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Unity in diversity, a systems approach to regulating plant cell physiology by 2-oxoglutarate-dependent dioxygenases.

Kundu S - Front Plant Sci (2015)

Bottom Line: The domain profile of a protein sequence was used as an index of miscellaneous reaction chemistry and interpreted alongside existent kinetic data in a linear model of integrated function.The collated information was categorized on the basis of existing annotation schema.The data suggests that 2OG-dependent enzymes incorporate several desirable features of a systems level player.

View Article: PubMed Central - PubMed

Affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University New Delhi, India.

ABSTRACT
Could a disjoint group of enzymes synchronize their activities and execute a complex multi-step, measurable, and reproducible response? Here, I surmise that the alpha-ketoglutarate dependent superfamily of non-haem iron (II) dioxygenases could influence cell physiology as a cohesive unit, and that the broad spectra of substrates transformed is an absolute necessity to this portrayal. This eclectic group comprises members from all major taxa, and participates in pesticide breakdown, hypoxia signaling, and osmotic stress neutralization. The oxidative decarboxylation of 2-oxoglutarate to succinate is coupled with a concomitant substrate hydroxylation and, in most cases, is followed by an additional specialized conversion. The domain profile of a protein sequence was used as an index of miscellaneous reaction chemistry and interpreted alongside existent kinetic data in a linear model of integrated function. Statistical parameters were inferred by the creation of a novel, empirically motivated flat-file database of over 3800 sequences (DB2OG) with putative 2-oxoglutarate dependent activity. The collated information was categorized on the basis of existing annotation schema. The data suggests that 2OG-dependent enzymes incorporate several desirable features of a systems level player. DB2OG, is free, accessible without a login to all users, and available at the following URL (http://comp-biol.theacms.in/DB2OG.html).

No MeSH data available.


Related in: MedlinePlus

Domain analysis of sequences of DB2OG. (A) Taxonomic spread of catalytic domains in sequences, (B) Quartile representation of domains. Abbreviations: F, fungi; A, animals; GP, gram positive; GN, gram negative; P, plants and algae; NP, non-plants. Nomenclature for enzyme families, see abbreviations in Figure 2.
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Figure 3: Domain analysis of sequences of DB2OG. (A) Taxonomic spread of catalytic domains in sequences, (B) Quartile representation of domains. Abbreviations: F, fungi; A, animals; GP, gram positive; GN, gram negative; P, plants and algae; NP, non-plants. Nomenclature for enzyme families, see abbreviations in Figure 2.

Mentions: A comparative analysis of plant 2-oxoglutarate domains with sequences of other taxa (N = 1624; Figure 3, Tables T1, T2; S2A, S2B), conveys important information on the nature of enzymes that have specialized functions. The domains DACS (Deacetoxycephalosporin-S synthase/expandase), GIAC (Gibberellic acid metabolizing), HYOS/ALKO (Hyoscyamine transforming), NUHY (nucleotide/side hydroxylases), and THYE (Thymine dioxygenase) are exclusively high scoring (q4), in comparison to other organisms. Coupled mono- (DSAT; desaturase) or poly- (FLAV; 2S-flavones) hydrogen- abstracting, i.e., desaturases, have (q4) scores, but are shared with fungal spp. The domains SULF (sulfate cleaving), CHLO (chlorinating), and CYCL (cyclization) are uniformly high (q3, q4), in all sequences examined. In contrast, the low scoring plant GBBH (γ-butyrobetaine), COLY (collagen lysyl-dioxygenases), and TFDA (enzymes catalyzing the degradation of phenoxyalkanoic acid herbicides) (q1), and XANT domains (Xanthine hydroxylase; q2) have high valued equivalents (q4) in fungal, animal, and bacterial sequences. Homogenous low scoring CP3H (collagen prolyl 3-hydroxylase) and THYD (Thymidine dioxygenases) (q1, q2) were also part of this profile. These results suggest that while collagen lysyl-hydroxylases (COLY) predominate, expectedly in animal tissues, gibberellic acids (GIAC), alkaloids (HYOS), deacetyl/deacetoxycephalopsorin-C synthases/expandase domains (DACS) populate plant sequences. The susceptibility of plant DNA to undergo modifications is reflected by the presence of the NUHY and related THYE domains.


