Literature DB >> 26958612

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

Aminur Rahman1, Noor Nahar2, Neelu N Nawani3, Jana Jass4, Sibdas Ghosh5, Björn Olsson2, Abul Mandal2.   

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.

Entities:  

Year:  2015        PMID： 26958612      PMCID： PMC4773391          DOI： 10.1016/j.dib.2015.09.040

Source DB:  PubMed          Journal:  Data Brief        ISSN： 2352-3409


Specifications table 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 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. nameNo. of nucleotideStartEndFunction
Gene 759754066002Metal ion binding
Gene 33146434,17135,634Metal ion binding
Gene 46197745,92347,899Metal ion binding
Gene 7776879,28880,055Metal ion binding
Gene 1171995127,168129,162Metal ion binding
Gene 1711125184,513185,637Metal ion binding
Gene 1771425190,919192,343Metal ion binding
Gene 1882004204,045206,048Metal ion binding
Gene 223876242,015242,890Metal ion binding
Gene 2261674244,232245,905Metal ion binding
Gene 2381233254,866256,098Metal ion binding
Gene 3101587328,134329,720Metal ion binding
Gene 3131131331,292332,422Metal ion binding
Gene 353936369,982370,917Metal ion binding
Gene 366921381,327382,247Metal ion binding
Gene 507849521,560522,408Metal ion binding
Gene 541987552,963553,949Metal ion binding
Gene 5761110596,085597,194Metal ion binding
Gene 578918598,123599,040Metal ion binding
Gene 600741615,128615,868Metal ion binding
Gene 6031716617,978619,693Metal ion binding
Gene 6371164651,099652,262Metal ion binding
Gene 7651506798,894800,399Metal ion binding
Gene 8351047884,978886,024Metal ion binding
Gene 8451173896,350897,522Metal ion binding
Gene 866639913,115913,753Metal ion binding
Gene 877552926,277926,828Metal ion binding
Gene 8851113935,597936,709Metal ion binding
Gene 95313591,012,8681,014,226Metal ion binding
Gene 10106691,072,2021,072,870Metal ion binding
Gene 10118851,072,8731,073,757Metal ion binding
Gene 101411431,076,5161,077,658Metal ion binding
Gene 10397741,105,7121,106,485Metal ion binding
Gene 110934351,174,4501,177,884Metal ion binding
Gene 114716681,212,6571,214,324Metal ion binding
Gene 118511851,255,8291,257,013Metal ion binding
Gene 120617401,277,5621,279,301Metal ion binding
Gene 121820671,294,0771,296,143Metal ion binding
Gene 12447951,319,1411,319,935Metal ion binding
Gene 127135101,348,5761,352,085Metal ion binding
Gene 129425111,372,9371,375,447Metal ion binding
Gene 132223641,399,7901,402,153Metal ion binding
Gene 13892041,481,6001,481,803Metal ion binding
Gene 139710021,491,4721,492,473Metal ion binding
Gene 140832491,500,3391,503,587Metal ion binding
Gene 14268731,523,1691,524,041Metal ion binding
Gene 143213081,534,2941,535,601Metal ion binding
Gene 14677651,563,5041,564,268Metal ion binding
Gene 148520791,582,0411,584,119Metal ion binding
Gene 14885461,586,6611,587,206Metal ion binding
Gene 153611461,627,8581,629,003Metal ion binding
Gene 156416681,656,7991,658,466Metal ion binding
Gene 157112721,667,0801,668,351Metal ion binding
Gene 157213021,668,3481,669,649Metal ion binding
Gene 158015601,676,2691,677,828Metal ion binding
Gene 161212691,708,5121,709,780Metal ion binding
Gene 166719951,762,6611,764,655Metal ion binding
Gene 16845581,776,6721,777,229Metal ion binding
Gene 17999061,887,4951,888,400Metal ion binding
Gene 18744171,959,6731,960,089Metal ion binding
Gene 18895071,974,3211,974,827Metal ion binding
Gene 19058371,986,7941,987,630Metal ion binding
Gene 192512632,011,4402,012,702Metal ion binding
Gene 202812032,120,0072,121,209Metal ion binding
Gene 20826152,173,1722,173,786Metal ion binding
Gene 213214282,225,1792,226,606Metal ion binding
Gene 217712122,268,1582,269,369Metal ion binding
Gene 222311612,313,7152,314,875Metal ion binding
Gene 222717132,316,6372,318,349Metal ion binding
Gene 24505042,494,7012,495,204Metal ion binding
Gene 24772372,515,8222,516,058Metal ion binding
Gene 26249842,622,8042,623,787Metal ion binding
Gene 263519172,628,9542,630,870Metal ion binding
Gene 28599692,848,8242,849,792Metal ion binding
Gene 300727062,987,0302,989,735Metal ion binding
Gene 30354593,008,2093,008,667Metal ion binding
Gene 30363663,008,7003,009,065Metal ion binding
Gene 321626073,159,4743,162,080Metal ion binding
Gene 32505913,187,3493,187,939Metal ion binding
Gene 325210173,188,4653,189,481Metal ion binding
Gene 32969093,231,2703,232,178Metal ion binding
Gene 330017463,235,8923,237,637Metal ion binding
Gene 332311733,258,1733,259,345Metal ion binding
Gene 333114103,268,1813,269,590Metal ion binding
Gene 333716713,276,3003,277,970Metal ion binding
