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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

Physiological model of 2-oxoglutarate dependent catalysis in influencing plant cell function. These enzymes have well established roles as catalysts and possess an asymmetric cellular distribution. Any model that spans an activity profile requires multiple interfacing points. These levels could be active site-, reaction-, threshold-, or compartment-specific. Suitable examples from this superfamily, able to work in a concerted manner to accomplish a systemic role are highlighted.
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Figure 5: Physiological model of 2-oxoglutarate dependent catalysis in influencing plant cell function. These enzymes have well established roles as catalysts and possess an asymmetric cellular distribution. Any model that spans an activity profile requires multiple interfacing points. These levels could be active site-, reaction-, threshold-, or compartment-specific. Suitable examples from this superfamily, able to work in a concerted manner to accomplish a systemic role are highlighted.

Mentions: A pan-systemic role for AKG-dependent dioxygenases may only be envisaged if members populate, and thereby, influence the cascade at all possible levels (Figures 4, 5). This would, in turn only be feasible if, supplemental to the variations discussed, vide supra, there were examples of graded responders to a particular stimulus or substrate. The enzymes prolyl 4-hydroxylase (P4HY; Figures 5, 7B) and ACCO might serve to facilitate these effects as sensors and terminators of a particular response. An analysis of kinetic data for oxygen in P4Hs (EC 1.14.11.2) suggests that at Km values greater than 0.065 mM, the enzyme may function as a index for declining cytosolic oxygen (De Jong and Kemp, 1984; Hirsila et al., 2003; Myllyharju, 2008), while the higher affinity forms, i.e., <0.065 mM function as efficient catalysts (Hutton et al., 1967; Kivirikko and Myllyla, 1980; Tanaka et al., 1980; Chrispeels, 1984; Myllyharju, 2008). Another salient feature of P4Hs, at least in plants is the almost complete sequestration (≈85%; N = 22) of this enzyme in various organelles. Since, proline/hydroxyproline-rich glycoproteins (PRPs) are abundant (≈20%; Hijazi et al., 2014) in cell walls, this may impose a measure of sensitivity to 4-hydroxyproline levels. Any insult to P4H activity in the form of insufficient co-factors or transporters could weaken the cell wall, and initiate a downstream response.


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

Kundu S - Front Plant Sci (2015)

Physiological model of 2-oxoglutarate dependent catalysis in influencing plant cell function. These enzymes have well established roles as catalysts and possess an asymmetric cellular distribution. Any model that spans an activity profile requires multiple interfacing points. These levels could be active site-, reaction-, threshold-, or compartment-specific. Suitable examples from this superfamily, able to work in a concerted manner to accomplish a systemic role are highlighted.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Physiological model of 2-oxoglutarate dependent catalysis in influencing plant cell function. These enzymes have well established roles as catalysts and possess an asymmetric cellular distribution. Any model that spans an activity profile requires multiple interfacing points. These levels could be active site-, reaction-, threshold-, or compartment-specific. Suitable examples from this superfamily, able to work in a concerted manner to accomplish a systemic role are highlighted.
Mentions: A pan-systemic role for AKG-dependent dioxygenases may only be envisaged if members populate, and thereby, influence the cascade at all possible levels (Figures 4, 5). This would, in turn only be feasible if, supplemental to the variations discussed, vide supra, there were examples of graded responders to a particular stimulus or substrate. The enzymes prolyl 4-hydroxylase (P4HY; Figures 5, 7B) and ACCO might serve to facilitate these effects as sensors and terminators of a particular response. An analysis of kinetic data for oxygen in P4Hs (EC 1.14.11.2) suggests that at Km values greater than 0.065 mM, the enzyme may function as a index for declining cytosolic oxygen (De Jong and Kemp, 1984; Hirsila et al., 2003; Myllyharju, 2008), while the higher affinity forms, i.e., <0.065 mM function as efficient catalysts (Hutton et al., 1967; Kivirikko and Myllyla, 1980; Tanaka et al., 1980; Chrispeels, 1984; Myllyharju, 2008). Another salient feature of P4Hs, at least in plants is the almost complete sequestration (≈85%; N = 22) of this enzyme in various organelles. Since, proline/hydroxyproline-rich glycoproteins (PRPs) are abundant (≈20%; Hijazi et al., 2014) in cell walls, this may impose a measure of sensitivity to 4-hydroxyproline levels. Any insult to P4H activity in the form of insufficient co-factors or transporters could weaken the cell wall, and initiate a downstream response.

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