20+ Million Readerbase
Indexed In
  • Academic Journals Database
  • Genamics JournalSeek
  • Academic Keys
  • JournalTOCs
  • China National Knowledge Infrastructure (CNKI)
  • Scimago
  • Access to Global Online Research in Agriculture (AGORA)
  • Electronic Journals Library
  • RefSeek
  • Directory of Research Journal Indexing (DRJI)
  • Hamdard University
  • OCLC- WorldCat
  • SWB online catalog
  • Virtual Library of Biology (vifabio)
  • Publons
  • MIAR
  • University Grants Commission
  • Geneva Foundation for Medical Education and Research
  • Euro Pub
  • Google Scholar
Share This Page
Journal Flyer
Flyer image

Research Article - (2017) Volume 9, Issue 5

Genome Sequencing Revealed Chromium and Other Heavy Metal Resistance Genes in E. cloacae B2-Dha

Aminur R1,2*, Björn O1, Jana J2, Neelu NN3, Sibdas G4 and Abul M1
1Systems Biology Research Center, School of Bioscience, University of Skövde, Skövde, Sweden
2The Life Science Center, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden
3Microbial Diversity Research Centre, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Tathawade, Pune-411033, India
4School of Arts and Science, Iona College, New Rochelle, NY 10801, USA
*Corresponding Author: Aminur R, Department of Molecular Biology, Systems Biology Research Center, School of Bioscience, University of Skövde, Sweden, Tel: +46-500 448679, +46-7389 81928 Email:


The previously described chromium resistant bacterium, Enterobacter cloacae B2-DHA, was isolated from leather manufacturing tannery landfill in Bangladesh. Here we report the entire genome sequence of this bacterium containing chromium and other heavy metal resistance genes. The genome size and the number of genes, determined by massive parallel sequencing and comparative analysis with other known Enterobacter genomes, are predicted to be 4.22 Mb and 3958, respectively. Nearly 160 of these genes were found to be involved in binding, transport, and catabolism of ions as well as efflux of inorganic and organic compounds. Specifically, the presence of two chromium resistance genes, chrR and chrA was verified by polymerase chain reaction. The outcome of this research highlights the significance of this bacterium in bioremediation of chromium and other toxic metals from the contaminated sources.

Keywords: Bioremediation; Toxic metals; Enterobacter cloacae; Genome sequencing; De novo assembly; Gene annotation


The global urbanization and industrialization creates increasing levels of pollution including toxic heavy metal contamination [1]. In particular, chromium toxicity is generated through widespread anthropogenic activity via leather processing, steel production, wood preservation, chromium/electroplating, metal processing, alloy formation, textiles, ceramics and thermonuclear weapons manufacturing, and together with agronomic practices such as the use of organic biomass (sewage sludge or fertilizers), which continues to be a major threat to the environment [2-6]. Furthermore, chromium exerts damage directly on human health through toxic and mutagenic effects causing severe DNA damage [7]. However, chromium has multiple effects on bacteria including competitive inhibition of sulphate transport, DNA mutagenesis and protein damage [8]. Microorganisms have developed various mechanisms to survive chromium toxicity: (i) transmembrane efflux of chromate (ii) the ChrR transport system (iii) the reduction of chromate (iv) protection against oxidative stress and (v) DNA repair systems [3,9-15]. In addition, chromate resistance is attributed to the functions of a series of chromosomal or plasmid encoded genes, including the chromium resistance (chr) operon comprising of either chrBAC or chrBACF in bacteria [9,16,17]. The ChrA protein, a member of the CHR superfamily of transporters appears to be active in chromate efflux driven by the membrane potential, whereas the chrB gene encodes for a membrane bound protein necessary for the regulation of chromate resistance [18-20]. The chrC gene encodes a protein almost similar to iron-containing superoxide dismutase, while the chrE gene encodes a protein resembling a rhodanese type enzyme in Orthrobacterium tritici 5bvI1 [20]. The chrF gene likely encodes a repressor of chromatedependent induction, whereas the ChrR protein catalyzes one-electron shuttle followed by a two-electron transfer to Cr6+ [21].

Previously, we have characterized E. cloacae B2-DHA, a soilborne bacterium, that can survive and grow on medium containing up to 5.5 mM chromate. By using inductively coupled plasma atomic emission spectroscopy (ICP-AES) we have shown that after 120 h of exposure to 100 μg/mL chromium the B2-DHA cells can accumulate 320 μg of chromium per gram dry weight of bacterial biomass thus the concentration of chromium in the cell free growth medium is decreased from 100 μg/mL to 19 μg/mL (81%) [6]. In addition, B2-DHA, can grow on medium containing sodium arsenate, ferric chloride, manganese chloride, zinc chloride, nickel chloride and silver nitrate. However, the mechanisms by which this chromium-adapted B2-DHA survives were not elucidated. Thus, the present study was aimed at demonstrating whether the strain B2-DHA harbored genes that were responsible for chromium and other metal resistance. In this study, we have performed massive parallel genome sequencing of E. cloacae B2-DHA to investigate the metal responsive genes. All the genes involved in metal binding activity and reduction of metal by the E. cloacae B2-DHA strain were predicted by Rapid Annotations using Subsystems Technology, RAST and/or Blast2GO [22,23]. Furthermore, we have conducted comparative genome analyses of E. cloacae B2-DHA with other known Enterobacter genome sequences and characterized the genetic rearrangement among the various lineages to understand the evolutionary processes involved in shaping the genomes.

