The effect of simulated copper stress on genes associated with the metabolism of polyphosphates and polyhydroxyalkanoates in Bacillus thuringiensis Y1

Aims: Bacillus thuringiensis Y1 is a copper-tolerant bacterium that can serve as a model for the elucidation of the mechanism of energy metabolism under simulated copper stress. This study aimed to elucidate the effects of simulated copper stress on the genes associated with the biosynthesis of polyhydroxyalkanoates (PAH) and the metabolism of polyphosphates (PP). Methodology and results: The gene expression study involved the growth of the bacterium in nutrient broth supplemented with two concentrations of copper sulphate (0.4 mM and 0.8 mM), followed by RNA extraction and quantification of four and 11 genes associated with the metabolism of polyphosphate (PP) and polyhydroxyalkanoates (PAHs) respectively, using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Three genes associated with polyphosphate metabolism, which are polyphosphate kinase (ppk), exopolyphosphatase (ppx) and NAD kinase (ppnk), were all shown to be upregulated by both 0.4 mM and 0.8 mM copper, except for the 5’-nucleotidase (surE) gene that was downregulated under the second treatment. Among the 11 genes associated with the metabolism of polyhydroxyalkanoates, only the 3-ketoacyl-CoA-thiolase (phaA) gene was upregulated in both treatments and highly expressed in the second treatment; the majority were downregulated and repressed. Conclusion, significance and impact of study: The study demonstrated that copper induces the metabolism of polyphosphates in B. thuringiensis Y1 that serve as an alternative source of energy under copper stress. This model can be extended to the study of other species of Bacillus under environmental stress

Genomic data of two bacillus and two pseudomonas strains isolated from the acid mine drainage site at Mamut Copper Mine, Ranau, Malaysia

The genomic data of four bacteria strains isolated from the abandoned Mamut Copper Mine, an Acid Mine Drainage (AMD) site is presented in this report. Two of these strains belong to the genus Bacillus , while the other two belong to the genus Pseudomonas. The draft genome size of Pseu- domonas sp. strain MCMY3 was 6,396,595 bp (GC: 63.3%), Bacillus sp. strain MCMY6 was 6,815,573 bp (GC: 35.2%), Bacillus sp. strain MCMY13 was 5,559,059 bp (GC: 35.5%) and Pseudomonas sp. strain MCMY15 was 7,381,777 bp (GC: 64.8%). These four genomes contained 4 93, 4 95, 4 95 and 579 annotated subsystems, respectively. The sequence data are available at GenBank sequence read archive with ac- cessions numbers SRX7859406, SRX7859404, SRX7859405 and SRX7293032 for strains MCMY3, MCMY6, MCMY13 and MCMY15, respectively

Bacterial diversity of the abandoned Mamut Copper Mine in Sabah, Malaysia and its correlation with copper contamination

The former Mamut Copper Mine, acid mine drainage site represents an anthropogenic altered landscape characterized by its acidic topsoil which is contaminated primarily with copper. Even though the mining operation was ceased at 1999, the bacterial diversity in this area has never been investigated. This study was conducted to ascertain the bacterial diversity of this abandoned copper mine and correlate it to the copper concentration in the soil. Methodology and results: Soil samples were collected from 7 sites near the mine pit and the vicinity. Soil samples were assessed for soil copper elemental concentration using inductively coupled plasma optical emission spectrometry and bacteria were isolated via serial dilution followed by culture on nutrient agar plates. Phylogenetic analysis was done based on the full-length sequences of 16S rRNA gene. Twenty-four phylotypes were obtained from the 7 locations which originated from the phyla Firmicutes, Actinobacteria, Bacteroidetes and Proteobacteria. The results of the study indicated that site 2 (6.030223°; 116.658030°), located in between the mine pit and the mine factory with a copper concentration of 88.96 ppm, possessed the most diverse bacterial community with a Shannon diversity index (H) of 1.68, evenness (EH) of 0.94 and richness (S) of 6. Conclusion, significance and impact of study: Current study revealed that there was a positive correlation between the copper concentration and the H index and the richness, but this was not reflected in the evenness. This is the first report of bacterial diversity from the former Mamut Copper Mine site. The data provided a valuable insight for the future monitoring of the bacterial community in this ecologically important niche

Adaptive Strategies of Bacillus thuringiensis Isolated from Acid Mine Drainage Site in Sabah, Malaysia

