scholarly journals The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1049
Author(s):  
Laurens Maertens ◽  
Natalie Leys ◽  
Jean-Yves Matroule ◽  
Rob Van Houdt
Keyword(s):  
Sulfur Metabolism ◽  
Model Organism ◽  
Gene Clusters ◽  
Resistance Mechanisms ◽  
Metal Resistance ◽  
Copper Resistance ◽  
Messenger Rnas ◽  
Antisense Transcripts ◽  
Cupriavidus Metallidurans Ch34 ◽  
Cupriavidus Metallidurans

Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of Cupriavidus metallidurans CH34 cells acutely exposed to copper by tagRNA-sequencing. C. metallidurans CH34 is a model organism for metal resistance, and its potential as a biosensor and candidate for metal bioremediation has been demonstrated in multiple studies. Several metabolic pathways were impacted by Cu exposure, and a broad spectrum of metal resistance mechanisms, not limited to copper-specific clusters, was overexpressed. In addition, several gene clusters involved in the oxidative stress response and the cysteine-sulfur metabolism were induced. In total, 7500 transcription start sites (TSSs) were annotated and classified with respect to their location relative to coding sequences (CDSs). Predicted TSSs were used to re-annotate 182 CDSs. The TSSs of 2422 CDSs were detected, and consensus promotor logos were derived. Interestingly, many leaderless messenger RNAs (mRNAs) were found. In addition, many mRNAs were transcribed from multiple alternative TSSs. We observed pervasive intragenic TSSs both in sense and antisense to CDSs. Antisense transcripts were enriched near the 5′ end of mRNAs, indicating a functional role in post-transcriptional regulation. In total, 578 TSSs were detected in intergenic regions, of which 35 were identified as putative small regulatory RNAs. Finally, we provide a detailed analysis of the main copper resistance clusters in CH34, which include many intragenic and antisense transcripts. These results clearly highlight the ubiquity of noncoding transcripts in the CH34 transcriptome, many of which are putatively involved in the regulation of metal resistance.

scholarly journals Transcriptomes of the Extremely Thermoacidophilic Archaeon Metallosphaera sedula Exposed to Metal “Shock” Reveal Generic and Specific Metal Responses

2016 ◽  
Vol 82 (15) ◽  
pp. 4613-4627 ◽  
Author(s):  
Garrett H. Wheaton ◽  
Arpan Mukherjee ◽  
Robert M. Kelly
Keyword(s):  
Metal Toxicity ◽  
Cellular Response ◽  
Sulfur Metabolism ◽  
Metal Resistance ◽  
Open Reading Frames ◽  
Copper Resistance ◽  
Natural Environments ◽  
Cluster Assembly ◽  
Content Type ◽  
Metallosphaera Sedula