Materials and Methods

Extraction of genomic DNA

Genomic DNA was extracted from E. cloacae B2-DHA using DNeasy Blood & Tissue Kit (Qiagen, Cat No 69506) according to manufacturer’s instructions with some modifications. The bacteria were cultured in Luria Bertani (LB) medium and pellets were collected from 1.0 ml of bacterial cultures by centrifugation at 8000 rpm for 10 min, the pellets were resuspended in TE buffer (10 mM Tris- HCl, 1 mM EDTA [pH 8.0]) containing RNase (50 mg/ml) and lysozyme (50 mg/ml) and incubated at 37°C for 2 h instead of using ATL (a tissue lysis buffer). The purity and concentration of the extracted DNA were measured using the Nanodrop® ND-1000 Spectrophotometer (Saveen Werner, USA). The DNA sample exhibiting a clear band in agarose gel electrophoresis was selected for sequencing of the whole genome.

Genome sequencing

The entire genome sequencing of E. cloacae B2-DHA was assisted by the Otogenetics Corporation (GA, USA) as follows: (i) Purified 0.5- 1.0 μg of genomic DNA sample was clipped into smaller fragments with a Covaris E210 ultrasonicator; (ii) the library of genomic DNA was prepared according to standard protocol of the NEB library preparation kit (New England Biolabs) for the Illumina sequencer with a single sequencing index; (iii) the sequencing was accomplished with the Illumina HiSeq2500 PE106 (106 bp paired-end) read format; (iv) properly paired reads (≥ 30 bp) were separated from the corrected read pool and the remaining singleton reads were combined as singleend reads; and (v) both of the single-end reads and corrected pairedend reads were used in the subsequent de novo assembly as described previously [24].

de novo assembly

The de novo assembly started with Illumina 106 bp paired-end reads of genomic DNA with an insert length of 300 bp and the read quality was measured with FastQC, version 1.10.1 [25]. Adapter and quality trimming on raw reads were conducted with cutAdapt and K-mer error correction was performed on the adapter-free reads using Quake, version 0.3.5 [26,27]. The paired reads were extracted from the corrected read pool and the remaining singleton reads were listed as single-end reads. Both corrected paired-end and single-end reads were used in the k-mer-based de novo assembly. SOAPDenovo, version 2.04 was utilized to perform de novo assembly optimization with the error corrected reads [28]. A wide range of K-mers (29-99) were used to identify the scaffold sequences with the largest N50. The optimal scaffold sequences were further subjected to gap closing by utilizing the corrected pairedend reads, and the resulting scaffolds of length ≥ 300 bp were chosen as the final assembly. The largest N50 of 492,970 bp was produced at the k-mer 97. All the scaffolds were ordered by finding the location of the best Blastn hit for each scaffold on the reference genome E. cloacae ECNIH2 [NCBI accession number CP008823]. A total of 13 scaffolds were used to order the contigs from a draft genome by comparison to a reference genome performed by following the Mauve Contigs Mover (http://darlinglab.org/mauve/user-guide/reordering.html).

Comparative analysis with other E-bacter genomes

The Whole Genome Shotgun project has been deposited at DDBJ/ EMBL/GenBank under the GenBank accession LFJA00000000 [29]. The progressive MAUVE algorithm in the MAUVE genome alignment software, version 2.3.1was used to study genome rearrangements in E. cloacae B2-DHA and related bacteria. Furthermore, another nucleotidebased dot plot analysis was performed with the Gepard software to (i) compare the 4.21 Mbp chromosomal scaffolds of E. cloacae B2-DHA with that of 4.85 Mbp chromosomes in E. cloacae ECNIH2, and (ii) investigate the possible genome rearrangements in these strains.

Prediction and annotation of metal responsive genes

The prediction of all genes in B2-DHA genome was carried out using FGenesB and GeneMark. ARAGORN, version 1.2.36 employed to predict tRNA genes in B2-DHA genome. We have applied Blast2GO pipeline using all translated protein coding sequences resulting from the FGenesB to execute all functional annotation analyses. In Blast2GO, the BlastP option was chosen to find the closest homologs in the nonredundant protein databases (nr), followed by employment of Gene Ontology (GO) annotation terms to each gene [30]. An InterPro scan was then performed through the Blast2GO interface with the InterPro IDs for obtaining integrated annotation results [31]. Annotation of all putative metal responsive genes was manually curated. The assembled genome sequence was annotated with RAST which uses (i) the GLIMMER algorithm to predict protein-coding genes (ii) the tRNAscan-SE to predict tRNA genes [32], (iii) an internal script for identification of rRNA genes and (iv)the RNAmmer prediction server version 1.2, to identify rRNA genes [33]. Furthermore, RAST (i) infers putative function(s) of the protein coding genes based on homology with known protein families in phylogenetic neighbor species, and (ii) detects subsystems represented in the genome, and helps to reconstruct the metabolic networks. RAST results obtained in prediction of protein coding genes were compared with the GeneMark and the FGenesB algorithms. Circular plot of ordered contigs of B2-DHA was generated with DNAPlotter to predict the graphical map of the genome [34].

