Abstract
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
| Subject area | Biology |
| More specific subject area | 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
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Complete genome sequencing of a highly arsenic resistant bacteria L. sphaericus, strain B1-CDA.
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Annotation of bacterial genes involved in binding and transport of toxic metals such as arsenics.
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Data presented in this article can be used to remove toxic metals from the contaminated sources thus protecting human health and the environment.
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In a longer term these data can also contribute to socio-economic development of a society.
1. 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.
2. 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 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).
Table 1.
Genes involved in metal ion binding and metal ion transport in B1-CDA predicted by RAST and/or Blast2GO.
| Seq. name | No. of nucleotide | Start | End | Function |
|---|---|---|---|---|
| Gene 7 | 597 | 5406 | 6002 | Metal ion binding |
| Gene 33 | 1464 | 34,171 | 35,634 | Metal ion binding |
| Gene 46 | 1977 | 45,923 | 47,899 | Metal ion binding |
| Gene 77 | 768 | 79,288 | 80,055 | Metal ion binding |
| Gene 117 | 1995 | 127,168 | 129,162 | Metal ion binding |
| Gene 171 | 1125 | 184,513 | 185,637 | Metal ion binding |
| Gene 177 | 1425 | 190,919 | 192,343 | Metal ion binding |
| Gene 188 | 2004 | 204,045 | 206,048 | Metal ion binding |
| Gene 223 | 876 | 242,015 | 242,890 | Metal ion binding |
| Gene 226 | 1674 | 244,232 | 245,905 | Metal ion binding |
| Gene 238 | 1233 | 254,866 | 256,098 | Metal ion binding |
| Gene 310 | 1587 | 328,134 | 329,720 | Metal ion binding |
| Gene 313 | 1131 | 331,292 | 332,422 | Metal ion binding |
| Gene 353 | 936 | 369,982 | 370,917 | Metal ion binding |
| Gene 366 | 921 | 381,327 | 382,247 | Metal ion binding |
| Gene 507 | 849 | 521,560 | 522,408 | Metal ion binding |
| Gene 541 | 987 | 552,963 | 553,949 | Metal ion binding |
| Gene 576 | 1110 | 596,085 | 597,194 | Metal ion binding |
| Gene 578 | 918 | 598,123 | 599,040 | Metal ion binding |
| Gene 600 | 741 | 615,128 | 615,868 | Metal ion binding |
| Gene 603 | 1716 | 617,978 | 619,693 | Metal ion binding |
| Gene 637 | 1164 | 651,099 | 652,262 | Metal ion binding |
| Gene 765 | 1506 | 798,894 | 800,399 | Metal ion binding |
| Gene 835 | 1047 | 884,978 | 886,024 | Metal ion binding |
| Gene 845 | 1173 | 896,350 | 897,522 | Metal ion binding |
| Gene 866 | 639 | 913,115 | 913,753 | Metal ion binding |
| Gene 877 | 552 | 926,277 | 926,828 | Metal ion binding |
| Gene 885 | 1113 | 935,597 | 936,709 | Metal ion binding |
| Gene 953 | 1359 | 1,012,868 | 1,014,226 | Metal ion binding |
| Gene 1010 | 669 | 1,072,202 | 1,072,870 | Metal ion binding |
| Gene 1011 | 885 | 1,072,873 | 1,073,757 | Metal ion binding |