ABSTRACTThe extremely thermoacidophilic archaeonMetallosphaera sedulamobilizes metals by novel membrane-associated oxidase clusters and, consequently, requires metal resistance strategies. This issue was examined by “shocking”M. sedulawith representative metals (Co2+, Cu2+, Ni2+, UO22+, Zn2+) at inhibitory and subinhibitory levels. Collectively, one-quarter of the genome (554 open reading frames [ORFs]) responded to inhibitory levels, and two-thirds (354) of the ORFs were responsive to a single metal. Cu2+(259 ORFs, 106 Cu2+-specific ORFs) and Zn2+(262 ORFs, 131 Zn2+-specific ORFs) triggered the largest responses, followed by UO22+(187 ORFs, 91 UO22+-specific ORFs), Ni2+(93 ORFs, 25 Ni2+-specific ORFs), and Co2+(61 ORFs, 1 Co2+-specific ORF). While one-third of the metal-responsive ORFs are annotated as encoding hypothetical proteins, metal challenge also impacted ORFs responsible for identifiable processes related to the cell cycle, DNA repair, and oxidative stress. Surprisingly, there were only 30 ORFs that responded to at least four metals, and 10 of these responded to all five metals. This core transcriptome indicated induction of Fe-S cluster assembly (Msed_1656-Msed_1657), tungsten/molybdenum transport (Msed_1780-Msed_1781), and decreased central metabolism. Not surprisingly, a metal-translocating P-type ATPase (Msed_0490) associated with a copper resistance system (Cop) was upregulated in response to Cu2+(6-fold) but also in response to UO22+(4-fold) and Zn2+(9-fold). Cu2+challenge uniquely induced assimilatory sulfur metabolism for cysteine biosynthesis, suggesting a role for this amino acid in Cu2+resistance or issues in sulfur metabolism. The results indicate thatM. sedulaemploys a range of physiological and biochemical responses to metal challenge, many of which are specific to a single metal and involve proteins with yet unassigned or definitive functions.IMPORTANCEThe mechanisms by which extremely thermoacidophilic archaea resist and are negatively impacted by metals encountered in their natural environments are important to understand so that technologies such as bioleaching, which leverage microbially based conversion of insoluble metal sulfides to soluble species, can be improved. Transcriptomic analysis of the cellular response to metal challenge provided both global and specific insights into how these novel microorganisms negotiate metal toxicity in natural and technological settings. As genetics tools are further developed and implemented for extreme thermoacidophiles, information about metal toxicity and resistance can be leveraged to create metabolically engineered strains with improved bioleaching characteristics.

Copper Resistance Mechanisms of Biomining Bacteria and Archaea Living under Extremely High Concentrations of Metals

2009 ◽  
Vol 71-73 ◽  
pp. 279-282 ◽  
Author(s):  
A. Orell ◽  
C.A. Navarro ◽  
Carlos A. Jerez
Keyword(s):  
Resistance Mechanisms ◽  
Metal Resistance ◽  
Copper Resistance ◽  
Inorganic Polyphosphate ◽  
Resistance Determinants ◽  
High Metal ◽  
Pi Complex ◽  
Cu Resistance ◽  
High Concentrations ◽  
Cu Tolerance

Extremophiles such as the acidophilic Sulfolobus metallicus (Archaea) and Acidithiobacillus ferrooxidans (Bacteria) can resist Cu (CuSO4) concentrations of 200 mM and 800 mM respectively. These microorganisms are important in biomining processes to extract copper and other metals. A. ferrooxidans grown at low Cu concentrations (5 mM) expressed genes coding for ATPases most likely involved in pumping the metal from the cytoplasm to the periplasm of the bacterium. At 100 mM Cu the previous systems were repressed and there was a great induction in the expression of efflux systems known to use the proton motive force energy to export the metal outside the cell. These Cu-resistance determinants from A. ferrooxidans were found to be functional since when expressed in Escherichia coli they conferred higher Cu tolerance to it. Novel Cu-resistance determinants for A. ferrooxidans were found and characterized. S. metallicus possessed at least 2 CopM metallochaperones and 2 CopA ATPases whose expressions were induced by Cu (5 to 50 mM). Furthermore, we previously reported that both microorganisms accumulate high levels of inorganic polyphosphate (PolyP) and that intracellular Cu concentration stimulates polyP hydrolysis. The resulting Pi would then be transported out of the cell as a metal-Pi complex to detoxify the cells. In addition, our results suggest that at high Cu concentrations polyP could also provide energy for the metal efflux. All the data suggest that both biomining microorganisms use different systems to respond to Cu depending on the extracellular concentrations of the metal and suggest that the presence of different additional systems to respond to Cu may explain the extremely high metal resistance of these extremophiles.

scholarly journals Streptococcus agalactiaefrom pregnant women: antibiotic and heavy-metal resistance mechanisms and molecular typing

2016 ◽  
Vol 144 (15) ◽  
pp. 3205-3214 ◽  
Author(s):  
B. ROJO-BEZARES ◽  
J. M. AZCONA-GUTIÉRREZ ◽  
C. MARTIN ◽  
M. S. JAREÑO ◽  
C. TORRES ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Pregnant Women ◽  
Heavy Metal Resistance ◽  
Resistance Mechanisms ◽  
Metal Resistance ◽  
Copper Resistance ◽  
Cross Resistance ◽  
Northern Spain ◽  
Single Strain ◽  
Genetic Lineages