PCR amplification of chromium-responsive genes

Primers for the gene chrR and chrA were designed by using the Primer3Plus web tool [35]. The two primer pairs, chrR-F/chrR-R (5'-ATGTCTGATACGTTGAAAGTTGTTA- 3'/5'-CAGGCCTTCACCCGCTTA- 3') and chrA-F/chrA-R (5'-TGAAAAGCTGTTTACCCCACT- 3'/5'-TTACAGTGAAGGGTAGTCGGTATAA-3') were selected for the detection of chrR and chrA genes, respectively. PCR amplification of chromium-related marker genes was performed using bacterial genomic DNA as a template in a piko thermal cycler (Finzymes) under the following cycling conditions: 5 min of denaturation at 95°C, followed by 30 cycles of 1 min of denaturation at 95°C, 45 s of annealing at 54.5°C and primer extension at 72°C for 1 min of each Kb product size. All PCR reaction mixtures contained approximately 50 ng DNA templates, 0.2 mM of each deoxyribonucleoside triphosphate, 1X PCR buffer, 0.5 mM of each primer, and 1 U Taq DNA polymerase in a final volume of 50 μl. The final extension reaction was conducted at 72°C for 15 min. PCR products were purified with a QIAquick PCR Purification Kit (Qiagen, Cat No 28104).


Sequencing and de novo genome assembly

Illumina deep sequencing analysis revealed that the genome of B2-DHA consists of 1,756,877,072 bases containing 16,574,312 pairs of reads with an overall GC content of 55%. After quality trimming error correction followed by removal of the TruSeq adaptor sequence, 15,708,650 read pairs (94.78%) and 331,106 single end sequences remained for further analysis. Analysis of the raw reads with FastQC showed that the mean scores per base Phred and per sequence Phred were ≥ 36 and 36, respectively for all positions. The set of scaffold sequences with maximal N50 (492,970 bp) was detected at k-mer 97. The corresponding scaffold sequences were subjected to gap closure using the corrected paired-end reads and the resulting scaffolds (≥ 24300 bp) were defined as the final assembly. The genome summary including the nucleotide content and the gene count is posted in Table 1. The scaffolds were ordered by finding the location of the best Blastn hit for each scaffold on the reference genome Enterobacter cloacae ECNIH2. The final assembly of 4,218,945 bp was comprised of 13 scaffolds ranging from 72,208 to 777,700 bp.

Attribute Value % of total
Genome size (bp) 4 218 945 100
DNA GC content (bp) 2 353 515 55
DNA coding region (bp) 3 768779 89,33
Number of replicons 1  
Total scaffolds 13 100
Total genes 4043 100
rRNA genes 22 0,54
tRNA genes 66 1,63
Protein coding genes 3958 97,82
Genes assigned to RAST functional categories 3954 97,79
Genes assigned Gene Ontology terms by Blast2GO 3159 79,87
Largest N50* 492970  
Largest N90* 111054  

Table 1: Summary of the genome of B2-DHA with nucleotide content and gene count.

Comparative genome analysis

The chromosomal arrangement of E. cloacae B2-DHA was compared to E. cloacae ECNIH2 by employing progressive Mauve from the Mauve software [36] and Gepard dot plot software [37]. While the alignment remained almost identical in chromosomal rearrangement, the progressive Mauve analysis found several inversions in scaffolds of E. cloacae B2-DHA compared to that in E. cloacae ECNIH2 (Figure 1A). The dot plot performed with E. cloacae B2-DHA and E. cloacae ECNIH2 depicted a similar observation of inversions in scaffolds of E. cloacae B2-DHA (Figure 1B). Furthermore, several large segments of high similarity were obtained when most parts of the chromosomes of E. cloacae B2-DHA and E. cloacae ECNIH2 were mapped onto each other (Figure 1B).


Figure 1: (A) Nucleotide-based alignment of a 4.21 Mbp chromosomal assembly of E. cloacae B2-DHA (upper) and 4.85 Mbp chromosomes of E. cloacae ECNIH2 (lower). A total of 12 homologous blocks are shown as identically colored regions and linked across the sequences. Regions that are inverted relative to E. cloacae B2-DHA are shifted to the right of center axis of the sequence. (B) Dot plot of nucleotide sequences of E. cloacae B2-DHA (X-axis) and E. cloacae ECNIH2 (Y-axis). Aligned segments are represented as dots, with regions of conservation appearing as lines.

Gene predictions

The genome and the locations of all genes were predicted through RAST server and the results of this prediction are shown via a circular plot in Figure 2. The prediction of rRNA coding genes showed 22 rRNA genes including four LSU, four SSU, eight 16S and six 23S genes in E. cloacae B2-DHA (Figure 2). ARAGORN, version 1.2.36 [38], employed to predict tRNA genes, identified 66 tRNA genes with a GC content ranging from 48.0% to 67.5% in E. cloacae B2-DHA.


Figure 2: Circular plot of ordered contigs, generated with DNAPlotter. Tracks indicate (from outside inwards) protein coding genes in forward direction (blue) and protein coding genes in reverse direction (green), tRNA genes (red), rRNA genes (dark blue), metal responsive genes (black), GC ratio and GC skew.

