Heavy Metal Binding Domain Research Articles

Genome-wide analysis elucidates the roles of GhHMA genes in different abiotic stresses and fiber development in upland cotton

The heavy metal-binding domain is involved in heavy metal transporting and plays a significant role in plant detoxification. However, the functions of HMAs are less well known in cotton. In this study, a total of 143 GhHMAs (heavy metal-binding domain) were detected by genome-wide identification in G. hirsutum L. All the GhHMAs were classified into four groups via phylogenetic analysis. The exon/intron structure and protein motifs indicated that each branch of the GhHMA genes was highly conserved. 212 paralogous GhHMA gene pairs were identified, and the segmental duplications were the main role to the expansion of GhHMAs. The Ka/Ks values suggested that the GhHMA gene family has undergone purifying selection during the long-term evolutionary process. GhHMA3 and GhHMA75 were located in the plasma membrane, while GhHMA26, GhHMA117 and GhHMA121 were located in the nucleus, respectively. Transcriptomic data and qRT-PCR showed that GhHMA26 exhibited different expression patterns in each tissue and during fiber development or under different abiotic stresses. Overexpressing GhHMA26 significantly promoted the elongation of leaf trichomes and also improved the tolerance to salt stress. Therefore, GhHMA26 may positively regulate fiber elongation and abiotic stress. Yeast two-hybrid assays indicated that GhHMA26 and GhHMA75 participated in multiple biological functions. Our results suggest some genes in the GhHMAs might be associated with fiber development and the abiotic stress response, which could promote further research involving functional analysis of GhHMA genes in cotton.

Characterization of a Novel Variant of the Quinolone-Resistance Gene qnrB (qnrB89) Carried by a Multi-Drug Resistant Citrobacter gillenii Strain Isolated from Farmed Salmon in Chile.

The main objective of this study was to characterize using whole-genome sequencing analysis, a new variant of the qnrB gene (qnrB89) carried by a fluoroquinolone-susceptible bacterium isolated from mucus of farmed Salmo salar fingerling in Chile. Citrobacter gillenii FP75 was identified by using biochemical tests and 16S ribosomal gene analysis. Nucleotide and amino acid sequences of the qnrB89 gene exhibited an identity to qnrB of 81.24% and 91.59%, respectively. The genetic environment of qnrB89 was characterized by the upstream location of a sequence encoding for a protein containing a heavy metal-binding domain and a gene encoding for a N-acetylmuramoyl-L-alanine amidase protein, whereas downstream to qnrB89 gene were detected the csp and cspG genes, encoding cold-shock proteins. The qnrB89 gene was located on a large chromosomal contig of the FP75 genome and was not associated with the 10-kb plasmid and class 1 integron harbored by the FP75 strain. This study reports for the first time the carriage of a qnrB gene by the C. gillenii species, and its detection in a bacterial strain isolated from farmed salmon in Chile.

Simulation of Copper-Dependent Regulation Dynamics in ATP7B

Membrane proteins control the flow of ions across biological membranes by selective import or export and are of vital importance for all living cells. ATP7B is a human P-type ATPase that exports copper from the cytoplasm for excretion or incorporation into proteins, and mutations in ATP7B lead to the copper metabolism disorder Wilson's disease. ATP7B activity is regulated by an N-terminal heavy metal binding domain (HMBD), which is believed to display different dynamics and interaction patterns of its six metal binding domains (MBDs) in response to changes in copper concentration. Because the HMBD is highly dynamic, does not form a compact structure, and contain MBDs that move as rigid bodies with transient copper-dependent interactions, experimental characterization is highly challenging. Despite much effort it is still unknown how the HMBD is arranged around the core protein, and the mechanism of regulation by copper binding is poorly understood. To determine copper-dependent differences in the HMBD structural dynamics, and possible interactions with the core protein, we simulated a homology model of ATP7B in an E2 ion-free state in a membrane environment in the presence and absence of HMBD-bound copper. The results show that the HMBD interacts extensively with the core protein, with distinct differences between the apo and holo state. Specifically, the HMBD adopts more extended conformations in the holo state, with MBD2 and MBD3 showing the greatest differences. The observed results support a regulation mechanism where copper binding results in loss of MBD1-3 interactions as a first step of enzyme activation.