SUMMARYWe investigated the antibiotic and heavy-metal resistance mechanisms, virulence genes and clonal relationships of macrolide- and/or lincosamide-resistant (M+/−LR)Streptococcus agalactiae(group BStreptococcus, GBS) isolates from pregnant women in La Rioja in Northern Spain, a region with a significant immigrant population. In total 375 GBS isolates were recovered during 2011. About three-quarters of isolates were from European nationals and the remainder distributed among 23 other nationalities. Seventy-five (20%) were classified as M+/−LRstrains and 28 (37%) of these were resistant to ⩾3 classes of antibiotics. Capsular serotypes III (29·3%), V (21·3%) and II (12%) were the most frequent. A wide variety of antibiotic resistance genes were detected in M+/−LRstrains; notably, 5·3% harboured thelsa(C) gene associated with cross-resistance, andtet(W) was identified in a single strain. We report, for the first time, the detection of cadmium and copper resistance encoded bytcrB+cadA+cadCgenes in 20 M+/−LRstrains, which raises the possibility of co-selection of antibiotic and heavy-metal resistance disseminated through mobile genetic elements. The M+/−LRstrains were highly diverse by DNA macrorestriction profiles (65 patterns) and 16 multilocus sequence types (STs) distributed among six clonal complexes; the most frequent were ST1, ST19, and ST12, and two strains were novel (ST586 and ST601). In conclusion, a wide diversity of genetic lineages of macrolide, lincosamide and heavy-metal- resistant GBS strains was observed in an ethnically diverse maternal population.

scholarly journals The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11373
Author(s):  
Claudia Clavero-León ◽  
Daniela Ruiz ◽  
Javier Cillero ◽  
Julieta Orlando ◽  
Bernardo González
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Growth ◽  
Growth Promotion ◽  
Growth Parameters ◽  
Primary Root ◽  
Metal Mobility ◽  
Copper Resistance ◽  
Specific Gene ◽  
Cupriavidus Metallidurans Ch34 ◽  
Cupriavidus Metallidurans

Copper (Cu) is important for plant growth, but high concentrations can lead to detrimental effects such as primary root length inhibition, vegetative tissue chlorosis, and even plant death. The interaction between plant-soil microbiota and roots can potentially affect metal mobility and availability, and, therefore, overall plant metal concentration. Cupriavidus metallidurans CH34 is a multi metal-resistant bacterial model that alters metal mobility and bioavailability through ion pumping, metal complexation, and reduction processes. The interactions between strain CH34 and plants may affect the growth, metal uptake, and translocation of Arabidopsis thaliana plants that are exposed to or not exposed to Cu. In this study, we looked also at the specific gene expression changes in C. metallidurans when co-cultured with Cu-exposed A. thaliana. We found that A. thaliana’s rosette area, primary and secondary root growth, and dry weight were affected by strain CH34, and that beneficial or detrimental effects depended on Cu concentration. An increase in some plant growth parameters was observed at copper concentrations lower than 50 µM and significant detrimental effects were found at concentrations higher than 50 µM Cu. We also observed up to a 90% increase and 60% decrease in metal accumulation and mobilization in inoculated A. thaliana. In turn, copper-stressed A. thaliana altered C. metallidurans colonization, and cop genes that encoded copper resistance in strain CH34 were induced by the combination of A. thaliana and Cu. These results reveal the complexity of the plant-bacteria-metal triad and will contribute to our understanding of their applications in plant growth promotion, protection, and phytoremediation strategies.

