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Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology.

Kundu S - Front Plant Sci (2015)

Bottom Line: Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores.Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared.The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function.

View Article: PubMed Central - PubMed

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

ABSTRACT
Can the stimulus-driven synergistic association of 2-oxoglutarate dependent dioxygenases be influenced by the kinetic parameters of binding and catalysis?In this manuscript, I posit that these indices are necessary and specific for a particular stimulus, and are key determinants of a dynamic clustering that may function to mitigate the effects of this trigger. The protein(s)/sequence(s) that comprise this group are representative of all major kingdoms of life, and catalyze a generic hydroxylation, which is, in most cases accompanied by a specialized conversion of the substrate molecule. Iron is an essential co-factor for this transformation and the response to waning levels is systemic, and mandates the simultaneous participation of molecular sensors, transporters, and signal transducers. Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores. Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared. The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function. This is achieved by the establishment of transient metabolic conduits, wherein the flux is dictated by kinetic compatibility of the participating enzymes. The approach adopted, i.e., predictive mathematical modeling, is integral to the hypothesis-driven acquisition of experimental data points and, in association with suitable visualization aids may be utilized for exploring complex plant biochemical systems.

No MeSH data available.


Related in: MedlinePlus

Biochemical machinery during compensated/ early onset iron deficiency. As the cytosolic levels of ferrous iron decline, the differential activity profile of 2OG-dependent enzymes influences the cellular response. These are depicted in reference to the non-linear regression model of predicted iron affinity data (NLR_KmFe). Key players include prolyl 4-hydroxylase, despite being almost entirely organellar; secondary metabolites (GAs, bioflavonoids, alkaloids) and monotonic incremental- and decremental-responders; and dual-origin ethylene formation (enzymatic and FETs). Much of this cellular biochemistry is directed toward diminishing the resistance of the cell wall in preparation for growth, development, and the release of rhizosphere influencing metabolites.
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Figure 3: Biochemical machinery during compensated/ early onset iron deficiency. As the cytosolic levels of ferrous iron decline, the differential activity profile of 2OG-dependent enzymes influences the cellular response. These are depicted in reference to the non-linear regression model of predicted iron affinity data (NLR_KmFe). Key players include prolyl 4-hydroxylase, despite being almost entirely organellar; secondary metabolites (GAs, bioflavonoids, alkaloids) and monotonic incremental- and decremental-responders; and dual-origin ethylene formation (enzymatic and FETs). Much of this cellular biochemistry is directed toward diminishing the resistance of the cell wall in preparation for growth, development, and the release of rhizosphere influencing metabolites.

Mentions: A biological response when graded temporally might be categorized as early (minutes to hours) or late (days), and is characterized by sequential changes in the levels of stored and newly synthesized proteins (Figures 3, 4). An analysis of putative protein products of the transcription factor genes (ABI −3, −4, −5), implicated in the development of absicisic acid (ABA) insensitive mutants (N = 26; Table T4A; S1A, S1B, S2 in Supplementary Material) was undertaken to map 2OG function onto these sequences. An examination suggests that the generic AKG domain is present in a majority of sequences (≈ 57%, N = 15). Interestingly, only putative ABI4- (100%, N = 2) and ABI5- (≈ 60%, N = 13) sequences possess the same (Figure 5). A distribution of substrate specific specialized regions is tabulated (Table T4B in Supplementary Material; Figure 5).


Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology.

Kundu S - Front Plant Sci (2015)

Biochemical machinery during compensated/ early onset iron deficiency. As the cytosolic levels of ferrous iron decline, the differential activity profile of 2OG-dependent enzymes influences the cellular response. These are depicted in reference to the non-linear regression model of predicted iron affinity data (NLR_KmFe). Key players include prolyl 4-hydroxylase, despite being almost entirely organellar; secondary metabolites (GAs, bioflavonoids, alkaloids) and monotonic incremental- and decremental-responders; and dual-origin ethylene formation (enzymatic and FETs). Much of this cellular biochemistry is directed toward diminishing the resistance of the cell wall in preparation for growth, development, and the release of rhizosphere influencing metabolites.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4502536&req=5

Figure 3: Biochemical machinery during compensated/ early onset iron deficiency. As the cytosolic levels of ferrous iron decline, the differential activity profile of 2OG-dependent enzymes influences the cellular response. These are depicted in reference to the non-linear regression model of predicted iron affinity data (NLR_KmFe). Key players include prolyl 4-hydroxylase, despite being almost entirely organellar; secondary metabolites (GAs, bioflavonoids, alkaloids) and monotonic incremental- and decremental-responders; and dual-origin ethylene formation (enzymatic and FETs). Much of this cellular biochemistry is directed toward diminishing the resistance of the cell wall in preparation for growth, development, and the release of rhizosphere influencing metabolites.
Mentions: A biological response when graded temporally might be categorized as early (minutes to hours) or late (days), and is characterized by sequential changes in the levels of stored and newly synthesized proteins (Figures 3, 4). An analysis of putative protein products of the transcription factor genes (ABI −3, −4, −5), implicated in the development of absicisic acid (ABA) insensitive mutants (N = 26; Table T4A; S1A, S1B, S2 in Supplementary Material) was undertaken to map 2OG function onto these sequences. An examination suggests that the generic AKG domain is present in a majority of sequences (≈ 57%, N = 15). Interestingly, only putative ABI4- (100%, N = 2) and ABI5- (≈ 60%, N = 13) sequences possess the same (Figure 5). A distribution of substrate specific specialized regions is tabulated (Table T4B in Supplementary Material; Figure 5).

Bottom Line: Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores.Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared.The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function.

View Article: PubMed Central - PubMed

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

ABSTRACT
Can the stimulus-driven synergistic association of 2-oxoglutarate dependent dioxygenases be influenced by the kinetic parameters of binding and catalysis?In this manuscript, I posit that these indices are necessary and specific for a particular stimulus, and are key determinants of a dynamic clustering that may function to mitigate the effects of this trigger. The protein(s)/sequence(s) that comprise this group are representative of all major kingdoms of life, and catalyze a generic hydroxylation, which is, in most cases accompanied by a specialized conversion of the substrate molecule. Iron is an essential co-factor for this transformation and the response to waning levels is systemic, and mandates the simultaneous participation of molecular sensors, transporters, and signal transducers. Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores. Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared. The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function. This is achieved by the establishment of transient metabolic conduits, wherein the flux is dictated by kinetic compatibility of the participating enzymes. The approach adopted, i.e., predictive mathematical modeling, is integral to the hypothesis-driven acquisition of experimental data points and, in association with suitable visualization aids may be utilized for exploring complex plant biochemical systems.

No MeSH data available.


Related in: MedlinePlus