The fundamental chemistry of trace elements dictates the molecular speciation and reactivity both within cells and the environment at large. Using protein structure and comparative genomics, we elucidate several major influences this chemistry has had upon biology. All of life exhibits the same proteome size-dependent scaling for the number of metal-binding proteins within a proteome. This fundamental evolutionary constant shows that the selection of one element occurs at the exclusion of another, with the eschewal of Fe for Zn and Ca being a defining feature of eukaryotic proteomes. Early life lacked both the structures required to control intracellular metal concentrations and the metal-binding proteins that catalyze electron transport and redox transformations. The development of protein structures for metal homeostasis coincided with the emergence of metal-specific structures, which predominantly bound metals abundant in the Archean ocean. Potentially, this promoted the diversification of emerging lineages of Archaea and Bacteria through the establishment of biogeochemical cycles. In contrast, structures binding Cu and Zn evolved much later, providing further evidence that environmental availability influenced the selection of the elements. The late evolving Zn-binding proteins are fundamental to eukaryotic cellular biology, and Zn bioavailability may have been a limiting factor in eukaryotic evolution. The results presented here provide an evolutionary timeline based on genomic characteristics, and key hypotheses can be tested by alternative geochemical methods.Archean-Proterozoic | biogeochemistry | bioinorganic chemistry | evolution | metal homeostasis M etalloproteins contain one or more ions of an inorganic element in their 3D structure and are said to comprise 30% of all proteins (1). Many biological pathways contain at least one metalloenzyme (2) and consequently require Mg, K, Ca, Fe, Mn, and Zn to sustain life (3). Other elements, like Cu, Mo, Ni, Se, and Co, are required by many-though not all-organismal lineages, and the utilization of trace elements varies greatly between species (3). The different elements have a range of affinities for most coordinating environments in the order Mg +2 /Ca +2 < Mn +2 < Fe +2 < Co +2 < Ni +2 < Cu +2 ∼Zn +2 , an equilibrium series known as the Irving-Williams Series (4). This array of outer-sphere chemistry provides significant catalytic diversity, yet has consequences for both biological and environmental chemistry. Within the cell, metals compete for protein binding sites; hence, extensive protein networks involving transporters and metalsensing regulatory proteins are required to maintain the proper subcellular concentrations of each element, and in some cases directly shuttle each metal to its requisite metalloprotein in the proper cellular compartment (1, 5, 6). It has been hypothesized that the establishment of a metal homeostasis system is required for distinct phylotypes of cells to develop (7).Environmentally, for similar fundamental chemical reasons, the...

EchoLOCATION is a database that provides a comprehensive analysis of the subcellular locations of Escherichia coli K-12 proteins. Locations are predicted by integrating data from a range of publicly available algorithms combined with extensive curation of experimental literature. The data can be searched in a variety of ways and can generate lists of subcellular proteomes for analysis. Experimental evidence supports the locations of over 500 envelope proteins (periplasm, inner and outer membrane). From analysis of disagreements between in silico predictions and experimental data, we provide an analysis of protein types where subcellular prediction algorithms are currently not accurate.

It is coníirmed that the loss of HO' from the molecular ion of enitrotoluene involves exclusively a hydrogen from the methyl group. However, in higher homologues hydrogen atoms from non-benzylic sites are also implicated. With such compounds this fragmentation mode is shown not only by the ortho but, to a lesser extent, by the meta and para isomers as well. The proportion of the total ion current borne by the fM-17]+ ion follows the order orrho> meta> para, which is attributed to suhstiíuent migration around the ring with a hydroxyl radical only being lost when the groups are on adjecent ring atoms. Other ions present in the spectra point to interaction between substituents to form a new heterocyclic nng.