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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

Profile based search of sequences in DB2OG. Users may query the database for putative 2-OG dependent sequences using one or more of the pre-defined HMM profiles (N = 26). A structured query of this nature (simple or complex), without an inclusion score will list all sequences with the profile of interest. Other sequences corresponding to variable subcellular locations may also be downloaded by clicking on the appropriate hyperlinks. NOTE: The browser window displaying the search results needs to be refreshed for each query.
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Figure 1: Profile based search of sequences in DB2OG. Users may query the database for putative 2-OG dependent sequences using one or more of the pre-defined HMM profiles (N = 26). A structured query of this nature (simple or complex), without an inclusion score will list all sequences with the profile of interest. Other sequences corresponding to variable subcellular locations may also be downloaded by clicking on the appropriate hyperlinks. NOTE: The browser window displaying the search results needs to be refreshed for each query.

Mentions: The GUI introduces and summarizes the salient features of alpha-KG dependent enzymes, and provides general instructions of use. The user may opt to download various categories of sequences or search the database for combinations of previously computed profiles (twenty-six functional hidden Markov model profiles; Kundu, 2012). Since, most sequences of the database have more than one assigned profile, there are several examples of overlapping data. This may be minimized by usage of the logical OR/AND functions to filter the profiles (Figure 1). The matched list is presented as a simple text file, which may be downloaded or viewed online. Users are encouraged to refresh their browsers to visualize the latest search results.


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

Kundu S - Front Plant Sci (2015)

Profile based search of sequences in DB2OG. Users may query the database for putative 2-OG dependent sequences using one or more of the pre-defined HMM profiles (N = 26). A structured query of this nature (simple or complex), without an inclusion score will list all sequences with the profile of interest. Other sequences corresponding to variable subcellular locations may also be downloaded by clicking on the appropriate hyperlinks. NOTE: The browser window displaying the search results needs to be refreshed for each query.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Profile based search of sequences in DB2OG. Users may query the database for putative 2-OG dependent sequences using one or more of the pre-defined HMM profiles (N = 26). A structured query of this nature (simple or complex), without an inclusion score will list all sequences with the profile of interest. Other sequences corresponding to variable subcellular locations may also be downloaded by clicking on the appropriate hyperlinks. NOTE: The browser window displaying the search results needs to be refreshed for each query.
Mentions: The GUI introduces and summarizes the salient features of alpha-KG dependent enzymes, and provides general instructions of use. The user may opt to download various categories of sequences or search the database for combinations of previously computed profiles (twenty-six functional hidden Markov model profiles; Kundu, 2012). Since, most sequences of the database have more than one assigned profile, there are several examples of overlapping data. This may be minimized by usage of the logical OR/AND functions to filter the profiles (Figure 1). The matched list is presented as a simple text file, which may be downloaded or viewed online. Users are encouraged to refresh their browsers to visualize the latest search results.

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