Gene 33939633,326,9013,327,863Metal ion binding
Gene 34374143,376,0603,376,473Metal ion binding
Gene 344121543,379,5793,381,732Metal ion binding
Gene 344216923,381,7293,383,420Metal ion binding
Gene 346813683,410,1153,411,482Metal ion binding
Gene 357611043,514,6913,515,794Metal ion binding
Gene 359017163,530,1713,531,886Metal ion binding
Gene 365412273,602,0573,603,283Metal ion binding
Gene 36606153,606,9783,607,592Metal ion binding
Gene 368012063,634,4743,635,679Metal ion binding
Gene 370211163,656,3863,657,501Metal ion binding
Gene 37119573,667,1713,668,127Metal ion binding
Gene 37129603,668,4493,669,408Metal ion binding
Gene 373819323,693,3643,695,295Metal ion binding
Gene 37975943,750,0783,750,671Metal ion binding
Gene 38579813,810,5173,811,497Metal ion binding
Gene 388911463,839,8583,841,003Metal ion binding
Gene 39089153,862,1173,863,031Metal ion binding
Gene 39645733,917,6463,918,218Metal ion binding
Gene 40205703,969,3873,969,956Metal ion binding
Gene 403021213,978,5483,980,668Metal ion binding
Gene 403817313,986,1323,987,862Metal ion binding
Gene 40589694,006,2804,007,248Metal ion binding
Gene 40709064,023,8914,024,796Metal ion binding
Gene 421510714,157,5504,158,620Metal ion binding
Gene 421816354,160,1344,161,768Metal ion binding
Gene 427211074,218,9544,220,060Metal ion binding
Gene 429513804,241,9154,243,294Metal ion binding
Gene 429823614,245,2364,247,596Metal ion binding
Gene 430621244,254,4844,256,607Metal ion transport
Gene 434610834,294,1064,295,188Metal ion binding
Gene 435713864,307,3214,308,706Metal ion binding
Gene 44007294,354,2644,354,992Metal ion binding
Gene 44549574,410,5034,411,459Metal ion binding
Gene 449013774,445,1264,446,502Metal ion binding
Gene 449514614,450,5414,452,001Metal ion binding
Gene 45426544,490,4484,491,101Metal 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. nameNo. of nucleotideStartEndFunction
Gene 75202876,02278,049Metalloendopeptidase activity
Gene 90106592,20193,265Metalloexopeptidase activity
Gene 95101796,13597,151Metalloendopeptidase activity
Gene 248756266,333267,088Metalloexopeptidase activity
Gene 435675456,865457,539Metallopeptidase activity
Gene 5971509612,142613,650Metalloexopeptidase activity
Gene 8901230940,132941,361Metallopeptidase activity
Gene 125118181,324,3671,326,184Metalloendopeptidase activity
Gene 153712631,629,0501,630,312Metalloendopeptidase activity
Gene 155312241,648,6581,649,881Metalloendopeptidase activity
Gene 182512871,914,9341,916,220Metalloendopeptidase activity
Gene 200914972,101,8322,103,328Metallocarboxypeptidase activity
Gene 206218152,151,8412,153,655Metalloendopeptidase activity
Gene 208712332,180,5742,181,806Metallopeptidase activity
Gene 21537322,244,0872,244,818Metallopeptidase activity
Gene 24425552,489,7392,490,293Metallopeptidase activity
Gene 26656302,656,7432,657,372Metallochaperone activity
Gene 322310893,166,4983,167,586Metalloexopeptidase activity
Gene 343411163,372,1973,373,312Metallopeptidase activity
Gene 347810623,416,7703,417,831Metalloexopeptidase activity
Gene 35879273,526,6863,527,612Metalloexopeptidase activity
Gene 360912693,548,3633,549,631Metallopeptidase activity
Gene 370310893,657,5533,658,641Metalloexopeptidase activity
Gene 38746123,828,5983,829,209Metalloendopeptidase activity
Gene 397310173,924,9983,926,014Metalloendopeptidase activity
Gene 40314743,980,6773,981,150Metalloendopeptidase activity
Gene 411012124,067,5374,068,748Metallopeptidase activity
Gene 425516984,199,1614,200,858Metalloendopeptidase activity
Gene 438114614,331,0314,332,491Metallopeptidase activity
Gene 443311914,384,1764,385,366Metallocarboxypeptidase 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.

Subject areaBiology
More specific subject areaMolecular biology, Microbiology. Studies of arsenic responsive genes as well as other metal responsive genes in bacteria
Type of dataTables and figure
How data was acquiredThe data was derived by NGS as a raw data then de novo assembly and gene annotation was performed
Data formatAnalyzed
Experimental factorsBacterial isolate Lysinibacillus sphaericus B1-CDA was cultured in the presence of 100 mM arsenate and then DNA was isolated from these cells
Experimental featuresGenome sequencing and annotation of metal responsive genes in L. sphaericus B1-CDA
Data source locationBacterial 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 accessibilityThe genome information is available in EMBL as follows: [GenBank accession number LJYY01000000, http://www.ncbi.nlm.nih.gov/nuccore/LJYY00000000]
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