The Genetic Organisation and Control of Putative Dehalogenase Gene Expression in Bacillus megaterium WSH-002
Putative Dehalogenase Gene Expression in Bacillus megaterium
DOI:
https://doi.org/10.11594/jtls.13.02.15Keywords:
Bacillus megaterium WSH-002, Dehalogenase gene (dehWSH002), Ge-netic organisation, Haloacid uptake gene (dehP), Regulatory gene (dehR)Abstract
Dehalogenase-producing bacterium has been extensively studied due to their ability to reduce pollution in the environment. A previous study reported that Bacillus megaterium WSH-002 contains a putative haloacid dehalogenase type II gene, therefore, the presence of other genes associated with the dehalogenase regulatory gene function and uptake of halogenated compounds are expected. In the Bacillus megaterium WSH-002 whole genome, type II dehalogenase (DehWSH002) and two other genes related to dehalogenase regulatory and haloacid uptake genes were identified suggesting its ability to control the expression of putative dehalogenase(s) and the uptake of halogenated compounds into the cells. The phylogenetic analysis showed that DehWSH002 shared common features with DehLBHS1 of Bacillus megaterium strain BHS1 and Had protein of Bacillus megaterium strain ATCC12872/QMB1551. The study concluded that the genome of Bacillus megaterium WSH-002 contains a dehalogenase gene designated as dehWSH002 that is useful for biodegradation. In addition, further investigation of the adjacent genes suggested the presence of dehalogenase regulatory gene (dehR) and an uptake gene (dehP) in a single genetic organisation.
References
Weissermel K, HJ Arpe (2008) Industrial organic chemistry. John Wiley & Sons.
Goldberg ED (1991) Halogenated hydrocarbons: past, present and near-future problems. Science of the total environment 100:17-28. doi:10.1016/0048-9697(91)90371-K
Janssen DB, Oppentocht JE, Poelarends GJ (2001) Microbial dehalogenation. Current Opinion in Biotechnology 12(3):254-258. doi:10.1016/S0958-1669(00)00208-1
Abel E, Pakingking Jr RV, Gregoria G, Wint MT, Huyop F (2012), Characteristics of dehalogenase from bacteria isolated from the gut of pond-reared rohu (Labeo rohita) juveniles in Myanmar. Advances in Biosciences and Biotechnology 3(4): 353–361. doi:10.4236/abb.2012.34051
Adamu A, Wahab RA, Huyop F (2016) L-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1. Springerplus 5 (1): 1-17. doi:10.1186/s40064-016-2328-9
Edbeib MFA, Wahab RA, Huyop F (2016) Characterization of an α-haloalkanoic acid–degrading Pseudomonas aeruginosa MX1 isolated from contaminated seawater. Bioremediation Journal 20(2): 89-97. doi:10.1080/10889868.2015.1114464
Edbeib MFA, Wahab RA, Kaya Y, Huyop F (2017) In silico characterization of a novel dehalogenase (DehHX) from the halophile Pseudomonas halophila HX isolated from Tuz Gölü Lake, Turkey: insights into a hypersaline-adapted dehalogenase. Annals of Microbiology 67(5): 371-382. doi:10.1007/s13213-017-1266-2
Akcay K, Kaya Y (2019) Isolation, characterization and molecular identification of a halotolerant Bacillus megaterium CTBmeg1 able to grow on halogenated compounds. Biotechnology & Biotechnological Equipment 33 (1): 945-953. doi:10.1080/13102818.2019.1631717
Heidarrezaei M, Shokravi H, Huyop F, Koloor SSR, Petrů M (2020) Isolation and characterization of a novel bacterium from the marine environment for trichloroacetic acid bioremediation. Applied Sciences 10 (13): 4593. doi:10.3390/app10134593
Oyewusi HA, Wahab RA, Huyop F (2020) Dehalogenase-producing halophiles and their potential role in bioremediation. Marine Pollution Bulletin 160: 111603. doi:10.1016/j.marpolbul.2020.111603
Muslem WH, Edbeib MFA, Aksoy HM, Kaya Y, Hamid AAA, Hood MHM, Wahab RA, Huyop F (2020) Biodegradation of 3-chloropropionic acid (3-CP) by Bacillus cereus WH2 and its in silico enzyme-substrate docking analysis. Journal of Biomolecular Structure and Dynamics 38 (11): 3432-3441. doi:10.1080/07391102.2019.1655482
Huyop F, Cooper RA (2011) Regulation of dehalogenase E (DehE) and expression of dehalogenase regulator gene (DehR) from Rhizobium sp. RC1 in E. coli. Biotechnology & Biotechnological Equipment 25 (1): 2237-2242. doi:10.5504/BBEQ.2011.0009
Wahhab BHA, Samsulrizal NH, Edbeib MFA, Wahab RA, Al-Nimer MS, Hamid AAA, Oyewusi HA, Kaya Y, Notarte KIR, Shariff AHM (2021), Genomic analysis of a functional haloacid-degrading gene of Bacillus megaterium strain BHS1 isolated from Blue Lake (Mavi Gölü, Turkey), Annals of Microbiology, 71 (1): 1-11. doi:10.1186/s13213-021-01625-9
Zulkarnain LA, Huyop FZ (2022) Genomic Analysis for Haloacid Dehalogenase in Bacillus megaterium WSH-002. Journal of Tropical Life Science, 12 (1) 73-82. doi:10.11594/jtls.12.01.07
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M (2014) The seed and the rapid annotation of microbial genomes using Subsystems Technology (RAST), Nucleic acids Research 42 (D1): D206-D214. doi:10.1093/nar/gkt1226
Patwardhan A, Ray S, Roy A (2014) Molecular markers in phylogenetic studies-A Review. Journal of Phylogenetics and Evolutionary Biology 2(2):1-9. doi:10.4172/2329-9002.1000131
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and evolution, 35 (6): 1547. doi:10.1093/molbev/msy096
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4 (4): 406-425. doi:10.1093/oxfordjournals.molbev.a040454
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4): 783-791. doi:10.1111/j.15585646.1985.tb00420.
