NmerA, the metal binding domain of mercuric ion reductase, removes Hg2+ from proteins, delivers it to the catalytic core, and protects cells under glutathione-depleted conditions

Redox control of protein conformation in flavoproteins

Flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are two flavin prosthetic groups utilized as the redox centers of various proteins. The conformations and chemical properties of these flavins can be affected by their redox states as well as by photoreactions. Thus, proteins containing flavin (flavoproteins) can function not only as redox enzymes, but also as signaling molecules by using the redox- and/or light-dependent changes of the flavin. Redox and light-dependent conformational changes of flavoproteins are critical to many biological signaling systems. In this review, we summarize the molecular mechanisms of the redox-dependent conformational changes of flavoproteins and discuss their relationship to signaling functions. The redox-dependent (or light-excited) changes of flavin and neighboring residues in proteins act as molecular "switches" that "turn on" various conformational changes in proteins, and can be classified into five types. On the basis of the present analysis, we recommend future directions in molecular structural research on flavoproteins and related proteins.

An initial characterization of the mercury resistance (mer) system of the thermophilic bacterium Thermus thermophilus HB27

The evolutionary origin of the broadly distributed mer system, which plays an important role in mercury detoxification and biogeochemistry, is presently unknown. The phylum Deinococcus/Thermus was found to be one of the deepest-branching bacterial lineage to have a homolog of merA, which specifies reduction of ionic to elemental mercury, and the mercuric reductase (MerA) of Thermus thermophilus HB27 was found to be basal to all bacterial MerA when this protein's phylogeny was constructed. A merA mutant of HB27 was fourfolds more sensitive to mercury toxicity than the wild type (wt), and lost detectable MerA-specific activities. The merA gene in HB27 was transcribed on a polycistronic message downstream from ORF encoding for homologs of O-acetyl-l-homoserine/O-acetyl-serine (OAH/OAS) sulfhydrylase and MerR, the mer operon transcription regulator, from a promoter located 69 nucleotides upstream of the sulfhydrylase translation start codon. The transcription of the putative mer operon in HB27 was induced 66.8+/-15.8-fold by exposure to 1 muM HgCl2. The optimal temperature for MerA-specific activity corresponded to this strain's optimal growth temperature, 70 degrees C. Thus, T. thermophilus is the earliest mercury-resistant bacterium identified to date, a finding consistent with the hypothesis that the mer system originated among thermophilic microorganisms from geothermal environments.

Chromofluorescent indicator for intracellular Zn2+/Hg2+ dynamic exchange

The fluorescence of NABQ increases remarkably in the presence of Zn(2+) and is quenched by Hg(2+). As shown by confocal imaging, NABQ-Zn(2+) can penetrate cells, where the bound Zn(2+) is exchanged for Hg(2+). This results in the concomitant export of Hg(2+) from the cells, showing that NABQ can act as a Zn(2+) carrier and as a Hg(2+) extracting agent in living cells.

The multiple functions of the thiol-based electron flow pathways of Escherichia coli: Eternal concepts revisited

Electron flow via thiols is a theme with many variations in all kingdoms of life. The favourable physichochemical properties of the redox active couple of two cysteines placed in the optimised environment of the thioredoxin fold allow for two electron transfers in between top biological reductants and ultimate oxidants. The reduction of ribonucleotide reductases by thioredoxin and thioredoxin reductase of Escherichia coli (E. coli) was one of the first pathways to be elucidated. Diverse functions such as protein folding in the periplasm, maturation of respiratory enzymes, detoxification of hydrogen peroxide and prevention of oxidative damage may be based on two electron transfers via thiols. A growing field is the relation of thiol reducing pathways and the interaction of E. coli with different organisms. This concept combined with the sequencing of the genomes of different bacteria may allow for the identification of fine differences in the systems employing thiols for electron flow between pathogens and their corresponding mammalian hosts. The emerging possibility is the development of novel antibiotics.

High diversity of bacterial mercuric reductase genes from surface and sub-surface floodplain soil (Oak Ridge, USA)