RAST analysis using the GLIMMER algorithm predicted a total of 3958 protein coding genes of which 3401 could be annotated by RAST’s automated homology analysis procedure and assigned to functional categories (Figure 3) [27]. For confirmation of the number of protein coding genes, the FGenesB and the GeneMark algorithms were also applied, yielding 3955 and 3764 genes, respectively [39,40]. By using RAST, we observed that the strain E. cloacae B2-DHA contained a large number of genes involved in the ion binding, transport, catabolism and efflux of inorganic as well as organic compounds. More specifically, B2-DHA strain contains many specific metal resistance genes, such as arsenic, chromium, cadmium, cobalt, lead and nickel (Table 2). The Blast2GO pipeline analysis also indicated that B2-DHA contains many genes that are directly responsive to toxic metal ions like arsenic, chromium, cadmium, cobalt, lead and nickel (Table 2). Moreover, these analyses revealed that B2-DHA strain also possesses many genes encoding binding and/or transport of calcium, copper, iron, magnesium, potassium and sodium ions as well as several trace elements like manganese, molybdenum and tellurite (Table 3). Also, a large number of zinc ion binding and/or transporter proteins are retained in this strain (Data not shown). Besides zinc the B2-DHA genome contains a total of 104 proteins involved in binding and transport of other metal ions (Data not shown).


Figure 3: RAST analysis of genes connected to subsystems and their distribution in different functional categories.

      Predicted by
Start (bp) End (bp) Predicted function RAST Blast2GO
36960 37526 Chromate reductase   X
242454 243404 Magnesium and cobalt transport protein CorA X X
495488 496147 ArsR family X  
615926 616912 Cobalt, zinc, magnesium ion binding   X
964298 965137 Nickel, Cobalt cation transporter activity   X
997848 1000430 Copper, lead, cadmium, zinc, mercury transporting ATPase X X
1100748 1099984 Ferric enterobactin transport protein FepC X X
1101770 1100781 Ferric enterobactin transport protein FepG X X
1102774 1101770 Ferric enterobactin transport protein FepD X X
1105147 1104188 Ferric enterobactin transport protein FepB X X
1251060 1252157 Chromate reductase X X
1510555 1509272 Ferrous iron transport peroxidase EfeB X X
1511686 1510559 Ferrous iron transport periplasmic protein EfeO, X  
1512560 1511727 Ferrous iron transport permease EfeU X X
1703726 1704046 Arsenite resistance operon repressor X X
1704087 1705376 Arsenite efflux pump protein X X
1705389 1705820 Arsenate reductase X X
1834407 1835345 Cobalt-zinc-cadmium resistance, Zinc transporter ZitB X X
1919484 1921043 Magnesium and cobalt efflux protein CorC X  
2058555 2059283 Ferric siderophore transport protein TonB X  
2216754 2216455 Transcriptional regulator, ArsR family X  
2304506 2303766 Cobalt-zinc-cadmium resistance X  
2591739 2592824 Cobalt-zinc-cadmium resistance X  
2592824 2595886 Cobalt-zinc-cadmium resistance protein CzcA X  
2735411 2736391 Nickel, Cobalt cation transporter activity   X
2810083 2809727 Arsenate reductase X X
3168971 3169588 Nickel cation binding   X
3169598 3170242 Nickel cation binding   X
3170821 3171285 Nickel cation binding   X
3171295 3172998 Nickel cation binding   X
3173316 3173618 Nickel cation binding   X
3173629 3174456 Nickel cation binding   X
3170811 3170272 Transport of Nickel and Cobalt, Urea decomposition X  
3500732 3499869 Nickel incorporation-associated protein HypB X X
3505195 3506904 Nickel cation binding   X
3501086 3500736 Nickel incorporation protein HypA X X
3516192 3517214 Nickel/cobalt transporter X X
3892272 3892499 Ferrous iron transport protein A X X
3892530 3894848 Ferrous iron transport protein B X  
3951655 3953826 Copper, lead, cadmium, zinc, mercury transporting ATPase X X
4172744 4173628 Cobalt-zinc-cadmium resistance protein X X
4176907 4178211 Arsenic efflux pump protein X  

Table 2: Heavy metals responsive proteins in B2-DHA predicted by RAST and/or Blast2GO.

Gene Start End Term
Gene 802 858022 859119 manganese ion binding
Gene 196 202800 204344 manganese ion binding
Gene 209 215336 216379 manganese ion binding
Gene 271 277278 279605 molybdenum ion binding
Gene 597 628652 630154 manganese ion binding
Gene 626 664374 665294 manganese ion binding
Gene 720 771440 772036 manganese ion binding
Gene 861 919680 921458 manganese ion binding
Gene 1016 1088133 1089044 Manganese transporter protein SitA
Gene 1017 1089047 1089853 Manganese transporter protein SitB
Gene 1018 1089850 1090701 Manganese transporter protein SitC
Gene 1019 1090695 1091534 Manganese transporter protein SitD
Gene 1049 1125413 1124667 Molybdenum transport protein ModB
Gene 1071 1148010 1150448 molybdenum ion binding
Gene 1223 1294800 1296950 molybdenum ion binding
Gene 1504 1570809 1571876 molybdenum ion binding
Gene 1548 1623197 1625641 molybdenum ion binding
Gene 1610 1694840 1695742 manganese ion binding
Gene 1725 1822796 1821738 Molybdenum transport protein ModC
Gene 1726 1823488 1822796 Molybdenum transport protein ModB
Gene 1727 1824261 1823485 Molybdenum-binding protein ModA
Gene 1729 1824720 1825508 molybdate ion transport
Gene 1756 1853924 1855090 manganese ion binding
Gene 1818 1924327 1924905 manganese ion binding
Gene 1903 2021204 2023633 molybdenum ion binding
Gene 1908 2029753 2033496 molybdenum ion binding
Gene 2091 2224133 2227873 molybdenum ion binding
Gene 2098 2235200 2237611 molybdenum ion binding
Gene 2209 2348836 2349429 Tellurite resistance protein TehB
Gene 2210 2349429 2350424 Tellurite resistance protein TehA
Gene 2610 2758489 2760867 molybdenum ion binding
Gene 2650 2805061 2806479 manganese ion binding
Gene 2682 2845329 2847608 manganese ion binding
Gene 2713 2876204 2877379 Manganese transport protein MntH
Gene 2785 2950966 2953689 molybdenum ion binding
Gene 3085 3280624 3281571 manganese ion binding
Gene 3130 3326886 3328205 manganese ion binding
Gene 3151 3347474 3349207 manganese ion binding
Gene 3540 3756054 3757565 manganese ion binding
Gene 3885 4139417 4141831 molybdenum ion binding
Gene 3886 4141880 4142467 molybdenum ion binding