Murdiyatmo U, Asmara W, Tsang JS, Baines AJ, Bull AT, Hardman DJ (1992) Molecular biology of the 2-haloacid halidohydrolase IVa from Pseudomonas cepacia MBA4. Biochemical Journal 284(1): 87-93. doi:10.1042/bj2840087
van Der Ploeg JG, van Hall, Janssen DB (1991) Characterization of the haloacid dehalogenase from Xanthobacter autotrophicus GJ10 and sequencing of the dhlB gene. Journal of Bacteriology 173(24): 7925-7933. doi:10.1128/jb.173.24.7925-7933.1991
Brokamp A, Happe B, Schmidt FRJ (1996) Cloning and nucleotide sequence of a D,L-haloalkanoic acid dehalogenase encoding gene from Alcaligenes xylosoxidans ssp. denitrificans ABIV. Biodegradation 7 (5): 383-396. doi:10.1007/BF00056422
Barth, PT, Bolton L, Thomson JC (1992) Cloning and partial sequencing of an operon encoding two Pseudomonas putida haloalkanoate dehalogenases of opposite stereospecificity. Journal of Bacteriology 174 (8): 2612-2619. doi:10.1128/jb.174.8.2612-2619.1992
Nardi-Dei, V, Kurihara T, Okamura T, Liu JQ, Koshikawa, H, Ozaki H, Terashima Y, Esaki N, Soda K (1994) Comparative studies of genes encoding thermostable L-2-halo acid dehalogenase from Pseudomonas sp. strain YL, other dehalogenases, and two related hypothetical proteins from Escherichia coli. Applied and Environmental Microbiology 60(9): 3375-3380. doi:10.1128/aem.60.9.3375-3380.1994
Kawasaki H, Toyama T, Maeda T, Nishino H, Tonomura K (1994) Cloning and sequence analysis of a plasmid-encoded 2-haloacid dehalogenase gene from Pseudomonas putida no. 109. Bioscience Biotechnology and Biochemistry 58 (1): 160-163. doi:10.1271/bbb.58.160
Hill KE, Marchesi JR, Weightman AJ, (1999), Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. Journal of Bacteriology 181 (8): 2535-2547. doi:10.1128/JB.181.8.2535-2547.1999
Cairns SS, Cornish A, Cooper RA (1996) Cloning, sequencing and expression in Escherichia coli of two Rhizobium sp. genes encoding haloalkanoate dehalogenases of opposite stereospecificity. European Journal of Biochemistry 235(3): 744-749. doi:10.1111/j.1432-1033.1996.t01-1-00744.x
Schneider B, Müller R, Frank R, Lingens F (1991) Complete nucleotide sequences and comparison of the structural genes of two 2-haloalkanoic acid dehalogenases from Pseudomonas sp. strain CBS3. Journal of Bacteriology 173 (4): 1530-1535. doi:10.1128/jb.173.4.1530-1535.1991
Ratnaningsih E, Idris, I (2017) Cloning and expression of haloacid dehalogenase gene from Bacillus cereus IndB1. Indonesian Journal of Biotechnology 22 (2): 55-60.
Mashitah M, Roslan D, Huyop F, (2011) Molecular analysis of dehalogenase gene in genomic DNA of Bacillus megaterium strain GS1 isolated from volcanic area Gunung Sibayak. Journal of Biological Sciences 11 (5): 394-398.
Eppinger M, Bunk B, Johns MA, Edirisinghe JN, Kutumbaka KK, Koenig SSK, Creasy HH, Rosovitz MJ, Riley DR et al., (2011) Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319. Journal of Bacteriology 193 (16): 4199-4213. doi:10.1128/JB.00449-11
Lever J (1992) Cell and molecular biology of Na+/glucose symport: In Membrane Transport in Biology. Springer 56-72.
Madej MG, Kaback HR (2013) Evolutionary mix-and-match with MFS transporters II. Proceedings of the National Academy of Sciences, 110 (50): E4831-E4838. doi:10.1073/pnas.1319754110
Jing, NH, Wahab RA, Hamdan S, Huyop, F. (2010) Cloning and DNA Sequence Analysis of the Haloalkanoic Permease Uptake Gene from Rhizobium sp. RC 1. Biotechnology 9 (3): 319-325. doi: 10.3923/biotech.2010.319.325
Tse YM, Yu M, Tsang JS (2009) Topological analysis of a haloacid permease of a Burkholderia sp. bacterium with a PhoA-LacZ reporter. BMC Microbiology 9(1): 1-12. doi:10.1186/1471-2180-9-233
Saier Jr MH, Reddy VS, Tsu BV, Ahmed MS, Li C, Moreno-Hagelsieb G (2016) The transporter classifica-tion database (TCDB): recent advances. Nucleic Acids Research 44 (D1): D372-D379. doi: 10.1093/nar/gkv1103
Musa MA, Wahab RA, Huyop F (2018) Homology modelling and in silico substrate-binding analysis of a Rhizobium sp. RC1 haloalkanoic acid permease. Biotech-nology and Biotechnological Equipment 32(2): 339-349. doi: ttps://doi.org/10.1080/13102818.2018.1432417.
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