In silico prediction of potential metallothioneins and metallohistins in actinobacteria

Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance

Metallothionein (MT) genes are valuable genetic materials for developing metal bioremediation tools. Currently, a limited number of prokaryotic MTs have been experimentally identified, which necessitates the expansion of bacterial MT diversity. In this study, we conducted a metagenomics-guided analysis for the discovery of potential bacterial MT genes from the soil microbiome. More specifically, we combined resistance gene enrichment through diversity loss, metagenomic mining with a dedicated MT database, evolutionary trace analysis, DNA chemical synthesis, and functional genomic validation to identify novel MTs. Results showed that Cu stress induced a compositional change in the soil microbiome, with an enrichment of metal-resistant bacteria in soils with higher Cu concentrations. Shotgun metagenomic sequencing was performed to obtain the gene pool of environmental DNA (eDNA), which was subjected to a local BLAST search against an MT database for detecting putative MT genes. Evolutional trace analysis led to the identification of 27 potential MTs with conserved cysteine/histidine motifs different from those of known prokaryotic MTs. Following chemical synthesis of these 27 potential MT genes and heterologous expression in Escherichia coli, six of them were found to improve the hosts' growth substantially and enhanced the hosts' sorption of Cu, Cd, and Zn, among which MT5 led to a 13.7-fold increase in Cd accumulation. Furthermore, four of them restored Cu and/or Cd resistance in two metal-sensitive E. coli strains.IMPORTANCE The metagenomics-guided procedure developed here bypasses the difficulties encountered in classic PCR-based approaches and led to the discovery of novel MT genes, which may be useful in developing bioremediation tools. The procedure used here expands our knowledge on the diversity of bacterial MTs in the environment and may also be applicable to identify other functional genes from eDNA.

Pb2+ tolerance by Frankia sp. strain EAN1pec involves surface-binding

Several Frankia strains have been shown to be lead-resistant. The mechanism of lead resistance was investigated for Frankia sp. strain EAN1pec. Analysis of the cultures by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDAX) and Fourier transforming infrared spectroscopy (FTIR) demonstrated that Frankia sp. strain EAN1pec undergoes surface modifications and binds high quantities of Pb+2. Both labelled and unlabelled shotgun proteomics approaches were used to determine changes in Frankia sp. strain EAN1pec protein expression in response to lead and zinc. Pb2+ specifically induced changes in exopolysaccharides, the stringent response, and the phosphate (pho) regulon. Two metal transporters (a Cu2+-ATPase and cation diffusion facilitator), as well as several hypothetical transporters, were also upregulated and may be involved in metal export. The exported Pb2+ may be precipitated at the cell surface by an upregulated polyphosphate kinase, undecaprenyl diphosphate synthase and inorganic diphosphatase. A variety of metal chaperones for ensuring correct cofactor placement were also upregulated with both Pb+2 and Zn+2 stress. Thus, this Pb+2 resistance mechanism is similar to other characterized systems. The cumulative interplay of these many mechanisms may explain the extraordinary resilience of Frankia sp. strain EAN1pec to Pb+2. A potential transcription factor (DUF156) binding site was identified in association with several proteins identified as upregulated with heavy metals. This site was also discovered, for the first time, in thousands of other organisms across two kingdoms.

Microbially supported phytoremediation of heavy metal contaminated soils: strategies and applications

Heavy metal contamination of soil as a result of, for example, mining operations, evokes worldwide concern. The use of selected metal-accumulating plants to clean up heavy metal contaminated sites represents a sustainable and inexpensive method for remediation approaches and, at the same time, avoids destruction of soil function. Within this scenario, phytoremediation is the use of plants (directly or indirectly) to reduce the risks of contaminants in soil to the environment and human health. Microbially assisted bioremediation strategies, such as phytoextraction or phytostabilization, may increase the beneficial aspects and can be viewed as potentially useful methods for application in remediation of low and heterogeneously contaminated soil. The plant-microbe interactions in phytoremediation strategies include mutually beneficial symbiotic associations such as mycorrhiza, plant growth promoting bacteria (PGPB), or endophytic bacteria that are discussed with respect to their impact on phytoremediation approaches.