Transcriptome Analysis Reveals Cotton (Gossypium hirsutum) Genes That Are Differentially Expressed in Cadmium Stress Tolerance.

High concentrations of heavy metals in the soil should be removed for environmental safety. Cadmium (Cd) is a heavy metal that pollutes the soil when its concentration exceeds 3.4 mg/kg. Although the potential use of cotton to remediate heavy Cd-polluted soils is known, little is understood about the molecular mechanisms of Cd tolerance. In this study, transcriptome analysis was used to identify Cd tolerance genes and their potential mechanisms in cotton. We exposed cotton plants to excess Cd and identified 4627 differentially expressed genes (DEGs) in the root, 3022 DEGs in the stem and 3854 DEGs in the leaves through RNA-Seq analysis. Among these genes were heavy metal transporter coding genes (ABC, CDF, HMA, etc.), annexin genes and heat shock genes (HSP), amongst others. Gene ontology (GO) analysis showed that the DEGs were mainly involved in the oxidation–reduction process and metal ion binding. The DEGs were mainly enriched in two pathways, the influenza A and pyruvate pathway. GhHMAD5, a protein containing a heavy-metal binding domain, was identified in the pathway to transport or to detoxify heavy metal ions. We constructed a GhHMAD5 overexpression system in Arabidopsis thaliana that showed longer roots compared to control plants. GhHMAD5-silenced cotton plants showed more sensitivity to Cd stress. The results indicate that GhHMAD5 is involved in Cd tolerance, which gives a preliminary understanding of the Cd tolerance mechanism in upland cotton. Overall, this study provides valuable information for the use of cotton to remediate soils polluted with Cd and potentially other heavy metals.

A repeat region from the Brassica juncea HMA4 gene BjHMA4R is specifically involved in Cd2+ binding in the cytosol under low heavy metal concentrations

BackgroundHMA4 transporters are involved in the transport and binding of divalent heavy metals (Cd, Zn, Pb [lead] and Co [cobalt]). In general, as efflux pumps, HMA4 transporters can increase the heavy metal tolerance of yeast and Escherichia coli. Additional research has shown that the C-terminus of HMA4 contains a heavy metal-binding domain and that heterologous expression of a portion of peptides from this C-terminal domain in yeast provides a high level of Cd tolerance and Cd hyperaccumulation.ResultsWe cloned BjHMA4 from Brassica juncea, and quantitative real-time PCR analysis revealed that BjHMA4 was upregulated by Zn and Cd in the roots, stems and leaves. Overexpression of BjHMA4 dramatically affects Zn/Cd distribution in rice and wheat seedlings. Interestingly, BjHMA4 contains a repeat region named BjHMA4R within the C-terminal region; this repeat region is not far from the last transmembrane domain. We further characterized the detailed function of BjHMA4R via yeast and E. coli experiments. Notably, BjHMA4R greatly and specifically improved Cd tolerance, and BjHMA4R transformants both grew on solid media that contained 500 μM CdCl2 and presented improved Cd accumulation (approximately twice that of wild-type [WT] strains). Additionally, visualization via fluorescence microscopy indicated that BjHMA4R clearly localizes in the cytosol of yeast. Overall, these findings suggest that BjHMA4R specifically improves Cd tolerance and Cd accumulation in yeast by specifically binding Cd2+ in the cytosol under low heavy metal concentrations. Moreover, similar results in E. coli experiments corroborate this postulation.ConclusionBjHMA4R can specifically bind Cd2+ in the cytosol, thereby substantially and specifically improving Cd tolerance and accumulation under low heavy metal concentrations.