Unity in diversity, a systems approach to regulating plant cell physiology by 2-oxoglutarate-dependent dioxygenases.

Kundu S - Front Plant Sci (2015)

Domain analysis of sequences of DB2OG. (A) Taxonomic spread of catalytic domains in sequences, (B) Quartile representation of domains. Abbreviations: F, fungi; A, animals; GP, gram positive; GN, gram negative; P, plants and algae; NP, non-plants. Nomenclature for enzyme families, see abbreviations in Figure 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356072&req=5

Figure 3: Domain analysis of sequences of DB2OG. (A) Taxonomic spread of catalytic domains in sequences, (B) Quartile representation of domains. Abbreviations: F, fungi; A, animals; GP, gram positive; GN, gram negative; P, plants and algae; NP, non-plants. Nomenclature for enzyme families, see abbreviations in Figure 2.
Mentions: A comparative analysis of plant 2-oxoglutarate domains with sequences of other taxa (N = 1624; Figure 3, Tables T1, T2; S2A, S2B), conveys important information on the nature of enzymes that have specialized functions. The domains DACS (Deacetoxycephalosporin-S synthase/expandase), GIAC (Gibberellic acid metabolizing), HYOS/ALKO (Hyoscyamine transforming), NUHY (nucleotide/side hydroxylases), and THYE (Thymine dioxygenase) are exclusively high scoring (q4), in comparison to other organisms. Coupled mono- (DSAT; desaturase) or poly- (FLAV; 2S-flavones) hydrogen- abstracting, i.e., desaturases, have (q4) scores, but are shared with fungal spp. The domains SULF (sulfate cleaving), CHLO (chlorinating), and CYCL (cyclization) are uniformly high (q3, q4), in all sequences examined. In contrast, the low scoring plant GBBH (γ-butyrobetaine), COLY (collagen lysyl-dioxygenases), and TFDA (enzymes catalyzing the degradation of phenoxyalkanoic acid herbicides) (q1), and XANT domains (Xanthine hydroxylase; q2) have high valued equivalents (q4) in fungal, animal, and bacterial sequences. Homogenous low scoring CP3H (collagen prolyl 3-hydroxylase) and THYD (Thymidine dioxygenases) (q1, q2) were also part of this profile. These results suggest that while collagen lysyl-hydroxylases (COLY) predominate, expectedly in animal tissues, gibberellic acids (GIAC), alkaloids (HYOS), deacetyl/deacetoxycephalopsorin-C synthases/expandase domains (DACS) populate plant sequences. The susceptibility of plant DNA to undergo modifications is reflected by the presence of the NUHY and related THYE domains.

Bottom Line: The domain profile of a protein sequence was used as an index of miscellaneous reaction chemistry and interpreted alongside existent kinetic data in a linear model of integrated function.The collated information was categorized on the basis of existing annotation schema.The data suggests that 2OG-dependent enzymes incorporate several desirable features of a systems level player.

View Article: PubMed Central - PubMed

Affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University New Delhi, India.

ABSTRACT
Could a disjoint group of enzymes synchronize their activities and execute a complex multi-step, measurable, and reproducible response? Here, I surmise that the alpha-ketoglutarate dependent superfamily of non-haem iron (II) dioxygenases could influence cell physiology as a cohesive unit, and that the broad spectra of substrates transformed is an absolute necessity to this portrayal. This eclectic group comprises members from all major taxa, and participates in pesticide breakdown, hypoxia signaling, and osmotic stress neutralization. The oxidative decarboxylation of 2-oxoglutarate to succinate is coupled with a concomitant substrate hydroxylation and, in most cases, is followed by an additional specialized conversion. The domain profile of a protein sequence was used as an index of miscellaneous reaction chemistry and interpreted alongside existent kinetic data in a linear model of integrated function. Statistical parameters were inferred by the creation of a novel, empirically motivated flat-file database of over 3800 sequences (DB2OG) with putative 2-oxoglutarate dependent activity. The collated information was categorized on the basis of existing annotation schema. The data suggests that 2OG-dependent enzymes incorporate several desirable features of a systems level player. DB2OG, is free, accessible without a login to all users, and available at the following URL (http://comp-biol.theacms.in/DB2OG.html).

No MeSH data available.


Related in: MedlinePlus