The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia

BACKGROUND

Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb(2+), Al(+3), SeO2, Cu(2+), AsO4, and Zn(2+). With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison.

RESULTS

Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia.

CONCLUSIONS

Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.

Challenging conventional wisdom: single domain metallothioneins

Metallation studies of human metallothioneins support the role of single metal-binding-domains as commonplace with the typical two-domain-cluster structure as exceptional.

Responses of environmental Amycolatopsis strains to copper stress

Copper is a redox-active metal, which acts as a catalyst in the formation of Reactive Oxygen Species (ROS) encouraging oxidative stress. Protection against oxidants is intrinsic to every living cell; however, in stress conditions, cells are forced to increase and expand their antioxidative network. In this work, the novel copper-resistant strain Amycolatopsis tucumanensis and the copper-sensitive Amycolatopsis eurytherma were grown under copper increasing concentrations in order to elucidate the dissimilar effects of the metal on the strains viability, mainly on morphology and antioxidant capacity. Although biosorbed copper encouraged ROS production in a dose-dependent manner in both strains, the increase in ROS production from the basal level to the stress conditions in A. tucumanensis is lesser than in the copper-sensitive strain; likewise, in presence of copper A. eurytherma suffered inexorable morphological alteration while A. tucumanensis was not affected. The levels of antioxidant enzymes and metallothioneins (MT) were all greater in A. tucumanensis than in A. eurytherma; in addition MT levels as well as superoxide dismutase and thioredoxin reductase activities in A. tucumanensis, were higher as higher the concentration of copper in the culture medium. This work has given evidence that an efficient antioxidant defense system might aid microorganisms to survive in copper-stress conditions; besides it constitutes the first report of oxidative stress study in the genus Amycolatopsis and contributes to enlarge the knowledge on the copper-resistance mechanisms of A. tucumanensis.

GC content-independent amino acid patterns in bacteria and archaea

Every organism can be characterized by the amino acid composition of its proteome. So far it was assumed that these compositions are determined by the GC content of the DNA or, in some cases, by extreme lifestyles, like thermophily or halophily. Here, we focussed our analysis on eight amino acids, each of which is encoded by both, GC and AT rich codons, to identify finer amino acid patterns beyond the GC dominance. We investigated the conceptually translated proteomes of 1029 bacterial and archaeal strains with sequenced genomes for amino acid composition. Using correspondence analysis, we found that phylogenetic groups within bacteria and archaea generally can be discriminated from other groups due to their amino acid composition. In some cases, single organisms, e.g. Treponema pallidum strains or Mycoplasma penetrans, are characterized by extreme amino acid compositions. We assume that our data could provide a basis for a new approach to analyze evolution of bacterial and archaeal groups. Furthermore, for single organisms, the detailed knowledge of the amino acid composition of the entire proteome encoded in the genome could lead to a better understanding, important for pharmaceutical or biotechnological applications. We recommend that information about amino acid compositions should be provided in databases, comparable to the GC content of genomes.

Metallothionein protein evolution: a miniassay

Metallothionein (MT) evolution is one of the most obscure yet fascinating aspects of the study of these atypical metal-binding peptides. The different members of the extremely heterogeneous MT protein superfamily probably evolved through a web of duplication, functional differentiation, and/or convergence events leading to the current scenario, which is particularly hard to interpret in terms of molecular evolution. Difficulties in drawing straight evolutionary relationships are reflected in the lack of definite MT classification criteria. Presently, MTs are categorized either according to a pure taxonomic clustering or depending on their metal binding preferences and specificities. Extremely well documented MT revisions were recently published. But beyond classic approaches, this review of MT protein evolution will bring together new aspects that have seldom been discussed before. Hence, the emergence of life on our planet, since metal ion utilization is accepted to be at the root of the emergence of living organisms, and global trends that underlie structural and functional MT diversification, will be presented. Major efforts are currently being devoted to identifying rules for function-constrained MT evolution that may be applied to different groups of organisms.