Genomic Analysis of Mesorhizobium loti Strain TONO Reveals Dehalogenases for Bioremediation

Sefatullah Zakary, Habeebat Adekilekun Oyewusi, Fahrul Huyop

Abstract


Halogenated compounds are extensively utilized in different industrial applications such as pesticides and herbicides and cause severe environmental problems because of their toxicity and persistence. Degradation of these compounds by the biological method is a significant method to reduce these recalcitrant. Mesorhizobium loti is important for nitrogen fixation in legume roots. Up to now, there is no report to indicate M. loti can produce dehalogenase enzymes. Thus, a total of twenty-five genomes of M. loti strains from the National Center for Biotechnology Information (NCBI) were analyzed. These strains notably carry dehalogenase genes and were further investigated. The relative ratio of haloalkane and haloacid dehalogenase type II or L-type from all twenty-five genomes was 26% and 74%, respectively, suggesting type II dehalogenase is common. Surprisingly, only M. loti strain TONO carries four dehalogenases and therefore it was further characterized. The chromosome of M. loti strain TONO contains four haloacid dehalogenase type II genes namely, dehLt1 (MLTONO_2099), dehLt2 (MLTONO_3660), dehLt3 (MLTONO_4143), and dehLt4 (MLTONO_6945), and their corresponding enzymes were designated as DehLt1, DehLt2, DehLt3, and DehLt4, respectively. The only haloalkane dehalogenase gene (MLTONO_4828) was located upstream of the dehLt3 gene and its amino acid share 88% identity with DmlA of Mesorhizobium japonicum MAFF 303099. The putative haloacid permease gene designated as dehrPt (MLTONO_0284) was located downstream of the dehLt1 and its amino acids show 69% identity with haloacid permease of Rhizobium sp. RC1. The gene encoding helix-turn-helix (HTH) motif family DNA-binding protein regulator and LysR family transcriptional regulator genes were also identified, possibly for regulatory functions. The genomic studies as such, have good potential to be screened for ne


Keywords


Genomic analysis, Haloacid dehalogenase, Haloacid permease, Halogenated organic compounds, Mesorhizobium loti

Full Text:

PDF

References


Edbeib MF, Wahab RA, Huyop FZ et al. (2020) Further

Analysis of Burkholderia pseudomallei MF2 and

Identification of Putative Dehalogenase Gene by PCR.

Indonesian Journal of Chemistry 20 (2): 86 – 394. doi:

22146/ijc.43262.

Adamu A, Wahab RA, Aliyu F et al. (2020) Haloacid

dehalogenases of Rhizobium sp. and related enzymes:

catalytic properties and mechanistic analysis. Process

Biochemistry 92: 437 – 446. doi:

1016/j.procbio.2020.02.002.

Heidarrezaei M, Shokravi H, Huyop F et al. (2020)

Isolation and Characterization of a Novel Bacterium

from the Marine Environment for Trichloroacetic Acid

Bioremediation. Applied Sciences 10 (13): p. 4593. doi:

3390/app10134593.

Pries F, Kingma J, Pentenga M et al. (1994) SiteDirected Mutagenesis and Oxygen Isotope Incorporation

Studies of the Nucleophilic Aspartate of Haloalkane

Dehalogenase. Biochemistry 33 (5): 1242-1247. doi:

1021/bi00171a026.

Zhang Y, Li ZS, Wu JY et al. (2004) Homology

modeling and SN2 displacement reaction of

fluoroacetate dehalogenase from Burkholderia sp. FA1.

Biochemical and Biophysical Research Communications

(2): 414-420. doi: 10.1016/j.bbrc.2004.10.044.

Allison N, Skinner AJ, Cooper RA (1983) The

dehalogenases of a 2, 2-dichloropropionate-degrading

bacterium. Microbiology 129 (5): 1283-1293. doi:

1099/00221287-129-5-1283.