The adaptive process in bacteria is driven by specific genetic elements which regulate phenotypic characteristics such as tolerance to high metal ion concentrations and the secretion of protective biofilms. Extreme environments such as those associated with heavy metal pollution and extremes of acidity offer opportunities to study the adaptive mechanisms of microorganisms. This study focused on the genome analysis of Bacillus thuringiensis (Bt MCMY1), a gram positive rod shaped bacterium isolated from an acid mine drainage site in Sabah, Malaysia by using a combination of Single Molecule Real Time DNA Sequencing, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The genome size of Bt MCMY1 was determined to be 5,458,152 bases which was encoded on a single chromosome. Analysis of the genome revealed genes associated with resistance to Copper, Mercury, Arsenic, Cobalt, Zinc, Cadmium and Aluminum. Evidence from SEM and FTIR indicated that the bacterial colonies form distinct films which bear the signature of polyhydroxyalkanoates (PHA) and this finding was supported by the genome data indicating the presence of a genetic pathway associated with the biosynthesis of PHAs. This is the first report of a Bacillus sp. isolated from an acid mine drainage site in Sabah, Malaysia and the genome sequence will provide insights into the manner in which B. thuringiensis adapts to acid mine drainage

DUSP16 promotes cancer chemoresistance through regulation of mitochondria-mediated cell death

10.1038/s41467-021-22638-7NATURE COMMUNICATIONS12

Genome-wide association analyses identify three new susceptibility loci for primary angle closure glaucoma.

Primary angle closure glaucoma (PACG) is a major cause of blindness worldwide. We conducted a genome-wide association study including 1,854 PACG cases and 9,608 controls across 5 sample collections in Asia. Replication experiments were conducted in 1,917 PACG cases and 8,943 controls collected from a further 6 sample collections. We report significant associations at three new loci: rs11024102 in PLEKHA7 (per-allele odds ratio (OR)=1.22; P=5.33×10(-12)), rs3753841 in COL11A1 (per-allele OR=1.20; P=9.22×10(-10)) and rs1015213 located between PCMTD1 and ST18 on chromosome 8q (per-allele OR=1.50; P=3.29×10(-9)). Our findings, accumulated across these independent worldwide collections, suggest possible mechanisms explaining the pathogenesis of PACG

ABCC5, a Gene That Influences the Anterior Chamber Depth, Is Associated with Primary Angle Closure Glaucoma.

Anterior chamber depth (ACD) is a key anatomical risk factor for primary angle closure glaucoma (PACG). We conducted a genome-wide association study (GWAS) on ACD to discover novel genes for PACG on a total of 5,308 population-based individuals of Asian descent. Genome-wide significant association was observed at a sequence variant within ABCC5 (rs1401999; per-allele effect size = -0.045 mm, P = 8.17×10-9). This locus was associated with an increase in risk of PACG in a separate case-control study of 4,276 PACG cases and 18,801 controls (per-allele OR = 1.13 [95% CI: 1.06-1.22], P = 0.00046). The association was strengthened when a sub-group of controls with open angles were included in the analysis (per-allele OR = 1.30, P = 7.45×10-9; 3,458 cases vs. 3,831 controls). Our findings suggest that the increase in PACG risk could in part be mediated by genetic sequence variants influencing anterior chamber dimensions. PLoS Genet 2014 Mar 6; 10(3):e1004089

Genome-wide association analyses identify three new susceptibility loci for primary angle closure glaucoma

10.1038/ng.2390Nature Genetics44101142-1146NGEN

Association analysis between <i>ABCC5</i> rs1401999 and primary angle closure glaucoma in all chip-typed sample collections (top panel), de-novo genotyped sample collections (middle panel), and PACG cases and clinically certified controls with open angles (bottom panel).

<p>MAF case: Minor allele frequency in PACG cases.</p><p>MAF control: Minor allele frequency in controls.</p><p>OR: Odds ratio.</p><p><i>P</i>: <i>P</i>-value for association with PACG.</p><p>I²: I-squared index for between-collection heterogeneity.</p><p>* Results here are presented based on raw minor allele frequency counts without further adjustment.</p>†<p>PACG patients were recruited from the Beijing Tongren Hospital and controls were recruited from the Handan Eye Study (HES), a population-based study of eye disease in rural Chinese aged 30 years and over.</p