Cadmium Resistance, Microbial Biosorptive Performance and Mechanisms of a Novel Biocontrol Bacterium Paenibacillus sp. LYX-1

In order to explore whether the newly discovered biocontrol strain Paenibacillus sp., LYX-1 having antagonistic effect on peach brown rot was resistant to Cd2+, a series of growth of strain LYX-1 under different Cd concentration and biosorption experiments were conducted to living and dead strain LYX-1. Meanwhile, the Cd2+ resistance and biosorption mechanisms were further identified by Cd-resistant genes, TEM, SEM-EDS, FTIR and XPS analysis. The results showed that strain LYX-1 could resist 50 mg/L Cd2+ and the adsorption process of both living and dead strain LYX-1 all satisfied the pseudo-second kinetic equation. Under pH 8.0 and at a dose of 1.0 g/L strain, the removal capacities of living and dead cells were as high as 90.39% and 75.67% at 20 mg/L Cd2+, respectively. For the adsorption isotherm test, results revealed that both Langmuir (R2=0.9704) and Freundlich (R2=0.9915) model could describe the Cd2+ biosorption well for living strain LYX-1. The maximum equilibrium biosorption capacities of living and dead biomass were 30.6790 and 24.3752 mg/g, respectively. The adsorption mechanism was controlled by chemisorption with -OH, -NH, -C=O, O=C-O, C-N, S2− and phosphate functional groups on the cell surface of strain LYX-1, which were further identified by XPS. The insignificant biosorption difference of living and dead biomass was caused by CzcD gene in strain LYX-1 detoxifying cadmium through the heavy metal efflux system. The above results indicated that strain LYX-1 had higher tolerance and fixed capacity to Cd2+.

Cryo-EM Structures of CusA Reveal a Mechanism of Metal-Ion Export

ABSTRACT Gram-negative bacteria utilize the resistance-nodulation-cell division (RND) superfamily of efflux pumps to expel a variety of toxic compounds from the cell. The Escherichia coli CusA membrane protein, which recognizes and extrudes biocidal Cu(I) and Ag(I) ions, belongs to the heavy-metal efflux (HME) subfamily of RND efflux pumps. We here report four structures of the trimeric CusA heavy-metal efflux pump in the presence of Cu(I) using single-particle cryo-electron microscopy (cryo-EM). We discover that different CusA protomers within the trimer are able to bind Cu(I) ions simultaneously. Our structural data combined with molecular dynamics (MD) simulations allow us to propose a mechanism for ion transport where each CusA protomer functions independently within the trimer. IMPORTANCE The bacterial RND superfamily of efflux pumps mediate resistance to a variety of biocides, including Cu(I) and Ag(I) ions. Here we report four cryo-EM structures of the trimeric CusA pump in the presence of Cu(I). Combined with MD simulations, our data indicate that each CusA protomer within the trimer recognizes and extrudes Cu(I) independently.

Characterisation of multiple heavy metal resistance loci in the genome of the novel species Cupriavidus neocaledonicus STM 6070, a nickel- and zinc-tolerant Mimosa pudica microsymbiont isolated from mining site soil

Background Cupriavidus strain STM 6070 was isolated from nickel-rich mine roadside soil near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems. Results The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6,118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica -nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to five symbiotic and three non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance. Conclusions STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica -nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.

The NAD+-dependent deacetylase Sir2 enables evolution of new traits by regulating distinct gene sets in two yeast species, Saccharomyces cerevisiae and Kluyveromyces lactis

ABSTRACTEvolutionary adaptation increases the fitness of an organism in its environment. It can occur through rewiring of gene regulatory networks, such that an organism responds appropriately to environmental changes. We investigated whether sirtuin deacetylases, which repress transcription and require NAD+ for activity, could facilitate the evolution of potentially adaptive responses by serving as transcriptional rewiring points. If so, bringing genes under the control of sirtuins could enable organisms to mount appropriate responses to stresses that decrease NAD+ levels. To explore how the genomic targets of sirtuins shift over evolutionary time, we compared two yeast species, Saccharomyces cerevisiae and Kluyveromyces lactis that display differences in cellular metabolism and lifecycle timing in response to nutrient availability. We identified sirtuin-regulated genes through a combination of chromatin immunoprecipitation and RNA expression. In both species, regulated genes were associated with NAD+ homeostasis, mating, and sporulation, but the specific genes differed. In addition, regulated genes in K. lactis were associated with other processes, including utilization of non-glucose carbon sources, heavy metal efflux, DNA synthesis, and production of the siderophore pulcherrimin. Consistent with the species-restricted regulation of these genes, sirtuin deletion impacted relevant phenotypes in K. lactis but not S. cerevisiae. Finally, sirtuin-regulated gene sets were depleted for broadly-conserved genes, consistent with sirtuins regulating processes restricted to a few species. Taken together, these results are consistent with the notion that sirtuins serve as rewiring points that allow species to evolve distinct responses to low NAD+ stress.

Changes of enzyme activities related to oxidative stress in rice plants inoculated with random mutants of a Pseudomonas fluorescens strain able to improve plant fitness upon biotic and abiotic conditions

The Pseudomonas fluorescens strain used in this work (Aur 6) has demonstrated its ability to improve fitness of different plant species upon biotic and abiotic stress conditions. Random mutants of this strain were constructed with the Tn5 transposon technology, and biological tests to evaluate loss of salt protection were conducted with all the mutants (104 mutants) on rice seedlings. Mutant 33 showed an evident reduction in its ability to protect plants upon salt stress challenge, whereas mutant 19 was more effective than the wild type. Enzymes related with oxidative stress were studied in both mutants and wild type. Enzyme activities were decreased with mutant 33 with regard to wild type, whereas mutant 19 did not produce important changes suggesting involvement of redox balance associated to the observed modifications in these antioxidant enzymes as one of the probable mechanisms used by these strains. Data of malondialdehyde (MDA) were consistent with this fact. Mutants also affected accumulation of proline, the most common osmolyte in plants. A second experiment to evaluate the ability of both mutants and wild type to stimulate growth on tomato plants was conducted, as this feature was previously demonstrated by wild type. Similar results were obtained in growth of both species, suggesting that mutations of both mutants are related with the capacities of the wild type to stimulate growth. To reveal mutated genes, both mutants were mapped. Three mutated genes were found in mutant 33. A gene related with a general secretion pathway protein D, a gene related with a putative two-component system sensor kinase (ColS), and a gene related with flagellar motor switch protein (FliG). In mutant 19, two mutated genes were found. One gene related with heavy metal efflux pump Czca family, and other gene of 16s rRNA.