Slater JH, Bull AT, Hardman DJ (1996) Microbial

dehalogenation of halogenated alkanoic acids, alcohols

and alkanes. Advances in Microbial Physiology 38: 133-

doi: 10.1016/S0065-2911(08)60157-5.

Slater JH, Lovatt D, Weightman AJ et al. (1979) The

growth of Pseudomonas putida on chlorinated aliphatic

acids and its dehalogenase activity. Microbiology 114

(1): 125-136. doi: 10.1099/00221287-114-1-125.

Yang G, Liang PH, Dunaway-Mariano D (1994)

Evidence for Nucleophilic Catalysis in the Aromatic

Substitution Reaction Catalyzed by (4-Chlorobenzoyl)

coenzyme A Dehalogenase. Biochemistry 33 (28): 8527-

doi: 10.1021/bi00194a018.

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:

1128/JB.181.8.2535-2547.1999.

Slater JH, Bull AT, Hardman DJ (1995) Microbial

dehalogenation. Biodegradation 6 (3): 181-189. doi:

1007/BF00700456.

Muslem WH, Edbeib MF, Aksoy HM et al. (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:

1080/07391102.2019.1655482.

Mesri S, Wahab RA, Huyop F (2009) Degradation of 3-

chloropropionic acid (3CP) by Pseudomonas sp. B6P

isolated from a rice paddy field. Annals of Microbiology,

(3): 447-451. doi: 10.1007/bf03175129.

Chan WY, Wong M, Guthrie J et al. (2010) Sequenceand activity-based screening of microbial genomes for

novel dehalogenases. Microbial Biotechnology 3 (1):

-120. doi: 10.1111/j.1751-7915.2009.00155.x.

Adamu A, Wahab RA, Huyop F (2016) L-2-Haloacid

dehalogenase (DehL) from Rhizobium sp. RC1.

SpringerPlus 5 (1): 1-17.

Oyewusi HA, Huyop F, Wahab RA (2020) Molecular

docking and molecular dynamics simulation of Bacillus

thuringiensis dehalogenase against haloacids,

haloacetates and chlorpyrifos. Journal of Biomolecular

Structure and Dynamics: 1-16. doi:

1080/07391102.2020.1835727.

Wahhab BH, Anuar NFSK, Wahab RA et al. (2020)

Characterization of a 2,2-dichloropropionic acid (2,2-

DCP) degrading alkalotorelant Bacillus megaterium

strain BHS1 isolated from Blue Lake in Turkey. Journal

of Tropical Life Science 10 (3): 245 – 252. doi:

11594/jtls.10.03.08.

Zang H, Wang H, Miao L et al. (2020) Carboxylesterase,

a de-esterification enzyme, catalyzes the degradation of

chlorimuron-ethyl in Rhodococcus erythropolis D310-1.

Journal of Hazardous Materials, 387: p. 121684. doi:

1016/j.jhazmat.2019.121684.

Azam S, Parthasarathy S, Singh C et al. (2019) Genome

organization and adaptive potential of archetypal

organophosphate degrading Sphingobium fuliginis

ATCC 27551. Genome Biology and Evolution 11 (9):

-2562. doi: 10.1093/gbe/evz189.

Shimoda Y, Hirakawa H, Sato S et al. (2016) Wholegenome sequence of the nitrogen-fixing symbiotic

Rhizobium Mesorhizobium loti strain TONO. Genome

Announcements 4 (5). doi: 10.1128/genomeA.01016-16.

Yamaya‐Ito H, Shimoda Y, Hakoyama T et al. (2018)

Loss‐of‐function of Aspartic peptidase nodule‐induced 1

S Zakary, HA Oyewusi, F Huyop, 2021 / Genomic Analysis of Mesorhizobium loti Strain TONO for Bioremediation

JTLS | Journal of Tropical Life Science 76 Volume 11 | Number 1 | January | 2021

(APN 1) in Lotus japonicus restricts efficient nitrogen‐

fixing symbiosis with specific Mesorhizobium loti

strains. The Plant Journal 93 (1): 5-16. doi:

1111/tpj.13759.