Table 3: Manganese, molybdenum and tellurite resistant proteins in B2-DHA predicted by RAST and/or Blast2GO.

Detection of putative chromium resistance genes

The Blast2GO and RAST analyses detected two chromium reductase genes in B2-DHA. These gene were named as chrR and chrA (not to be confused with chromate transporter gene). Presence of these genes in this bacterium was verified by PCR amplification (Figure 4). In addition, a number of other chromate responsive genes were confirmed in B2-DHA. Most of these genes have NAD (P) H dependent oxidoreductase activity (Table 4).


Figure 4: Molecular analysis of chromium responsive genes of B2-DHA and gel electrophoresis. PCR amplification of chrR and chrA genes. L represents 2 log DNA marker, lane 1 and 2 are the amplified fragments of chrR gene in two replicates whereas lane 3 and 4 are the amplified fragments of chrA gene in two replicates.

Seq. Name Start End Predicted function
Gene- 207 213103 213432 Thioredoxin
Gene- 343 355848 356153 Cytochrome-c oxidase activity
Gene- 488 512342 513904 Oxidoreductase activity, reduced flavin or flavoprotein
Gene- 650 692191 693615 Dihydrolipoamide dehydrogenase
Gene- 1057 1135310 1134879 Universal stress protein G
Gene- 1121 1198337 1199287 Universal stress protein E
Gene- 1150 1228221 1230242 NAD(P)H dependent oxidoreductase activity
Gene- 1554 1634190 1635158 Thioredoxin reductase
Gene- 2184 2325505 2324840 Multiple antibiotic resistance protein MarC
Gene- 2185 2325818 2326195 Multiple antibiotic resistance protein MarR
Gene- 2186 2326216 2326596 Multiple antibiotic resistance protein MarA
Gene- 2187 2326629 2326844 Multiple antibiotic resistance protein MarB
Gene- 2364 2487111 2487539 Universal stress protein C
Gene- 2436 2553300 2556080 NADH: flavin oxidoreductase
Gene- 2463 2591265 2590834 Universal stress protein G
Gene- 2531 2669613 2672735 Multidrug resistance MdtB
Gene- 2533 2672736 2675813 Multidrug resistance MdtC
Gene- 2534 2675814 2677229 Multidrug resistance MdtD
Gene- 3334 3544616 3543069 Multidrug resistance MdtB
Gene- 3335 3545805 3544633 Multidrug resistance MdtA
Gene- 3582 3809416 3810390 Quinone oxidoreductase
Gene- 3638 3860171 3862714 Nitrite reductases
Gene- 3746 3974324 3973941 Polymyxin resistance protein PmrM
Gene- 3747 3974644 3974321 Polymyxin resistance protein PmrL,
Gene- 3749 3977186 3976284 Polymyxin resistance protein PmrJ
Gene- 3751 3980145 3979162 Polymyxin resistance protein ArnC
Gene- 3760 3989137 3988850 Universal stress protein B
Gene- 3761 3989469 3989906 Universal stress protein A

Table 4: Universal stress proteins, multiple antibiotic resistant proteins, multidrug resistance proteins and polymyxin resistance protein in B2-DHA as predicted by RAST and/or Blast2GO.

Prediction other proteins

Several polymyxin resistant proteins such as PmrM, PmrL, PmrJ and ArnC were aslo predicted by RAST and Blast2GO (Table 4). RAST analysis enabled us to detect several multidrug transporter proteins like MdtA, MdtB, MdtC and MdtD in B2-DHA strain (Table 4). This strain also contains universal stress proteins A, B, C, E and G, as well as several multiple antibiotic resistance proteins such as MarA, MarB, MarC and MarR (Table 4). Other proteins that catalyze binding and transport of the metal ions are metalloendopeptidase, metalloexopeptidase, metallopeptidase, metallocarboxypeptidase and metallochaperone. Some metallocenter assembly proteins such as HypA, HypB, HypC, HypD, HypE and HypF are also present in this strain.