| Gene 1014 | 1143 | 1,076,516 | 1,077,658 | Metal ion binding |
| Gene 1039 | 774 | 1,105,712 | 1,106,485 | Metal ion binding |
| Gene 1109 | 3435 | 1,174,450 | 1,177,884 | Metal ion binding |
| Gene 1147 | 1668 | 1,212,657 | 1,214,324 | Metal ion binding |
| Gene 1185 | 1185 | 1,255,829 | 1,257,013 | Metal ion binding |
| Gene 1206 | 1740 | 1,277,562 | 1,279,301 | Metal ion binding |
| Gene 1218 | 2067 | 1,294,077 | 1,296,143 | Metal ion binding |
| Gene 1244 | 795 | 1,319,141 | 1,319,935 | Metal ion binding |
| Gene 1271 | 3510 | 1,348,576 | 1,352,085 | Metal ion binding |
| Gene 1294 | 2511 | 1,372,937 | 1,375,447 | Metal ion binding |
| Gene 1322 | 2364 | 1,399,790 | 1,402,153 | Metal ion binding |
| Gene 1389 | 204 | 1,481,600 | 1,481,803 | Metal ion binding |
| Gene 1397 | 1002 | 1,491,472 | 1,492,473 | Metal ion binding |
| Gene 1408 | 3249 | 1,500,339 | 1,503,587 | Metal ion binding |
| Gene 1426 | 873 | 1,523,169 | 1,524,041 | Metal ion binding |
| Gene 1432 | 1308 | 1,534,294 | 1,535,601 | Metal ion binding |
| Gene 1467 | 765 | 1,563,504 | 1,564,268 | Metal ion binding |
| Gene 1485 | 2079 | 1,582,041 | 1,584,119 | Metal ion binding |
| Gene 1488 | 546 | 1,586,661 | 1,587,206 | Metal ion binding |
| Gene 1536 | 1146 | 1,627,858 | 1,629,003 | Metal ion binding |
| Gene 1564 | 1668 | 1,656,799 | 1,658,466 | Metal ion binding |
| Gene 1571 | 1272 | 1,667,080 | 1,668,351 | Metal ion binding |
| Gene 1572 | 1302 | 1,668,348 | 1,669,649 | Metal ion binding |
| Gene 1580 | 1560 | 1,676,269 | 1,677,828 | Metal ion binding |
| Gene 1612 | 1269 | 1,708,512 | 1,709,780 | Metal ion binding |
| Gene 1667 | 1995 | 1,762,661 | 1,764,655 | Metal ion binding |
| Gene 1684 | 558 | 1,776,672 | 1,777,229 | Metal ion binding |
| Gene 1799 | 906 | 1,887,495 | 1,888,400 | Metal ion binding |
| Gene 1874 | 417 | 1,959,673 | 1,960,089 | Metal ion binding |
| Gene 1889 | 507 | 1,974,321 | 1,974,827 | Metal ion binding |
| Gene 1905 | 837 | 1,986,794 | 1,987,630 | Metal ion binding |
| Gene 1925 | 1263 | 2,011,440 | 2,012,702 | Metal ion binding |
| Gene 2028 | 1203 | 2,120,007 | 2,121,209 | Metal ion binding |
| Gene 2082 | 615 | 2,173,172 | 2,173,786 | Metal ion binding |
| Gene 2132 | 1428 | 2,225,179 | 2,226,606 | Metal ion binding |
| Gene 2177 | 1212 | 2,268,158 | 2,269,369 | Metal ion binding |
| Gene 2223 | 1161 | 2,313,715 | 2,314,875 | Metal ion binding |
| Gene 2227 | 1713 | 2,316,637 | 2,318,349 | Metal ion binding |
| Gene 2450 | 504 | 2,494,701 | 2,495,204 | Metal ion binding |
| Gene 2477 | 237 | 2,515,822 | 2,516,058 | Metal ion binding |
| Gene 2624 | 984 | 2,622,804 | 2,623,787 | Metal ion binding |
| Gene 2635 | 1917 | 2,628,954 | 2,630,870 | Metal ion binding |
| Gene 2859 | 969 | 2,848,824 | 2,849,792 | Metal ion binding |
| Gene 3007 | 2706 | 2,987,030 | 2,989,735 | Metal ion binding |
| Gene 3035 | 459 | 3,008,209 | 3,008,667 | Metal ion binding |
| Gene 3036 | 366 | 3,008,700 | 3,009,065 | Metal ion binding |
| Gene 3216 | 2607 | 3,159,474 | 3,162,080 | Metal ion binding |