Roy SS, Dasgupta R, Bagchi A (2014) A review on

phylogenetic analysis: a journey through modern era.

Computational Molecular Bioscience 4 (03): 39. doi:

4236/cmb.2014.43005.

Kumar S, Stecher G, Tamura K (2016) MEGA7:

Molecular evolutionary genetics analysis version 7.0 for

bigger datasets. Molecular Biology and Evolution 33 (7):

-1874. doi: 10.1093/molbev/msw054.

Kumar S, Stecher G, Li M et al. (2018) MEGA X:

molecular evolutionary genetics analysis across

computing platforms. Molecular Biology and Evolution

(6): 1547-1549. doi: 10.1093/molbev/msy096.

Madeira F, Park YM, Lee J et al. (2019) The EMBL-EBI

search and sequence analysis tools APIs in 2019. Nucleic

Acids Research 47 (W1): W636-W641. doi:

1093/nar/gkz268.

Corpet F (1988) Multiple sequence alignment with

hierarchical clustering. Nucleic Acids Research 16 (22):

-10890. doi: 10.1093/nar/16.22.10881.

Robert X, Gouet P (2014) Deciphering key features in

protein structures with the new ENDscript server.

Nucleic Acids Research 42 (W1): W320-W324. doi:

1093/nar/gku316.

Salamov VSA, Solovyevand A (2011) Automatic

annotation of microbial genomes and metagenomic

sequences. In: Metagenomics and its Applications in

Agriculture, Biomedicine and Environmental Studies.

Hauppauge, Nova Science Publishers. 61-78.

Ribeiro FJ, Przybylski D, Yin S et al. (2012) Finished

bacterial genomes from shotgun sequence data. Genome

Research 22 (11): 2270 - 2277. doi:

1101/gr.141515.112.

Marcus S, Lee H, Schatz MC (2014) SplitMEM: a

graphical algorithm for pan-genome analysis with suffix

skips. Bioinformatics 30 (24): 3476-3483. doi:

1093/bioinformatics/btu756.

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:

1111/j.1432-1033.1996.t01-1-00744.x.

Stringfellow JM, Cairns SS, Cornish A, Cooper RA

(1997) Haloalkanoate dehalogenase II (DehE) of a

Rhizobium sp.—Molecular analysis of the gene and

formation of carbon monoxide from trihaloacetate by the

enzyme. European Journal of Biochemistry 250 (3): 789-

doi: 10.1111/j.1432-1033.1997.00789.x.

Kasai-Maita H, Hirakawa H, Nakamura Y et al. (2013)

Commonalities and differences among symbiosis islands

of three Mesorhizobium loti strains. Microbes and

Environments 28 (2): 275-278. doi:

1264/jsme2.ME12201.

Sallabhan R, Kerdwong J, Dubbs JM et al. (2013) The

hdhA gene encodes a haloacid dehalogenase that is

regulated by the LysR-type regulator, HdhR, in

Sinorhizobium meliloti. Molecular Biotechnology 54

(2): 148-157. doi: 10.1007/s12033-012-9556-1.

Krasper L, Lilie H, Kublik A et al. (2016) The MarRtype regulator Rdh2R regulates rdh gene transcription in

Dehalococcoides mccartyi strain CBDB1. Journal of

Bacteriology 198 (23): 3130-3141. doi:

1128/JB.00419-16.

Wagner A, Segler L, Kleinsteuber S et al. (2013)

Regulation of reductive dehalogenase gene transcription

in Dehalococcoides mccartyi. Philosophical

Transactions of the Royal Society B: Biological Sciences

(1616): 20120317. doi: 10.1098/rstb.2012.0317.

La Roche SD, Leisinger T (1991) Identification of

DcmR, the regulatory gene governing expression of

dichloromethane dehalogenase in Methylobacterium sp.

strain DM4. Journal of Bacteriology 173 (21): 6714-

doi: 10.1128/jb.173.21.6714-6721.1991.

