couple. Thus, minimisation of competition of Cd(2+) for Zn(2+) sites is of crucial importance for organisms that are in direct contact with soil. Amongst these, plants have an especially critical role, due to their importance for nutrition and energy. We have studied an embryo-specific, zinc-binding metallothionein (E(C)) from wheat by nuclear magnetic resonance, electrospray mass spectrometry, site-directed mutagenesis, and molecular modelling. Wheat E(C) exploits differences in affinities of Cys(4) and Cys(2)His(2) sites for Cd(2+) and Zn(2+) to achieve metal-selective protein folding. We propose that this may constitute a novel mechanism to discriminate between essential Zn(2+) and toxic Cd(2+).