| Gene 3250 | 591 | 3,187,349 | 3,187,939 | Metal ion binding |
| Gene 3252 | 1017 | 3,188,465 | 3,189,481 | Metal ion binding |
| Gene 3296 | 909 | 3,231,270 | 3,232,178 | Metal ion binding |
| Gene 3300 | 1746 | 3,235,892 | 3,237,637 | Metal ion binding |
| Gene 3323 | 1173 | 3,258,173 | 3,259,345 | Metal ion binding |
| Gene 3331 | 1410 | 3,268,181 | 3,269,590 | Metal ion binding |
| Gene 3337 | 1671 | 3,276,300 | 3,277,970 | Metal ion binding |
| Gene 3393 | 963 | 3,326,901 | 3,327,863 | Metal ion binding |
| Gene 3437 | 414 | 3,376,060 | 3,376,473 | Metal ion binding |
| Gene 3441 | 2154 | 3,379,579 | 3,381,732 | Metal ion binding |
| Gene 3442 | 1692 | 3,381,729 | 3,383,420 | Metal ion binding |
| Gene 3468 | 1368 | 3,410,115 | 3,411,482 | Metal ion binding |
| Gene 3576 | 1104 | 3,514,691 | 3,515,794 | Metal ion binding |
| Gene 3590 | 1716 | 3,530,171 | 3,531,886 | Metal ion binding |
| Gene 3654 | 1227 | 3,602,057 | 3,603,283 | Metal ion binding |
| Gene 3660 | 615 | 3,606,978 | 3,607,592 | Metal ion binding |
| Gene 3680 | 1206 | 3,634,474 | 3,635,679 | Metal ion binding |
| Gene 3702 | 1116 | 3,656,386 | 3,657,501 | Metal ion binding |
| Gene 3711 | 957 | 3,667,171 | 3,668,127 | Metal ion binding |
| Gene 3712 | 960 | 3,668,449 | 3,669,408 | Metal ion binding |
| Gene 3738 | 1932 | 3,693,364 | 3,695,295 | Metal ion binding |
| Gene 3797 | 594 | 3,750,078 | 3,750,671 | Metal ion binding |
| Gene 3857 | 981 | 3,810,517 | 3,811,497 | Metal ion binding |
| Gene 3889 | 1146 | 3,839,858 | 3,841,003 | Metal ion binding |
| Gene 3908 | 915 | 3,862,117 | 3,863,031 | Metal ion binding |
| Gene 3964 | 573 | 3,917,646 | 3,918,218 | Metal ion binding |
| Gene 4020 | 570 | 3,969,387 | 3,969,956 | Metal ion binding |
| Gene 4030 | 2121 | 3,978,548 | 3,980,668 | Metal ion binding |
| Gene 4038 | 1731 | 3,986,132 | 3,987,862 | Metal ion binding |
| Gene 4058 | 969 | 4,006,280 | 4,007,248 | Metal ion binding |
| Gene 4070 | 906 | 4,023,891 | 4,024,796 | Metal ion binding |
| Gene 4215 | 1071 | 4,157,550 | 4,158,620 | Metal ion binding |
| Gene 4218 | 1635 | 4,160,134 | 4,161,768 | Metal ion binding |
| Gene 4272 | 1107 | 4,218,954 | 4,220,060 | Metal ion binding |
| Gene 4295 | 1380 | 4,241,915 | 4,243,294 | Metal ion binding |
| Gene 4298 | 2361 | 4,245,236 | 4,247,596 | Metal ion binding |
| Gene 4306 | 2124 | 4,254,484 | 4,256,607 | Metal ion transport |
| Gene 4346 | 1083 | 4,294,106 | 4,295,188 | Metal ion binding |
| Gene 4357 | 1386 | 4,307,321 | 4,308,706 | Metal ion binding |
| Gene 4400 | 729 | 4,354,264 | 4,354,992 | Metal ion binding |
| Gene 4454 | 957 | 4,410,503 | 4,411,459 | Metal ion binding |
| Gene 4490 | 1377 | 4,445,126 | 4,446,502 | Metal ion binding |
| Gene 4495 | 1461 | 4,450,541 | 4,452,001 | Metal ion binding |
| Gene 4542 | 654 | 4,490,448 | 4,491,101 | Metal ion binding |
Table 2.
Genes involved in metalloendopeptidase, metalloexopeptidase, metallopeptidase, metallochaperone and metallocarboxypeptidase protein predicted by RAST and Blast2GO are present in B1-CDA.