scholarly journals Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34

Microbiology ◽  
2006 ◽  
Vol 152 (6) ◽  
pp. 1765-1776 ◽  
Author(s):  
Sébastien Monchy ◽  
Mohammed A. Benotmane ◽  
Ruddy Wattiez ◽  
Sébastien van Aelst ◽  
Vanessa Auquier ◽  
...  
Keyword(s):  
Survival Curve ◽  
Gene Clusters ◽  
Department Of Energy ◽  
Joint Genome Institute ◽  
Copper Resistance ◽  
Late Response ◽  
Two Dimensional Gel Electrophoresis ◽  
Proteomic Data ◽  
Cupriavidus Metallidurans ◽  
Related Plant

The four replicons of Cupriavidus metallidurans CH34 (the genome sequence was provided by the US Department of Energy–University of California Joint Genome Institute) contain two gene clusters putatively encoding periplasmic resistance to copper, with an arrangement of genes resembling that of the copSRABCD locus on the 2.1 Mb megaplasmid (MPL) of Ralstonia solanacearum, a closely related plant pathogen. One of the copSRABCD clusters was located on the 2.6 Mb MPL, while the second was found on the pMOL30 (234 kb) plasmid as part of a larger group of genes involved in copper resistance, spanning 17 857 bp in total. In this region, 19 ORFs (copVTMKNSRABCDIJGFLQHE) were identified based on the sequencing of a fragment cloned in an IncW vector, on the preliminary annotation by the Joint Genome Institute, and by using transcriptomic and proteomic data. When introduced into plasmid-cured derivatives of C. metallidurans CH34, the cop locus was able to restore the wild-type MIC, albeit with a biphasic survival curve, with respect to applied Cu(II) concentration. Quantitative-PCR data showed that the 19 ORFs were induced from 2- to 1159-fold when cells were challenged with elevated Cu(II) concentrations. Microarray data showed that the genes that were most induced after a Cu(II) challenge of 0.1 mM belonged to the pMOL30 cop cluster. Megaplasmidic cop genes were also induced, but at a much lower level, with the exception of the highly expressed MPL copD. Proteomic data allowed direct observation on two-dimensional gel electrophoresis, and via mass spectrometry, of pMOL30 CopK, CopR, CopS, CopA, CopB and CopC proteins. Individual cop gene expression depended on both the Cu(II) concentration and the exposure time, suggesting a sequential scheme in the resistance process, involving genes such as copK and copT in an initial phase, while other genes, such as copH, seem to be involved in a late response phase. A concentration of 0.4 mM Cu(II) was the highest to induce maximal expression of most cop genes.

scholarly journals The Response of Cupriavidus Metallidurans CH34 to Cadmium Involves a Decrease in Intracellular Levels of C-Di-GMP Probably Mediated by a Novel Metal Regulated Phosphodiesterase That Inhibits the Biofilm Lifestyle

2018 ◽  
Author(s):  
Pablo Alviz ◽  
Sebastian Fuentes ◽  
Luis Rojas ◽  
Raymond Turner ◽  
Michael Seeger ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Biofilm Formation ◽  
Bioinformatic Analysis ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Cadmium Resistance ◽  
Toxic Heavy Metal ◽  
Transcription Analysis ◽  
Cupriavidus Metallidurans Ch34 ◽  
Cupriavidus Metallidurans

Cadmium is a highly toxic heavy metal for biological systems. Cupriavidus metallidurans CH34 is a model strain for heavy metal resistance and bioremediation. The aim of this study was to determine the role of the c-di-GMP pathway in the C. metallidurans CH34 response to cadmium in both planktonic and biofilm cells. Increasing cadmium concentrations correlates with an inhibition of biofilm formation and EPS production in C. metallidurans cells. Planktonic and biofilm cells showed similar tolerance to cadmium. During exposure to cadmium an acute decrease of c-di-GMP levels in planktonic and biofilm cells was observed. Transcription analysis by RT-qPCR showed that cadmium induced in planktonic cells and strongly induced in biofilm cells the expression of the urf2 gene and the mercuric reductase encoding merA gene, which belong to the Tn501/Tn21 mer operon. After exposure to cadmium the cadA gene involved in cadmium resistance was equally upregulated in both lifestyles. Bioinformatic analysis and null mutant complementation assays indicated that the protein encoded by the urf2 gene is a functional phosphodiesterase involved in the c-di-GMP metabolism. We propose to rename the urf2 gene as mrp gene for metal regulated phosphodiesterase. An increase of the second messenger c-di-GMP content by the heterologous expression of the constitutively active diguanylate cyclase PleD* correlated with an increase in biofilm formation and cadmium susceptibility. These results indicate that the response to cadmium in C. metallidurans CH34 involves a decrease in c-di-GMP content that inhibits the biofilm lifestyle.

Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network

BioMetals ◽  
2011 ◽  
Vol 24 (6) ◽  
pp. 1133-1151 ◽  
Author(s):  
Pieter Monsieurs ◽  
Hugo Moors ◽  
Rob Van Houdt ◽  
Paul J. Janssen ◽  
Ann Janssen ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Transcriptional Network ◽  
Cupriavidus Metallidurans Ch34 ◽  
Cupriavidus Metallidurans

scholarly journals Cupriavidus metallidurans CH34, a historical perspective on its discovery, characterization and metal resistance

2020 ◽  
Author(s):  
Max Mergeay ◽  
Rob Van Houdt
Keyword(s):  
Type Strain ◽  
Historical Perspective ◽  
Bacterial Resistance ◽  
Metal Resistance ◽  
Early Research ◽  
Molecular Techniques ◽  
Ecological Niches ◽  
Cupriavidus Metallidurans Ch34 ◽  
Resistance Determinants ◽  
Cupriavidus Metallidurans

Abstract Cupriavidus metallidurans, and in particular type strain CH34, became a model bacterium to study bacterial resistance to metals. Although nowadays the routine use of a wide variety of omics and molecular techniques allow refining, deepening and expanding our knowledge on adaptation and resistance to metals, these were not available at the onset of C. metallidurans research starting from its isolation in 1976. This minireview describes the early research and legacy tools used to study its metal resistance determinants, characteristic megaplasmids, ecological niches and environmental applications.

scholarly journals Unintentional Genomic Changes Endow Cupriavidus metallidurans with an Augmented Heavy-Metal Resistance

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 551 ◽  
Author(s):  
Felipe Millacura ◽  
Paul Janssen ◽  
Pieter Monsieurs ◽  
Ann Janssen ◽  
Ann Provoost ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sequence Data ◽  
Gene Clusters ◽  
Metal Resistance ◽  
Model Organisms ◽  
Mercury Resistance ◽  
Genome Comparison ◽  
Nucleotide Polymorphisms ◽  
Entire Genome ◽  
Cupriavidus Metallidurans

For the past three decades, Cupriavidus metallidurans has been one of the major model organisms for bacterial tolerance to heavy metals. Its type strain CH34 contains at least 24 gene clusters distributed over four replicons, allowing for intricate and multilayered metal responses. To gain organic mercury resistance in CH34, broad-spectrum mer genes were introduced in a previous work via conjugation of the IncP-1β plasmid pTP6. However, we recently noted that this CH34-derived strain, MSR33, unexpectedly showed an increased resistance to other metals (i.e., Co2+, Ni2+, and Cd2+). To thoroughly investigate this phenomenon, we resequenced the entire genome of MSR33 and compared its DNA sequence and basal gene expression profile to those of its parental strain CH34. Genome comparison identified 11 insertions or deletions (INDELs) and nine single nucleotide polymorphisms (SNPs), whereas transcriptomic analysis displayed 107 differentially expressed genes. Sequence data implicated the transposition of IS1088 in higher Co2+ and Ni2+ resistances and altered gene expression, although the precise mechanisms of the augmented Cd2+ resistance in MSR33 remains elusive. Our work indicates that conjugation procedures involving large complex genomes and extensive mobilomes may pose a considerable risk toward the introduction of unwanted, undocumented genetic changes. Special efforts are needed for the applied use and further development of small nonconjugative broad-host plasmid vectors, ideally involving CRISPR-related and advanced biosynthetic technologies.

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