The Myxococcus xanthus two-component system CorSR regulates expression of a gene cluster involved in maintaining copper tolerance during growth and development

Adaptive Mechanisms of Shewanella xiamenensis DCB 2-1 Metallophilicity

The dose-dependent effects of single metals (Zn, Ni, and Cu) and their combinations at steady time-actions on the cell viability of the bacteria Shewanella xiamenensis DCB 2-1, isolated from a radionuclide-contaminated area, have been estimated. The accumulation of metals by Shewanella xiamenensis DCB 2-1 in single and multi-metal systems was assessed using the inductively coupled plasma atomic emission spectroscopy. To estimate the response of the bacteria's antioxidant defense system, doses of 20 and 50 mg/L of single studied metals and 20 mg/L of each metal in their combinations (non-toxic doses, determined by the colony-forming viability assay) were used. Emphasis was given to catalase and superoxide dismutase since they form the primary line of defense against heavy metal action and their regulatory circuit of activity is crucial. The effect of metal ions on total thiol content, an indicator of cellular redox homeostasis, in bacterial cells was evaluated. Genome sequencing of Shewanella xiamenensis DCB 2-1 reveals genes responsible for heavy metal tolerance and detoxification, thereby improving understanding of the potential of the bacterial strain for bioremediation.

Insights into the biodegradation and heavy metal resistance potential of the genus Brevibacillus through comparative genome analyses

Members of the genus Brevibacillus belonging to the familyPaenibacillaceae are Gram-positive/variable, endospore-forming, and rod-shaped bacteria that dwell in various environmental habitats. Brevibacillus spp. have a wide range of enzyme activities such as degradation of various carbohydrates, plastics, and they possess resistance against heavy metals. These characteristics make them encouraging contenders for biotechnological applications.In this work, we analyzed the reference genomes of 19Brevibacillusspecies, focusing on discovering the biodegradation and heavy metal resistance capabilities of this little studied genus from genomic data. The results indicate that several strain specific traits were identified. For example Brevibacillus halotolerans s-14, and Brevibacillus laterosporus DSM 25 have more glycoside hydrolases (GHs) compared to other carbohydrate-active enzymes, and therefore might be more suitable for biodegradation of carbohydrates. In contrast, strains such as Brevibacillus antibioticus TGS2-1, with a higher number of glycosyltransfereases (GTs) may aid in the biosynthesis of complex carbohydrates. Our results also suggest some correlation between heavy metal resistance and polyurethane degradation, thus indicating that heavy metal resistance strains (e.g. Brevibacillus reuszeri J31TS6) can be a promising source of enzymes for polyurethane degradation. These strain specific features make the members of this bacterial group potential candidates for further investigations with industrial implications. This work also represents the first exhaustive study of Brevibacillus at the genome scale.

Insight into soilless revegetation of oligotrophic and heavy metal contaminated gold tailing pond by metagenomic analysis

Soilless revegetation is an efficient way for gold tailing remediation, and micro-ecological environments in plant rhizosphere are important for vegetation establishment and pollution removal. In the present study, a field experiment of soilless revegetation has been carried out in a gold tailings pond, and the key genera and functional genes in the plant rhizosphere of gold mine tailings were revealed by metagenomics analysis. Soilless revegetation significantly decreased rhizosphere tailing pH from 8.54 to 7.43-7.87, reduced heavy metal (HM) concentration by 29.81-44.02% and enhanced the nutrient content by 50.30-169.50% averagely. Such improvements were strongly and closely correlated to microbial community and functional gene composition variation. The relative abundance of ecologically beneficial genus such as Actinobacteria (increased 9.7-18.8%) and functional genes involved in carbon, nitrogen and phosphorus cycling such as pyruvate metabolism (relatively increased 8.7-15.0%), assimilatory (increased to 1.44-2.08 times), phosphate ester mineralization (increased to 1.12-1.29 times) and phosphate transportation (increased to 1.28-1.85 times) were significantly increased. Moreover, the relative abundance of most As and Zn resistance genes were reduced, which may relate to the decrease of As and Zn concentration in the rhizosphere tailings. These results revealed the correlation among HM concentrations, microbial composition and functional genes, and provided clear strategies for improving gold mine tailing ecological restoration efficiency.

Antimicrobial Activity of Metals and Metalloids

Competition shapes evolution. Toxic metals and metalloids have exerted selective pressure on life since the rise of the first organisms on the Earth, which has led to the evolution and acquisition of resistance mechanisms against them, as well as mechanisms to weaponize them. Microorganisms exploit antimicrobial metals and metalloids to gain competitive advantage over other members of microbial communities. This exerts a strong selective pressure that drives evolution of resistance. This review describes, with a focus on arsenic and copper, how microorganisms exploit metals and metalloids for predation and how metal- and metalloid-dependent predation may have been a driving force for evolution of microbial resistance against metals and metalloids. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genome-Driven Discovery of Enzymes with Industrial Implications from the Genus Aneurinibacillus

Bacteria belonging to the genus Aneurinibacillus within the family Paenibacillaceae are Gram-positive, endospore-forming, and rod-shaped bacteria inhabiting diverse environments. Currently, there are eight validly described species of Aneurinibacillus; however, several unclassified species have also been reported. Aneurinibacillus spp. have shown the potential for producing secondary metabolites (SMs) and demonstrated diverse types of enzyme activities. These features make them promising candidates with industrial implications. At present, genomes of 9 unique species from the genus Aneurinibacillus are available, which can be utilized to decipher invaluable information on their biosynthetic potential as well as enzyme activities. In this work, we performed the comparative genome analyses of nine Aneurinibacillus species representing the first such comprehensive study of this genus at the genome level. We focused on discovering the biosynthetic, biodegradation, and heavy metal resistance potential of this under-investigated genus. The results indicate that the genomes of Aneurinibacillus contain SM-producing regions with diverse bioactivities, including antimicrobial and antiviral activities. Several carbohydrate-active enzymes (CAZymes) and genes involved in heavy metal resistance were also identified. Additionally, a broad range of enzyme classes were also identified in the Aneurinibacillus pan-genomes, making this group of bacteria potential candidates for future investigations with industrial applications.