DNA was extracted from different depth soils (0-5, 45-55 and 90-100 cm below surface) sampled at Lower East Fork Poplar Creek floodplain (LEFPCF), Oak Ridge (TN, USA). The presence of merA genes, encoding the mercuric reductase, the key enzyme in detoxification of mercury in bacteria, was examined by PCR targeting Actinobacteria, Firmicutes or beta/gamma-Proteobacteria. beta/gamma-Proteobacteria merA genes were successfully amplified from all soils, whereas Actinobacteria were amplified only from surface soil. merA clone libraries were constructed and sequenced. beta/gamma-Proteobacteria sequences revealed high diversity in all soils, but limited vertical similarity. Less than 20% of the operational taxonomic units (OTU) (DNA sequences > or = 95% identical) were shared between the different soils. Only one of the 62 OTU was > or = 95% identical to a GenBank sequence, highlighting that cultivated bacteria are not representative of what is found in nature. Fewer merA sequences were obtained from the Actinobacteria, but these were also diverse, and all were different from GenBank sequences. A single clone was most closely related to merA of alpha-Proteobacteria. An alignment of putative merA genes of genome sequenced mainly marine alpha-Proteobacteria was used for design of merA primers. PCR amplification of soil alpha-Proteobacteria isolates and sequencing revealed that they were very different from the genome-sequenced bacteria (only 62%-66% identical at the amino-acid level), although internally similar. In light of the high functional diversity of mercury resistance genes and the limited vertical distribution of shared OTU, we discuss the role of horizontal gene transfer as a mechanism of bacterial adaptation to mercury.

Evidence for direct interactions between the mercuric ion transporter (MerT) and mercuric reductase (MerA) from the Tn501 mer operon

Mercuric ion resistance in bacteria requires transport of mercuric ions (Hg(2+)) into the cytoplasmic compartment where they are reduced to the less toxic metallic mercury (Hg(0)) by mercuric reductase (MR). The long-established model for the resistance mechanism predicts interactions between the inner membrane mercuric ion transporter, MerT, and the N-terminal domain of cytoplasmic MR, but attempts to demonstrate this interaction have thus far been unsuccessful. A recently developed bacterial two-hybrid protein interaction detection system was used to show that the N-terminal region of MR interacts with the cytoplasmic face of MerT. We also show that the cysteine residues on the cytoplasmic face of the MerT protein are required for maximal mercuric ion transport but not for the interaction with mercuric reductase.

Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach

Metal-binding proteins play important roles in structural stability, signaling, regulation, transport, immune response, metabolism control, and metal homeostasis. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting metal-binding proteins irrespective of sequence similarity. This work explores support vector machines (SVM) as such a method. SVM prediction systems were developed by using 53,333 metal-binding and 147,347 non-metal-binding proteins, and evaluated by an independent set of 31,448 metal-binding and 79,051 non-metal-binding proteins. The computed prediction accuracy is 86.3%, 81.6%, 83.5%, 94.0%, 81.2%, 85.4%, 77.6%, 90.4%, 90.9%, 74.9% and 78.1% for calcium-binding, cobalt-binding, copper-binding, iron-binding, magnesium-binding, manganese-binding, nickel-binding, potassium-binding, sodium-binding, zinc-binding, and all metal-binding proteins respectively. The accuracy for the non-member proteins of each class is 88.2%, 99.9%, 98.1%, 91.4%, 87.9%, 94.5%, 99.2%, 99.9%, 99.9%, 98.0%, and 88.0% respectively. Comparable accuracies were obtained by using a different SVM kernel function. Our method predicts 67% of the 87 metal-binding proteins non-homologous to any protein in the Swissprot database and 85.3% of the 333 proteins of known metal-binding domains as metal-binding. These suggest the usefulness of SVM for facilitating the prediction of metal-binding proteins. Our software can be accessed at the SVMProt server http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi.

In silico identification of putative metal binding motifs

Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. In this study, we have performed an in silico analysis of metal binding proteins and have identified putative metal binding motifs for the ions of cadmium, cobalt, zinc, arsenic, mercury, magnesium, manganese, molybdenum and nickel. A pattern search against the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases yielded true positives in each case showing the high-specificity of the motifs. Motifs were also validated against PDB structures and site directed mutagenesis studies.

Hg(II) sequestration and protection by the MerR metal-binding domain (MBD)

MerR, the metalloregulator of the bacterial mercury resistance (mer) operon, binds Hg(II) with high affinity. To study the mechanism of metal-induced activation, a small protein was previously engineered embodying in a single polypeptide the metal-binding domain (MBD) ordinarily formed between two monomers of MerR. Here the physiological and biochemical properties of MBD expressed on the cell surface or in the cytosol were examined, to better understand the environments in which specific metal binding can occur with this small derivative. Over 20 000 surface copies of MBD were expressed per Escherichia coli cell, with metal stoichiometries of approximately 1.0 Hg(II) per MBD monomer. Cells expressing MBD on their surface in rich medium bound 6.1-fold more Hg(II) than those not expressing MBD. Although in nature cells use the entire mer operon to detoxify mercury, it was interesting to note that cells expressing only MBD survived Hg(II) challenge and recovered more quickly than cells without MBD. Cell-surface-expressed MBD bound Hg(II) preferentially even in the presence of a 22-fold molar excess of Zn(II) and when exposed to equimolar Cd(II) in addition. MBD expressed in the cystosol also afforded improved survival from Hg(II) exposure for E. coli and for the completely unrelated bacterium Deinococcus radiodurans.