Previously we have reported chromium-resistant bacterial strain E. cloacae B2-DHA isolated from the Hazaribagh tannery areas in Bangladesh [6]. In this paper we report the results of sequencing of the whole-genome of this bacterium. After quality trimming, error correction, and removal of the TruSeq adaptor sequence the genome was de novo assembled resulting an approximate genome length of 4.22 Mbp. Several other Enterobacter strains have been sequenced previously. For example, E. cloacae UW5 had a genome size of 4.9-Mbp and E. cloacae ENHKU01 had 4.72-Mbp [41,42]. Our strain E. cloacae B2-DHA contained a total of 3958 protein coding genes, whereas in E. cloacae ENHKU01 the total number of these genes was 4338. The results we obtained in B2-DHA are in agreement with those reported by other researchers, although the genome size and number of protein coding genes in B2-DHA are slightly smaller than those in E. cloacae ENHKU0. The difference in number of protein coding genes in the bacterial strains can be attributed to a common phenomenon. Even in a Gram-positive bacterium, Lysinibacillus sphaericus B1-CDA, the number of protein coding genes analyzed by different web tools was found to be different [43,44]. The goal of gene prediction in B2- DHA was to catalogue all the genes encoded within its genome. This prediction facilitates understanding of the mechanisms that might be involved in resistance of this bacterium to chromium and other toxic metals. The annotation of the assembled genome, number of tRNA and rRNA in B2-DHA varied from those found in the reference genome of E. cloacae ECNIH2. B2-DHA genome contained 22 rRNA and 66 tRNA genes, whereas in the reference genome ECNIH2 these were 25 and 87, respectively (http://www.ncbi.nlm.nih.gov/nuccore/CP008823). The difference in the number of tRNA genes is a common feature of bacterial and archaeal genomes [45]. These differences could likely be due to the draft status of their B2-DHA genome compared to the reference. However, sometimes annotation systems miss some RNA genes. Furthermore, the bacteria which have the highest number of 16S rRNA genes also have the highest number of tRNA genes [46].

Results obtained from RAST and Blast2GO analyses showed that the bacterium contains many metal resistance genes and there is no significant difference in the obtained results between these two methods (Table 2). Genome sequencing also revealed that B2-DHA harbors many other genes conferring resistance of this bacterium to polymyxins, multiple drugs and antibiotics. These type genes or their homologues have been identified previously in both Gram-positive and Gram-negative bacteria as well as archaea [47,48]. The proteins encoded by these genes contain many metal-binding residues, which may bind to several metal ions, primarily nickel ions [49,50]. Polymyxin resistance proteins are polycationic antimicrobial peptides that serve as antibiotics for the treatment of infectious diseases caused by multidrug-resistant Gram-negative bacteria. Several bacteria such as Serratia sp., Burkholderia sp. and Proteus sp. are naturally resistant to these antibiotics, whereas other bacteria like Pseudomonas aeruginosa, Acinetobacter baumannii and Klebsiella pneumoniae develop resistance to polymyxins through acquired resistance [51]. The B2-DHA strain contains many metalloproteinase or metalloprotease enzymes. The possible explanation for this is that the bacteria often need to protect themselves from adverse environmental stimuli, including exposure to stress factor, cationic antimicrobial peptides, and toxic metals [52]. To survive in these stress conditions bacteria develop various strategies mainly based on alterations of the lipopolysaccharides (LPSs) in their cell walls, which have overall negative charges and are the initial targets of polymyxins [53]. Other strategies may include efflux pumps and capsule formation [54,55]. Thus, the strain B2-DHA, isolated from highly chromium contaminated tannery industry area may have developed similar mechanisms to survive under adverse conditions.

We also report that B2-DHA contains 219 genes which are responsive to cell wall and capsule development as well as 164 genes which are involved in stress response (Figure 3). Presence of these genes in this bacterium might be accounted for its morphological changes when exposed to chromium. This type of changes is an advantageous trait for this bacterium and it facilitates accumulation of chromium inside the cells [6]. As described in the results, B2-DHA contains a number of chromate reductase genes and most of these have NAD(P) H-dependent oxidoreductase activity (Table 4). Similar kind of results has been reported previously by [56]. B2-DHA also harbors soluble quinone oxidoreductases that are expected to reduce Fe3+ and Cr6+ and counter oxidative stress [57]. In addition, B2-DHA possesses many other functional genes such as thioredoxin and thioredoxin reductase, dihydrolipoamide dehydrogenase, nitrite reductases, NADH: flavin oxidoreductase, quinones, cytochromes, flavoproteins and proteins with iron sulphur centers (Table 4). These genes are believed to be involved in metal oxidoreductase exhibiting Cr6+ reduction as reported previously [58-60]. The proteins encoded by these genes initially catalyze one-electron shuttle followed by a two-electron transfer to Cr6+ with the formation of intermediate(s) Cr5+ and/or Cr4+ before further reduction to Cr3+ which is a critical process involved in detoxification of chromium inside the cells [21]. Thus bacteria can survive and grow in a chromium contaminated environment. One of many possible ways to increase the effectiveness of chromium bioremediation by using bacteria is to alter the expression of these genes to minimize oxidative stress during chromate reduction. This approach has been proposed by several other researchers [12,48]. Previously, we have postulated that the B2-DHA is resistant to chromium and it can decrease chromium content significantly in the contaminated source by accumulating it in the cells [6]. Furthermore, we report that the bacterium can reduce Cr6+ to Cr3+, corroborating the presence of chromium resistance genes chrR and chrA as described in this paper.


In this paper we report the genome sequence and annotation of a chromium resistant bacterium, E. cloacae B2-DHA. Furthermore, bioinformatics analyses revealed that this bacterium harbours two chromium resistance genes, chrA and chrR among many metal resistance and other genes. Our previous findings of chromium accumulation and the recent data on genomics and functionality of the genes in B2-DHA (which is under investigation) will provide insights to establish the mechanism of chromium resistance in this strain. Altogether, our findings can be employed in bioremediation of these toxic metals in polluted environments especially industry effluents. In a long-term perspective, millions of people worldwide, in turn, can avoid many lethal diseases caused by chronic exposure of toxic metal poisoning. Therefore, our discoveries have a great potential through further investigations in contributing to a significant positive impact on the socioeconomic status of the people particularly in the developing world.