Copper and Melanin Play a Role in Myxococcus xanthus Predation on Sinorhizobium meliloti

Myxococcus xanthus is a soil myxobacterium that exhibits a complex lifecycle with two multicellular stages: cooperative predation and development. During predation, myxobacterial cells produce a wide variety of secondary metabolites and hydrolytic enzymes to kill and consume the prey. It is known that eukaryotic predators, such as ameba and macrophages, introduce copper and other metals into the phagosomes to kill their prey by oxidative stress. However, the role of metals in bacterial predation has not yet been established. In this work, we have addressed the role of copper during predation of M. xanthus on Sinorhizobium meliloti. The use of biosensors, variable pressure scanning electron microscopy, high-resolution scanning transmission electron microscopy, and energy dispersive X ray analysis has revealed that copper accumulates in the region where predator and prey collide. This accumulation of metal up-regulates the expression of several mechanisms involved in copper detoxification in the predator (the P_1B-ATPase CopA, the multicopper oxidase CuoA and the tripartite pump Cus2), and the production by the prey of copper-inducible melanin, which is a polymer with the ability to protect cells from oxidative stress. We have identified two genes in S. meliloti (encoding a tyrosinase and a multicopper oxidase) that participate in the biosynthesis of melanin. Analysis of prey survivability in the co-culture of M. xanthus and a mutant of S. meliloti in which the two genes involved in melanin biosynthesis have been deleted has revealed that this mutant is more sensitive to predation than the wild-type strain. These results indicate that copper plays a role in bacterial predation and that melanin is used by the prey to defend itself from the predator. Taking into consideration that S. meliloti is a nitrogen-fixing bacterium in symbiosis with legumes that coexists in soils with M. xanthus and that copper is a common metal found in this habitat as a consequence of several human activities, these results provide clear evidence that the accumulation of this metal in the soil may influence the microbial ecosystems by affecting bacterial predatory activities.

The complex global response to copper in the multicellular bacterium Myxococcus xanthus

The complex copper response of the multicellular proteobacterium M. xanthus includes structural genes similar to those described in other bacteria, such as P1B-type ATPases, multicopper oxidases, and heavy metal efflux systems. However, the two time-dependent expression profiles of the different copper systems are unique. There are a number of genes responsible for an immediate response, whose expression increases after the addition of copper, but rapidly decreases thereafter to basal levels. The regulatory element that controls this early response is CorE, a novel extracytoplasmic function σ factor that is activated by Cu2+ and inactivated by Cu+. Other genes are part of a maintenance response. These genes show a profile that slows up after the copper addition and reaches a plateau at 24-48 h incubation. Most of the genes involved in this response are encoded by the operon curA, which is regulated by the two-component system CorSR. Moreover, other genes involved in the maintenance response are regulated by different regulatory elements that remain unknown. Additionally, copper activates the transcription of the structural genes for carotenoid synthesis through a mechanism that requires the activation of the σ factor CarQ. Bearing in mind that M. xanthus is not very resistant to copper, it is speculated that the complexity of its copper response might be related to its complex life cycle.

Dissection of the sensor domain of the copper-responsive histidine kinase CorS from Myxococcus xanthus

Myxococcus xanthus CorSR is a two-component system responsible for maintaining the response of this bacterium to copper. In the presence of this metal it upregulates, among others, the genes encoding the multicopper oxidase CuoA and the P1B -ATPase CopA. Dissection of the periplasmic sensor domain of the histidine kinase CorS by the analysis of a series of in-frame deletion mutants generated in this portion of the protein has revealed that copper sensing requires a region of 28 residues in the N terminus and another region of nine residues in the C terminus. Point mutations at His34, His38 and His171 demonstrate that they are essential for the ability of CorS to sense copper. Furthermore, the use of a bacterial two-hybrid system has revealed dimerization between monomers of CorS even in the absence of any metal, and that copper enhances this interaction. When dimerization was tested with proteins mutated at the three essential His residues, it was observed that these proteins maintain the intrinsic dimerization ability in the absence of metal. In contrast to the wild-type protein, copper did not strengthen the interaction, corroborating that copper binding to the three His residues of CorS is required for enhancing dimerization and transmitting the signal.

In depth analysis of the mechanism of action of metal-dependent sigma factors: characterization of CorE2 from Myxococcus xanthus

Extracytoplasmic function sigma factors represent the third pillar of signal-transduction mechanisms in bacteria. The variety of stimuli they recognize and mechanisms of action they use have allowed their classification into more than 50 groups. We have characterized CorE2 from Myxococcus xanthus, which belongs to group ECF44 and upregulates the expression of two genes when it is activated by cadmium and zinc. Sigma factors of this group contain a Cys-rich domain (CRD) at the C terminus which is essential for detecting metals. Point mutations at the six Cys residues of the CRD have revealed the contribution of each residue to CorE2 activity. Some of them are essential, while others are either dispensable or their mutations only slightly affect the activity of the protein. However, importantly, mutation of Cys174 completely shifts the specificity of CorE2 from cadmium to copper, indicating that the Cys arrangement of the CRD determines the metal specificity. Moreover, the conserved CxC motif located between the σ2 domain and the σ4.2 region has also been found to be essential for activity. The results presented here contribute to our understanding of the mechanism of action of metal-dependent sigma factors and help to define new common features of the members of this group of regulators.