A novel C1q-domain-containing (C1qDC) protein from Mytilus coruscus with the transcriptional analysis against marine pathogens and heavy metals

The C1q-domain-containing (C1qDC) proteins, which are involved in various processes of vertebrates, are important pattern recognition receptors in innate immunity of invertebrates. In present study, a novel C1qDC was identified from Mytilus coruscus (designated as McC1qDC), which was 917bp in length encoding 236 amino acids with a typical signal peptide of 19 amino acid residues in N-terminus. Based on its conserved C1q domain and molecular architecture of 10 β-strand jelly-roll folding topology structure, McC1qDC might be classified as a member of the C1q family. The mRNA transcript of McC1qDC was predominantly detectable in the hemocytes, and a less degree in gill, gonad and mantle, but trace in foot, adductor and digestive gland. Upon induction by Vibrio harveyi and Vibrio alginolyticus, McC1qDC expression was significantly up-regulated. Time-dependent mRNA expression of McC1qDC was found during copper and cadmium exposure for its heavy metal-binding domain. These results indicated that McC1qDC was a novel member of the C1qDC protein family as a pattern recognition receptor against pathogens, and might be developed as a potential indicator for monitoring heavy metals pollution.

Research highlights

Research highlights

Structural model of the CopA copper ATPase of Enterococcus hirae based on chemical cross-linking

The CopA copper ATPase of Enterococcus hirae belongs to the family of heavy metal pumping CPx-type ATPases and shares 43% sequence similarity with the human Menkes and Wilson copper ATPases. Due to a lack of suitable protein crystals, only partial three-dimensional structures have so far been obtained for this family of ion pumps. We present a structural model of CopA derived by combining topological information obtained by intramolecular cross-linking with molecular modeling. Purified CopA was cross-linked with different bivalent reagents, followed by tryptic digestion and identification of cross-linked peptides by mass spectrometry. The structural proximity of tryptic fragments provided information about the structural arrangement of the hydrophilic protein domains, which was integrated into a three-dimensional model of CopA. Comparative modeling of CopA was guided by the sequence similarity to the calcium ATPase of the sarcoplasmic reticulum, Serca1, for which detailed structures are available. In addition, known partial structures of CPx-ATPase homologous to CopA were used as modeling templates. A docking approach was used to predict the orientation of the heavy metal binding domain of CopA relative to the core structure, which was verified by distance constraints derived from cross-links. The overall structural model of CopA resembles the Serca1 structure, but reveals distinctive features of CPx-type ATPases. A prominent feature is the positioning of the heavy metal binding domain. It features an orientation of the Cu binding ligands which is appropriate for the interaction with Cu-loaded metallochaperones in solution. Moreover, a novel model of the architecture of the intramembranous Cu binding sites could be derived.

Heavy metal transport by AtHMA4 involves the N-terminal degenerated metal binding domain and the C-terminal His 11 stretch

The Arabidopsis thaliana AtHMA4 is a P 1B-type ATPase that clusters with the Zn/Cd/Pb/Co subgroup. It has been previously shown, by heterologous expression and the study of AtHMA4 knockout or overexpressing lines in Arabidopsis [1–3], that AtHMA4 is implicated in zinc homeostasis and cadmium tolerance. Here, we report the study of the heterologous expression of AtHMA4 in the yeast Saccharomyces cerevisiae. AtHMA4 expression resulted in an increased tolerance to Zn, Cd and Pb and to a phenotypic complementation of hypersensitive mutants. In contrast, an increased sensitivity towards Co was observed. An AtHMA4::GFP fusion protein was observed in endocytic vesicles and at the yeast plasma membrane. Mutagenesis of the cysteine and glutamate residues from the N-ter degenerated heavy metal binding domain impaired the function of AtHMA4. It was also the case when the C-ter His 11 stretch was deleted, giving evidence that these amino acids are essential for the AtHMA4 binding/translocation of metals.