This research was supported by a major grant (AKT-2010-018) from the Swedish International Development Cooperation Agency (SIDA), and partly by a small grant from the Nilsson-Ehle (The Royal Physiographic Society in Lund) foundation in Sweden.


  1. Rahman A, Nahar N, Nawani NN, Jass J, Desale P, et al. (2014) Isolation of a Lysinibacillus strain B1-CDA showing potentials for arsenic bioremediation. J Environ Sci Health A Tox Hazard Subst Environ Eng 49: 1349-1360
  2. Viti C, Pace A, and Giovannetti L (2003) Characterization of Cr (VI)-resistant bacteria isolated from chromium-contaminated soil by tannery activity. Curr Microbiol 46: 1-5
  3. Chourey K, Thompson MR, Morrell-Falvey J, VerBerkmoes NC, Brown SD, et al. (2006) Global molecular and morphological effects of 24 h chromium(vi) exposure on Shewanella oneidensis MR-1. Appl Environ Microbiol 72: 6331-6344
  4. Saha R, Nandi R, Saha B (2011) Sources and toxicity of hexavalent chromium: A review. J Coord Chem 64: 1782-1806
  5. Kamika I, Momba M (2013) Assessing the resistance and bioremediation ability of selected bacterial and protozoan species to heavy metals in metal-rich industrial wastewater. BMC Microbiol 13: 28
  6. Rahman A, Nahar N, Nawani NN, Jass J, Hossain K, et al. (2015a) Bioremediation of hexavalent chromium (VI) by a soil borne bacterium, Enterobacter cloacae B2-DHA. J Environ Sci Health A Tox Hazard Subst Environ Eng 50: 1136-1147
  7. Viti C, Marchi E, Decorosi F, Giovannetti L (2014) Molecular mechanisms of Cr(VI) resistance in bacteria and fungi. FEMS Microbiol Rev 38: 633-659
  8. He M, Li X, Guo L, Miller SJ and Rensing C (2010) Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1. BMC Microbiol. 10: 1-10
  9. Ramirez-Diaz M, Diaz-Perez C, Vargas E, Riveros-Rosas H, Campos-Garcia J, et al. (2008) Mechanisms of bacterial resistance to chromium compounds. Biometals 21: 321-332
  10. Saier MH (2003) Tracing pathways of transport protein evolution. Mol Microbiol 48: 1145-1156
  11. Cervantes C, Campos-Garcia J (2007) Reduction and efflux of chromate by bacteria. In: Nies, D. H., Silver S. (Eds.). Molecular Microbiology of Heavy Metals (ed. Nies DH, Silver S, Springer-Verlag), pp: 407-420.
  12. Ackerley DF, Barak Y, Lynch SV, Curtin J, Matin A (2006) Effect of chromate stress on Escherichia coli K-12. J Bacteriol 188: 3371-3381
  13. Brown SD, Thompson MR, Verberkmoes NC, Chourey K, Shah M, et al. (2006) Molecular dynamics of the Shewanella oneidensis response to chromate stress. Mol Cell Proteomics5: 1054-1071
  14. Henne KL, Nakatsu CH, Thompson DK, Konopka AE (2009) High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes. BMC Microbiol 9: 199
  15. Miranda AT, González MV, González EG, Vargas E, Campos-García J, et al. (2005) Involvement of DNA helicases in chromate resistance by Pseudomonas aeruginosa PAO1. Mutat Res 578: 202 - 209
  16. Nies A, Nies DH, Silver S (1990) Nucleotide sequence and expression of a plasmid encoded chromate resistance determinant from Alcaligens eutrophus. J Biol Chem265: 5648-5653.
  17. Branco R, Chung AP, Johnston T, Gurel V, Morais P, et al. (2008) The chromate-inducible chrBACF operon from the transposable element TnOtChr confers resistance to chromium(VI) and superoxide. J Bacteriol 190: 6996-7003
  18. Henson MW, Domingo JWS, Kourtev PS, Jensen RV, Dunn JA, et al. (2015) Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment. Peer J 3: e1395.
  19. Pimentel BE, Sa´nchez RM, Cervantes C (2002) Effux of chromate by Pseudomonas aeruginosa cells expressing the ChrA protein. FEMS Microbiol Lett 212: 249-254
  20. Morais PV, Branco R,Francisco R (2011) Chromium resistance strategies and toxicity: What makes Ochrobactrum tritici 5bvl1 a strain highly resistant. Biometals 24: 401-410
  21. Cheung KH, Ji-Dong G (2007) Mechanism of hexavalent chromium detoxification by microorganisms and bioremediation application potential: A review. Int Biodeterior Biodegrada 59: 8-15
  22. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST server: Rapid annotations using subsystems technology. BMC Genomics9: 75
  23. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420-3435
  24. Rahman A, Nahar N, Jass J, Olsson B, Mandal A (2016a) Complete genome sequence of Lysinibacillus sphaericusB1-CDA, a bacterium that accumulates arsenic. Genome Announc 4: e00999-15
  25. Andrews S (2010) FastQC: A quality control tool for high throughput sequence data
  26. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet 17:10-12
  27. Kelley DR, Schatz MC, Salzberg SL (2010) Quake: Quality-aware detection and correction of sequencing errors. Genome Biol 11: R116
  28. Luo R, Liu B, Xie Y, Li Z, Huang W, et al. (2012) SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. GigaScience 1: 18
  29. Rahman A, Nahar N, Olsson B, Mandal A (2016b) Complete genome sequence of Enterobacter cloacae B2-DHA, a chromium resistant bacterium. Genome Announc 4: e00483-16
