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. 2021 Jan 27;12(2):187.
doi: 10.3390/genes12020187.

Genomics Insights into Pseudomonas sp. CG01: An Antarctic Cadmium-Resistant Strain Capable of Biosynthesizing CdS Nanoparticles Using Methionine as S-Source

Carla Gallardo-Benavente  1   2 , Jessica L Campo-Giraldo  3 , Juan Castro-Severyn  4 , Andrés Quiroz  2   5 , José M Pérez-Donoso  3
Affiliations

Genomics Insights into Pseudomonas sp. CG01: An Antarctic Cadmium-Resistant Strain Capable of Biosynthesizing CdS Nanoparticles Using Methionine as S-Source

Carla Gallardo-Benavente et al. Genes (Basel). .

Abstract

Here, we present the draft genome sequence of Pseudomonas sp. GC01, a cadmium-resistant Antarctic bacterium capable of biosynthesizing CdS fluorescent nanoparticles (quantum dots, QDs) employing a unique mechanism involving the production of methanethiol (MeSH) from methionine (Met). To explore the molecular/metabolic components involved in QDs biosynthesis, we conducted a comparative genomic analysis, searching for the genes related to cadmium resistance and sulfur metabolic pathways. The genome of Pseudomonas sp. GC01 has a 4,706,645 bp size with a 58.61% G+C content. Pseudomonas sp. GC01 possesses five genes related to cadmium transport/resistance, with three P-type ATPases (cadA, zntA, and pbrA) involved in Cd-secretion that could contribute to the extracellular biosynthesis of CdS QDs. Furthermore, it exhibits genes involved in sulfate assimilation, cysteine/methionine synthesis, and volatile sulfur compounds catabolic pathways. Regarding MeSH production from Met, Pseudomonas sp. GC01 lacks the genes E4.4.1.11 and megL for MeSH generation. Interestingly, despite the absence of these genes, Pseudomonas sp. GC01 produces high levels of MeSH. This is probably associated with the metC gene that also produces MeSH from Met in bacteria. This work is the first report of the potential genes involved in Cd resistance, sulfur metabolism, and the process of MeSH-dependent CdS QDs bioproduction in Pseudomonas spp. strains.

Keywords: Antarctic bacteria; comparative genomics; nanoparticle biosynthesis; volatile sulfur compounds.

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Conflict of interest statement

The authors declare that this research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Genome characteristics of Pseudomonas sp. GC01. (a) Complete chromosome map of Pseudomonas sp. GC01. The chromosome map comprises six circles. The dark-blue and light-blue circles show the positions of the protein-coding genes on the plus and minus strands. The black bars on the third circle represent tRNA genes. The green bars on the fourth circle represent rRNA genes. The pink/red circle shows the GC content. The purple/yellow circle shows the GC skew. (b) Distribution of COG categories on the Pseudomonas sp. GC01 predicted proteins. The figure shows the number of CDSs assigned in each COG category depicted by color.
Figure 2
Figure 2
Heatmap displaying the relationships (hierarchical clustering) between the 28 Pseudomonas strains based on ANI analysis. The color gradients show the percentage of identity shared by each pair of genomes, from lowest (blue) to highest (red).
Figure 3
Figure 3
Phylogeny and pan-genome of 28 Pseudomonas strains. (a) Circular phylogenetic tree showing the relationships between all Pseudomonas strains, inferred based on the core-genome sequences alignment. (b) Flower diagram representing the amount of core and accessory clusters for each Pseudomonas strain considered in the pan-genome.
Figure 4
Figure 4
Heatmap of the metal-resistance genes present on the 28 Pseudomonas genomes. The scale shows the copy number of each gene in the corresponding genome, the metal(loid)/compound associated with the gene, and the database used.
Figure 5
Figure 5
Schematic representation of the cadmium-resistance mechanisms based on the Pseudomonas genomes results. Protein names in blue are those found in the genome of Pseudomonas sp. GC01.
Figure 6
Figure 6
Heatmap of the sulfur metabolic genes present in the 28 Pseudomonas genomes analyzed. (a) Sulfur metabolism genes. (b) Cysteine and methionine metabolism genes. The heat scale shows the copy number of each gene in the corresponding genome.
Figure 7
Figure 7
Sulfur metabolic pathways present in the genome of Pseudomonas sp. GC01. The schematic representation of protein identified in the genome of Pseudomonas sp. GC01 involved in sulfur assimilation, cysteine and methionine synthesis, and volatile sulfur compounds catabolic pathways. Protein names in red were not found in this strain but present in other Pseudomonas strains.
Figure 8
Figure 8
Schematic representation of the CdS QDs biosynthesis by Pseudomonas sp. GC01. The figure shows the proteins present in the Pseudomonas sp. GC01 genome involved in the biosynthesis of CdS nanoparticles when Cys (CysK and MetC) or Met (MetC) was used as the sulfur source as well as the Cd2+ efflux pumps CadA, ZntA, and PbrA.
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References

    1. Cary S.C., McDonald I.R., Barrett J.E., Cowan D.A. On the rocks: The microbiology of Antarctic dry valley soils. Nat. Rev. Microbiol. 2010;8:129–138. doi: 10.1038/nrmicro2281. - DOI - PubMed
    1. Wasley J., Robinson S.A., Lovelock C.E., Popp M. Climate change manipulations show Antarctic flora is more strongly affected by elevated nutrients than water. Glob. Chang. Biol. 2006;12:1800–1812. doi: 10.1111/j.1365-2486.2006.01209.x. - DOI
    1. Nichols D.S., Sanderson K., Buia A., Van de Kamp J., Holloway P., Bowman J.P., Smith M., Nichols C.M., Nichols P.D., McMeekin T.A. Bioprospecting and biotechnology in Antarctica. In: Jabour-Green J., Haward M., editors. The Antarctic: Past, Present and Future, Antarctic CRC Research Report 28. Antarctic CRC; Hobart, Australia: 2002. pp. 85–103.
    1. Romoli R., Papaleo M., de Pascale D., Tutino M., Michaud L., LoGiudice A., Bartolucci G. Characterization of the volatile profile of Antarctic bacteria by using solid-phase microextraction– gas chromatography-mass spectrometry. J. Mass Spectrom. 2011;46:1051–1059. doi: 10.1002/jms.1987. - DOI - PubMed
    1. Papaleo M., Fondi M., Maida I., Perrin E., Lo Giudice A., Michaud L., Mangano S., Bartolucci G., Romoli R., Fani R. Sponge-associated microbial Antarctic communities exhibiting antimicrobial activity against Burkholderia cepacia complex bacteria. Biotechnol. Adv. 2012;30:272–293. doi: 10.1016/j.biotechadv.2011.06.011. - DOI - PubMed

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