Characterization of a heavy metal ATPase from the apicomplexan Cryptosporidiumparvum

P1-ATPases are transporters which pump heavy metals across membranes, either to provide enzymes with essential cofactors or to remove excess, toxic metal cations from the cytosol. The first protist P1-ATPase (CpATPase2) has been isolated from the apicomplexan Cryptosporidiumparvum, an opportunistic pathogen of AIDS patients. This single copy gene encodes 1260 amino acids (aa), predicting a protein of 144.7 kDa. Reverse transcription-polymerase chain reaction (RT-PCR) and western blot analysis confirmed CpATPase2 expression. Immunofluorescence microscopy of C.parvum sporozoites using rabbit antiserum raised against a glutathione-S-transferase (GST) fusion protein suggests that CpATPase2 is associated with the plasma- and cytoplasmic membranes. The protein shares greatest overall sequence similarity to previously characterized copper P1-ATPases. Expression and subsequent biochemical analyses of the N-terminal heavy metal binding domain (HMBD, GMxCxxC) of CpATPase2 as a maltose-binding protein (MBP) in Escherichiacoli reveals that the protein specifically binds reduced copper, Cu(I), invitro and invivo, and that the cysteine residues of HMBD are responsible for heavy metal coordination. Overall, these data show that the apicomplexan C.parvum possesses a heavy metal P-ATPase transporter with a specificity for reduced copper. Since this discovery represents the first time a heavy metal P-ATPase has been identified and characterized from a protist, further molecular and biochemical studies are needed to understand the roles heavy metal P-ATPases play in heavy metal metabolism and potential virulence for this and other apicomplexa.

Lead Targets GRP78, a Molecular Chaperone, in C6 Rat Glioma Cells

Exposure to potentially neurotoxic levels of lead (Pb) occurs in about 9% of American children under 6 years of age. Astroglia in the brain serve as a Pb depot, sequestering Pb and preventing its contact with the more sensitive neurons. Astroglia have the capacity to adapt to Pb exposure, and as such are able to tolerate relatively high intracellular Pb accumulation. This tolerance mechanism has yet to be defined in biochemical terms. In the present study, we present evidence that glucose-regulated protein (GRP78), a molecular chaperone in the ER, participates directly or indirectly in the tolerance mechanism. Exposure of cultured C6 rat glioma cells, an astroglia-like cell line, to 1 μM Pb acetate for 1 week raised the intracellular levels of two proteins, one of which was identified by sequence analysis as GRP78. GRP78 accumulation started within 1 day and progressed with time of exposure. Studies in vitro showed that GRP78 bound tightly to affinity columns with Pb2+ as the affinity ligand and bound weakly when either Zn2+ or Ni2+ replaced the Pb2+. The reduced form of GSH and BSA did not compete with GRP78 to chelate Pb2+. However, the heavy metal binding domain (HMB) of Menkes protein competed with GRP78 for chelating Pb2+. The data provide evidence that GRP78 may be a component of the Pb tolerance mechanism through its direct interaction with Pb2+. Its increased synthesis could be part of the adaptive response to Pb exposure.

A Menkes P-type ATPase involved in copper homeostasis in the central nervous system of the rat.