  30. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29
  31. Zdobnov EM, Apweiler R (2001) InterProScan ? an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848
  32. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964
  33. Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, et al. (2007) RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35: 3100-3108
  34. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J (2009) DNAPlotter: Circular and linear interactive genome visualization. Bioinformatics (Oxford, England) 25: 119-120
  35. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, (2007) Leunissen: Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71-W74
  36. Darling AE, Mau B, Perna NT (2010) ProgressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE5: e11147
  37. Krumsiek J, Arnold R, Rattei T (2007) Gepard: A rapid and sensitive tool for creating dot plots on genome scale. Bioinformatics 23:1026-1028
  38. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32: 11-16
  39. Salzberg SL, Delcher AL, Kasif S, White O (1998) Microbial gene identification using interpolated Markov models. Nucleic acids Res 26: 544-548
  40. Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10: 516-522
  41. Borodovsky M, McIninch J (1993) GeneMark: parallel gene recognition for both DNA strands. Comput Chem 17: 123-133
  42. Coulson TJD, Patten CL (2015) Complete genome sequence of Enterobacter cloacae UW5, a Rhizobacterium capable of high levels of indole-3-acetic acid production. Genome Announc 3: e00843-15
  43. Liu WY, Wong CF, Chung KMK, Jiang JW, Leung FCC (2013) Comparative genome analysis of Enterobacter cloacae. PLoS ONE 8: e74487
  44. Rahman A, Nahar N, Nawani NN, Jass J, Ghosh S, et al. (2015b) Comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics. Genomics 106: 384-392
  45. Lee ZMP, Bussema C, Schmidt TM (2009) rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 37: D489-D493
  46. Vezzi A, Campanaro S, D’Angelo M, Simonato F, Vitulo N, et al. (2005) Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307: 1459-1461
  47. Paschos A, Bauer A, Zimmermann A, Zehelein E, Böck A (2002) HypF, a carbamoyl phosphate-converting enzyme involved in [NiFe] hydrogenase maturation. J Biol Chem 277: 49945-49951
  48. Rahman A, Nahar N, Nawani NN, Jass J, Ghosh S, et al. (2015c) Data in support of the comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics. Data Brief 5: 579-585
  49. Olaitan AO, Morand S, Rolain JM (2014)Mechanisms of polymyxin resistance: Acquired and intrinsic resistance in bacteria. A review article. Front Microbiol 5: 1-18
  50. Moffatt JH, Harper M, Harrison P, Hale JD, Vinogradov E, et al. (2010) Colistin resistance in Acinetobacter baumannii is mediated by complete loss of lipopolysaccharide production. Antimicrob Agents Chemother54: 4971-4977
  51. Campos MA, Vargas MA, Regueiro V, Llompart CM, Alberti S, et al. (2004) Capsule polysaccharide mediates bacterial resistance to antimicrobial peptides. Infect Immun 72: 7107-7114
  52. Padilla E, Llobet E, Domenech-Sanchez A, Martinez-Martinez L, Bengoechea JA, et al. (2010) Klebsiella pneumoniae AcrAB efflux pump contributes to antimicrobial resistance and virulence. Antimicrob Agents Chemother 54: 177-183
  53. McCord JM, Fridovich I (1988) Superoxide dismutase: the first twenty years (1968-1988). Free Radic. Biol Med 5: 363-369.
  54. Ramírez-Díaz MI, Díaz-Pérez C, Vargas E, Riveros-Rosas H, Campos-García J, et al. (2007) Mechanisms of bacterial resistance to chromium compounds. BioMetals 21: 321-332
  55. Myers CR, Carstens BP, Antholine WE, Myers JM (2000) Chromium (VI) reductase activity is associated with the cytoplasmic membrane of anaerobically grown Shewanella putrefaciens MR-1. J Appl Microbiol 88: 98-106
  56. Viamajala S, Peyton BM, Apel WA, Petersen JN (2002) Chromate/nitrite interactions in Shewanella oneidensis MR-1: Evidence for multiple hexavalent chromium [Cr(VI)] reduction mechanisms dependent on physiological growth conditions. Biotechnol Bioeng 78: 770-778
  57. Ackerley DF, Gonzalez CF, Keyhan M, Blake R, Matin A (2004) Mechanism of chromate reduction by the Escherichia coli protein, NfsA and the role of different chromate reductases in minimizing oxidative stress during chromate reduction. Environ Microbiol 6: 851-860
  58. Opperman DJ, Van Heerden E (2008) A membrane-associated protein with Cr(VI)-reducing activity from Thermus scotoductus SA-01. FEMS Microbiol Lett 280: 210-218
  59. Li X, Krumholz LR (2009) Thioredoxin is involved in U(VI) and Cr(VI) reduction in Desulfovibrio desulfuricans G20. J Bacteriol 191: 4924-4933
Citation: Aminur R, Björn O, Jana J, Neelu NN, Sibdas G, et al. (2017) Genome Sequencing Revealed Chromium and Other Heavy Metal Resistance Genes in E. cloacae B2-Dha. J Microb Biochem Technol 09:191-199.

Copyright: © 2017 Aminur R, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.