| Seq. name | No. of nucleotide | Start | End | Function |
|---|---|---|---|---|
| Gene 75 | 2028 | 76,022 | 78,049 | Metalloendopeptidase activity |
| Gene 90 | 1065 | 92,201 | 93,265 | Metalloexopeptidase activity |
| Gene 95 | 1017 | 96,135 | 97,151 | Metalloendopeptidase activity |
| Gene 248 | 756 | 266,333 | 267,088 | Metalloexopeptidase activity |
| Gene 435 | 675 | 456,865 | 457,539 | Metallopeptidase activity |
| Gene 597 | 1509 | 612,142 | 613,650 | Metalloexopeptidase activity |
| Gene 890 | 1230 | 940,132 | 941,361 | Metallopeptidase activity |
| Gene 1251 | 1818 | 1,324,367 | 1,326,184 | Metalloendopeptidase activity |
| Gene 1537 | 1263 | 1,629,050 | 1,630,312 | Metalloendopeptidase activity |
| Gene 1553 | 1224 | 1,648,658 | 1,649,881 | Metalloendopeptidase activity |
| Gene 1825 | 1287 | 1,914,934 | 1,916,220 | Metalloendopeptidase activity |
| Gene 2009 | 1497 | 2,101,832 | 2,103,328 | Metallocarboxypeptidase activity |
| Gene 2062 | 1815 | 2,151,841 | 2,153,655 | Metalloendopeptidase activity |
| Gene 2087 | 1233 | 2,180,574 | 2,181,806 | Metallopeptidase activity |
| Gene 2153 | 732 | 2,244,087 | 2,244,818 | Metallopeptidase activity |
| Gene 2442 | 555 | 2,489,739 | 2,490,293 | Metallopeptidase activity |
| Gene 2665 | 630 | 2,656,743 | 2,657,372 | Metallochaperone activity |
| Gene 3223 | 1089 | 3,166,498 | 3,167,586 | Metalloexopeptidase activity |
| Gene 3434 | 1116 | 3,372,197 | 3,373,312 | Metallopeptidase activity |
| Gene 3478 | 1062 | 3,416,770 | 3,417,831 | Metalloexopeptidase activity |
| Gene 3587 | 927 | 3,526,686 | 3,527,612 | Metalloexopeptidase activity |
| Gene 3609 | 1269 | 3,548,363 | 3,549,631 | Metallopeptidase activity |
| Gene 3703 | 1089 | 3,657,553 | 3,658,641 | Metalloexopeptidase activity |
| Gene 3874 | 612 | 3,828,598 | 3,829,209 | Metalloendopeptidase activity |
| Gene 3973 | 1017 | 3,924,998 | 3,926,014 | Metalloendopeptidase activity |
| Gene 4031 | 474 | 3,980,677 | 3,981,150 | Metalloendopeptidase activity |
| Gene 4110 | 1212 | 4,067,537 | 4,068,748 | Metallopeptidase activity |
| Gene 4255 | 1698 | 4,199,161 | 4,200,858 | Metalloendopeptidase activity |
| Gene 4381 | 1461 | 4,331,031 | 4,332,491 | Metallopeptidase activity |
| Gene 4433 | 1191 | 4,384,176 | 4,385,366 | Metallocarboxypeptidase activity |
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.
Fig. 1.
Molecular analysis of arsenic responsive genes of B1-CDA and gel electrophoresis: (A) PCR amplification of acr3 gene. L represents 50 bp DNA marker, whereas lane 1 and 2 are the amplified fragments of acr3 gene in two replicates. (B) PCR amplification of arsR gene. L represents 2-log DNA marker, whereas lane 1, 2 and 3 are the amplified fragments of arsR gene in three replicates. (C) PCR amplification of arsB gene. L represents 2-log DNA marker, whereas lane 1, 2, 3, 4, 5 and 6 are the amplified fragments of arsB gene in six replicates and (D) PCR amplification of arsC gene. L represents 2-log DNA marker, whereas lane 1, 2 and 3 are the amplified fragments of arsC gene in three replicates.
Acknowledgments
This research has been funded mainly by the Swedish International Development Cooperation Agency (SIDA, Grant number: AKT-2010-018) and partly by the Nilsson-Ehle (The Royal Physiographic Society in Lund) foundation in Sweden.
Contributor Information
Aminur Rahman, Email: aminur.rahman@his.se.
Noor Nahar, Email: noor.nahar@his.se.
Neelu N. Nawani, Email: neelunawani@yahoo.com.
Jana Jass, Email: jana.jass@oru.se.
Sibdas Ghosh, Email: sghosh@iona.edu.
Björn Olsson, Email: bjorn.olsson@his.se.
Abul Mandal, Email: abul.mandal@his.se.
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