Data in support of the comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics

This study is a part of our long term project on bioremediation of toxic metals and other pollutants for protection of human health and the environment from severe contamination. The information and results presented in this data article are based on both in vitro and in silico experiments. in vitro experiments were used to investigate the presence of arsenic responsive genes in a bacterial strain B1-CDA that is highly resistant to arsenics. However, in silico studies were used to annotate the function of the metal responsive genes. By using this combined study consisting of in vitro and in silico experiments we have identified and characterized specific genes from B1-CDA that can be used as a potential tool for removal of arsenics as well as other heavy metals from the contaminated environment.


Specifications table
Molecular biology, Microbiology. Studies of arsenic responsive genes as well as other metal responsive genes in bacteria Type of data Tables and figure How data was acquired The data was derived by NGS as a raw data then de novo assembly and gene annotation was performed Data format Analyzed Experimental factors Bacterial isolate Lysinibacillus sphaericus B1-CDA was cultured in the presence of 100 mM arsenate and then DNA was isolated from these cells Experimental features Genome sequencing and annotation of metal responsive genes in L. sphaericus B1-CDA Data source location Bacterial sample was collected from a highly arsenic-contaminated cultivated land located in the south-west region of Bangladesh. DNA analysis was performed at the University of Skövde, Sweden and NGS and de novo assembly at Otogenetics Corporation in Norcross, USA Data accessibility The genome information is available in EMBL as follows: [GenBank accession number LJYY01000000, http://www.ncbi.nlm.nih.gov/nuccore/ LJYY00000000]

Value of the data
Complete genome sequencing of a highly arsenic resistant bacteria L. sphaericus, strain B1-CDA. Annotation of bacterial genes involved in binding and transport of toxic metals such as arsenics. Data presented in this article can be used to remove toxic metals from the contaminated sources thus protecting human health and the environment.
In a longer term these data can also contribute to socio-economic development of a society.

Data
The information and results presented in this data article are derived from the in vitro experiments for investigation of the arsenic responsive genes. We also provide in silico data on gene annotation that can be potentially useful for conducting microbial bioremediation of toxic metals.

Experimental design, materials and methods
Lysinibacillus sphaericus B1-CDA strain was collected from a highly arsenic-contaminated region located in the south-west region of Bangladesh. Previously, we have reported that the strain L. sphaericus B1-CDA is highly resistant to arsenic and it accumulates arsenic inside the cells [1]. Genomic DNA was extracted from this bacterium, using Master pure™ Gram positive DNA purification kit (Epicenter, USA). Genome sequencing of the strain was performed by the Otogenetics Corporation (GA, USA). After sequencing the genome was assembled by de novo assembly employing SOAPDenovo, version 2.04 [2].
The assembled genome sequence was annotated with Rapid Annotations using Subsystems Technology, RAST [3]. Functional annotation analysis was also carried out by the Blast2GO pipeline [4] using all translated protein coding sequences resulting from the GeneMark. An InterPro scan [5] was performed through the Blast2GO interface and the InterPro IDs were merged with the Blast-derived GO-annotation for obtaining the integrated annotation results. The GO annotation of all putative metal responsive genes was manually curated. The functional annotation carried out by the RAST and Table 1 Genes involved in metal ion binding and metal ion transport in B1-CDA predicted by RAST and/or Blast2GO. Blast2GO indicates that B1-CDA contains many genes which are responsive to specific metal ions like arsenic, cobalt, copper, iron, nickel, potassium, manganese and zinc. Prediction by RAST and Blast2GO (Table 1) revealed that the B1-CDA genome contains additionally a total of 123 proteins involved in binding and transport of metal ions. Further, B1-CDA contains many other proteins (approximately 30) that catalyze binding and transport of the metal ions such as metalloendopeptidase, metalloexopeptidase, metallopeptidase, metallocarboxypeptidase and metallochaperone (Table 2). In this article, we have studied the presence of arsenic resistance genes in this bacterium by using PCR amplification. The strain B1-CDA was found to harbor acr3, arsR, arsB and arsC arsenic marker genes (Fig. 1). The arsC gene codes for the enzyme arsenate reductase, which is responsible for the biotransformation of arsenate [As(V)] to arsenite [As(III)] prior to efflux. ArsB, an integral membrane protein that pumps arsenite out of the cell, is often associated with an ATPase subunit, arsA [6]. It is hypothesized that the arsB/acr3 genes are the primary determinants in arsenite resistance [6]. The results of these studies could be used to cope with arsenic toxicity by removing it from the contaminated source or converting it to a less toxic harmless compound.