Whelan S, Goldman N (2001) A general empirical model

of protein evolution derived from multiple protein

families using a maximum-likelihood approach.

Molecular Biology and Evolution 18 (5): 691-699. doi:

1093/oxfordjournals.molbev.a003851.

Schmidberger JW, Wilce JA, Tsang JSH, Wilce MCJ

(2007) Crystal structures of the substrate free-enzyme,

and reaction intermediate of the HAD superfamily

member, haloacid dehalogenase DehIVa from

Burkholderia cepacia MBA4. Journal of Molecular

Biology 368 (3): 706-717. doi:

1016/j.jmb.2007.02.015.

Liu JQ, Kurihara T, Miyagi M et al. (1995) Reaction

mechanism of L-2-haloacid dehalogenase of

Pseudomonas sp. YL: identification of Asp10 as the

active site nucleophile by 18O incorporation

experiments. Journal of Biological Chemistry 270 (31):

-18312. doi: 10.1074/jbc.270.31.18309.

Ridder IS, Rozeboom HJ, Kalk KH et al. (1997) Threedimensional structure of L-2-haloacid dehalogenase

from Xanthobacter autotrophicus GJ10 complexed with

the substrate-analogue formate. Journal of Biological

Chemistry 272 (52): 33015-33022. doi:

1074/jbc.272.52.33015.

Hisano T, Hata Y, Fujii T et al. (1996) Crystal Structure

of L-2-Haloacid Dehalogenase from Pseudomonas sp.

YL An α/β hydrolase structure that is different from the

α/β hydrolase fold. Journal of Biological Chemistry 271

(34): 20322-20330. doi: 10.1074/jbc.271.34.20322.

Nakamura T, Yamaguchi A, Kondo H et al. (2009) Roles

of K151 and D180 in L‐2‐haloacid dehalogenase from

Pseudomonas sp. YL: Analysis by molecular dynamics

and ab initio fragment molecular orbital calculations.

Journal of Computational Chemistry 30 (16): 2625-

doi: 10.1002/jcc.21273.

Kurihara T, Liu JQ, Nardi-Dei V et al. (1995)

Comprehensive site-directed mutagenesis of L-2-halo

acid dehalogenase to probe catalytic amino acid residues.

The Journal of Biochemistry 117 (6): 1317-1322. doi:

1093/oxfordjournals.jbchem.a124861.

Kondo H, Nakamura T, Tanaka S (2014) A significant

role of Arg41 residue in the enzymatic reaction of

haloacid dehalogenase L-DEX YL studied by QM/MM

method. Journal of Molecular Catalysis B: Enzymatic

: 23-31.doi: 10.1016/j.molcatb.2014.09.006.

Pang BCM, Tsang JSH (2001) Mutagenic analysis of the

conserved residues in dehalogenase IVa of Burkholderia

cepacia MBA4. FEMS Microbiology Letters 204 (1):

-140. doi: 10.1111/j.1574-6968.2001.tb10876.x.

Nardi-Dei V, Kurihara T, Park C et al. (1997) Bacterial

DL-2-haloacid dehalogenase from Pseudomonas sp.

S Zakary, HA Oyewusi, F Huyop, 2021 / Genomic Analysis of Mesorhizobium loti Strain TONO for Bioremediation

JTLS | Journal of Tropical Life Science 77 Volume 11 | Number 1 | January | 2021

strain 113: gene cloning and structural comparison with

D-and L-2-haloacid dehalogenases. Journal of

Bacteriology 179 (13): 4232-4238. doi:

1128/jb.179.13.4232-4238.1997.

Musa MA, Wahab RA, Huyop F (2018) Homology

modelling and in silico substrate-binding analysis of a

Rhizobium sp. RC1 haloalkanoic acid permease.

Biotechnology & Biotechnological Equipment 32 (2):

-349. doi: 10.1080/13102818.2018.1432417.




DOI: http://dx.doi.org/10.11594/jtls.11.01.09

Copyright (c) 2021 Sefatullah Zakary