We previously reported that copper efflux from C6 rat glioma cells was blocked by a brief exposure to sulfhydryl reagents p-chloromercuribenzoate (PCMB) and iodoacetamide as well as dicyclohexylcarbodiimide, suggesting the possible involvement of a Cu-transporting ATPase in the efflux mechanism. In this report, we show that copper efflux from PC12 cells, a neuron-like cell line established from rat adrenal pheochromocytoma, is also inhibited by PCMB exposure. Furthermore, we show that both C6 and PC12 cells express a homolog of the Menkes gene (MNK) as detected by RT-PCR with primers designed from a mouse cDNA and confirmed by sequence analysis of the amplified product. An expected 760-bp fragment representing the transduction and phosphorylation domains and a 925-bp fragment encoding the heavy metal-binding domain of Atp7a were amplified from a RNA extract of C6 and PC12 cells. Sequence data revealed that 690 bp of the 760-bp fragment from C6 cells were an identical match to a similar fragment from PC12 cells. Both fragments encoded a 229 amino-acid polypeptide that had a 98.7% sequence homology to mouse Atp7a. In addition, 880 bp from the 925-bp fragment of the two cell lines were identical and encoded a 293 amino-acid polypeptide with 94.5% sequence homology to mouse Atp7a. These data establish that a Menkes-type Cu-transporting ATPase is expressed in rat C6 and PC12 cells and strongly support the hypothesis that both neurons and glia are involved in maintaining Cu homeostasis in the central nervous system.

A growth factor-inducible nuclear protein with a novel cysteine/histidine repetitive sequence.

Growth factors rapidly induce transcription of a set of genes that encode regulatory proteins, many of which have been identified by cDNA cloning. Here we report the analysis of a cDNA corresponding to a gene induced in mouse 3T3 cells by growth factors and a variety of other extracellular signaling agents. The cDNA encodes a proline-, serine-, and glycine-rich nuclear protein designated Nup475 of 319 amino acids that contains two tandemly repeated cysteine- and histidine-containing sequences (CX8CX5CX3H) suggestive of a novel heavy metal-binding domain. Nup475 produced in Escherichia coli binds zinc. Its mRNA is present in a number of mouse tissues and cell lines, being especially abundant in intestine, thymus, and regenerating liver and in a macrophage cell line stimulated by gamma-interferon. We hypothesize that Nup475 is a regulatory protein with a novel zinc finger structure.

Molecular cloning of a histidine-rich Ca2+-binding protein of sarcoplasmic reticulum that contains highly conserved repeated elements

We reported previously the purification of a 165-kDa muscle-specific protein identified by virtue of its ability to bind 125I-labeled low density lipoprotein with high affinity after sodium dodecyl sulfate-polyacrylamide gel electrophoresis (Hoffmann, S. L., Brown, M. S., Lee, E., Pathak, R. K., Anderson, R. G. W., and Goldstein, J. J. (1989) J. Biol. Chem. 264, 8260-8270). The protein is located in the lumen of the sarcoplasmic reticulum, where it has no access to plasma lipoproteins. It binds to 45Ca2+ on nitrocellulose blots and stains metachromatically blue with Stains-all, a cationic dye that stains Ca2+-binding proteins. In the current paper, we have isolated a full-length rabbit cDNA clone for the 165-kDa protein. The deduced amino acid sequence reveals a 852-amino acid protein with the following structural features: 1) an NH2-terminal 27-residue putative signal sequence; 2) a highly repetitive region containing nine nearly identical tandem repeats of 29 residues, each consisting of a histidine-rich sequence HRHRGH, a stretch of 10-11 acidic amino acids, and a sequence containing 2 serines and a threonine in a negatively charged context; 3) a 13-residue stretch of polyglutamic acid; and 4) a COOH-terminal cluster of 14 closely spaced cysteine residues with the repeating pattern of Cys-X-X-Cys suggestive of a heavy metal binding domain. Histidine, aspartic acid, and glutamic acid accounted, respectively, for 13, 12, and 19% of the amino acids. The protein does not share any significant sequence homology with the cell surface low density lipoprotein receptor. Stretches of acidic amino acids are a feature of two other luminal sarcoplasmic reticulum proteins, suggesting that these may be a general feature of luminal sarcoplasmic reticulum proteins. We suggest that the histidine-rich Ca2+-binding protein described in the current study be designated HCP. The role of HCP in Ca2+ homeostasis in the sarcoplasmic reticulum of skeletal and cardiac muscle remains to be determined.