Plasmids of the Chlorophenoxyacetic-Acid Degradation of Bacteria of the Genus Raoultella

Zharikova, N. V.; Ясаков, Т. Р.; Zhurenko, E. I.; Korobov, V. V.; Markusheva, T. V.

doi:10.1134/s0003683821030157

Cited by 5 publications

(2 citation statements)

References 29 publications

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“…They encode for enzymes involved in the degradation of 2,4dichlorophenoxyacetic acid (2,4-D) which has human health and ecological risks (Peterson et al, 2016;ATSDR, 2020), but is still used worldwide as an herbicide in agriculture (Islam et al, 2018). Continued exploration of microbial 2,4-D degradation in various environments in China (Xia et al, 2017;Xiang et al, 2020), Brazil (Brucha et al, 2021), Vietnam (Nguyen et al, 2021a;Nguyen et al, 2021b), Russia (Zharikova et al, 2021) and Japan (Hayashi et al, 2021) suggests that this problem is still in the spotlight.…”

Section: Introductionmentioning

confidence: 99%

Evolution end classification oftfdgene clusters mediating bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D)

Ясаков

2023

Preprint

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Thetfd(tfdIandtfdII) are gene clusters originally discovered in plasmid pJP4 which is involved in the bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) via the ortho-cleavage pathway of chlorinated catechols. They share this activity, with respect to substituted catechols, with clusterstcbandclc. Although great efforts have been devoted over nearly forty years to exploring the structural diversity of these clusters, their evolution has been poorly resolved to date, and their classification is clearly obsolete. Employing comparative genomic and phylogenetic approaches revealed that alltfdclusters can be classified as one of four different types. The following four-type classification and new nomenclature are proposed:tfdI,tfdII,tfdIIIandtfdIV(A,B,C). Horizontal gene transfer betweenBurkholderialesandSphingomonadalesprovided phenomenal linkage betweentfdI,tfdII,tfdIIIandtfdIVtype clusters and their mosaic nature. It is hypothesized that the evolution oftfdgene clusters proceeded within first (tcb,clcandtfdI), second (tfdIIandtfdIII) and third (tfdIV(A,B,C)) evolutionary lineages in each of which the genes were clustered in specific combinations. Their clusterization has been discussed through the prism of hot spots and driving forces of various models, theories, and hypotheses of cluster and operon formation. Two hypotheses about series of gene deletions and displacements have also been proposed to explain the structural variations across members of clusterstfdIIandtfdIII, respectively. Taking everything into account, these findings reconstructing the phylogeny oftfdclusters, have delineated their evolutionary trajectories, and allowed the contribution of various evolutionary processes to be assessed.

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Section: Introductionmentioning

confidence: 99%

Evolution end classification oftfdgene clusters mediating bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D)

Ясаков

2023

Preprint

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“…They encode for enzymes involved in the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) which has human health and ecological risks [ 1 , 2 ], but is still used worldwide as an herbicide in agriculture [ 3 ]. Continued exploration of microbial 2,4-D degradation in various environments in China [ 4 , 5 ], Brazil [ 6 ], Vietnam [ 7 , 8 ], Russia [ 9 ] and Japan [ 10 ] suggests that this problem is still in the spotlight.…”

Section: Introductionmentioning

confidence: 99%

Evolution End Classification of tfd Gene Clusters Mediating Bacterial Degradation of 2,4-Dichlorophenoxyacetic Acid (2,4-D)

Iasakov

2023

IJMS

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The tfd (tfdI and tfdII) are gene clusters originally discovered in plasmid pJP4 which are involved in the bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) via the ortho-cleavage pathway of chlorinated catechols. They share this activity, with respect to substituted catechols, with clusters tcb and clc. Although great effort has been devoted over nearly forty years to exploring the structural diversity of these clusters, their evolution has been poorly resolved to date, and their classification is clearly obsolete. Employing comparative genomic and phylogenetic approaches has revealed that all tfd clusters can be classified as one of four different types. The following four-type classification and new nomenclature are proposed: tfdI, tfdII, tfdIII and tfdIV(A,B,C). Horizontal gene transfer between Burkholderiales and Sphingomonadales provides phenomenal linkage between tfdI, tfdII, tfdIII and tfdIV type clusters and their mosaic nature. It is hypothesized that the evolution of tfd gene clusters proceeded within first (tcb, clc and tfdI), second (tfdII and tfdIII) and third (tfdIV(A,B,C)) evolutionary lineages, in each of which, the genes were clustered in specific combinations. Their clustering is discussed through the prism of hot spots and driving forces of various models, theories, and hypotheses of cluster and operon formation. Two hypotheses about series of gene deletions and displacements are also proposed to explain the structural variations across members of clusters tfdII and tfdIII, respectively. Taking everything into account, these findings reconstruct the phylogeny of tfd clusters, have delineated their evolutionary trajectories, and allow the contribution of various evolutionary processes to be assessed.

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Novel 4-chlorophenoxyacetate dioxygenase-mediated phenoxyalkanoic acid herbicides initial catabolism in Cupriavidus sp. DL-D2

Yang,

Liu,

Chen

et al. 2024

Journal of Hazardous Materials

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Plasmids of the Chlorophenoxyacetic-Acid Degradation of Bacteria of the Genus Raoultella

Cited by 5 publications

References 29 publications

Evolution end classification oftfdgene clusters mediating bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D)

Evolution end classification oftfdgene clusters mediating bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D)

Evolution End Classification of tfd Gene Clusters Mediating Bacterial Degradation of 2,4-Dichlorophenoxyacetic Acid (2,4-D)

Novel 4-chlorophenoxyacetate dioxygenase-mediated phenoxyalkanoic acid herbicides initial catabolism in Cupriavidus sp. DL-D2

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