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Genome-wide survey of DNA-binding proteins in Arabidopsis thaliana: analysis of distribution and functions.

Malhotra S, Sowdhamini R - Nucleic Acids Res. (2013)

Bottom Line: Performing a comprehensive survey of the sequenced genomes for DNA-binding proteins (DBPs) will help in understanding their distribution and the associated functions in a particular genome.This resulted in 4471 proteins, identified as DNA-binding in Arabidopsis genome, which are distributed across 300 different PFam families.The functions observed to be overrepresented in the plant genome harbour DNA-3-methyladenine glycosylase activity, alkylbase DNA N-glycosylase activity and DNA-(apurinic or apyrimidinic site) lyase activity, suggesting their role in specialized functions such as gene regulation and DNA repair.

View Article: PubMed Central - PubMed

Affiliation: National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India.

ABSTRACT
The interaction of proteins with their respective DNA targets is known to control many high-fidelity cellular processes. Performing a comprehensive survey of the sequenced genomes for DNA-binding proteins (DBPs) will help in understanding their distribution and the associated functions in a particular genome. Availability of fully sequenced genome of Arabidopsis thaliana enables the review of distribution of DBPs in this model plant genome. We used profiles of both structure and sequence-based DNA-binding families, derived from PDB and PFam databases, to perform the survey. This resulted in 4471 proteins, identified as DNA-binding in Arabidopsis genome, which are distributed across 300 different PFam families. Apart from several plant-specific DNA-binding families, certain RING fingers and leucine zippers also had high representation. Our search protocol helped to assign DNA-binding property to several proteins that were previously marked as unknown, putative or hypothetical in function. The distribution of Arabidopsis genes having a role in plant DNA repair were particularly studied and noted for their functional mapping. The functions observed to be overrepresented in the plant genome harbour DNA-3-methyladenine glycosylase activity, alkylbase DNA N-glycosylase activity and DNA-(apurinic or apyrimidinic site) lyase activity, suggesting their role in specialized functions such as gene regulation and DNA repair.

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Distribution of proteins: the proteins in Arabidopsis genome that were identified DNA-binding on performing searches using the structure-based families were studied for their distribution in structural groups and families. The highest populated group was helix-turn-helix.
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gkt505-F2: Distribution of proteins: the proteins in Arabidopsis genome that were identified DNA-binding on performing searches using the structure-based families were studied for their distribution in structural groups and families. The highest populated group was helix-turn-helix.

Mentions: In the set of proteins in At-Dbome identified using structural families, 20% (376) were identified by all three sequence search methods. Forty-seven per cent of the proteins were identified as DBP by only one of the methods and were validated by performing HMMScan against the PFam HMM models to check whether they identify the DBP family (Table 1). In the At-Dbome, we studied the distribution of proteins in structural groups and families. They were observed to belong to the eight groups and 57 structural families (Figure 2). The three most populated groups were helix-turn-helix, enzymes and β-propeller.Figure 2.


Genome-wide survey of DNA-binding proteins in Arabidopsis thaliana: analysis of distribution and functions.

Malhotra S, Sowdhamini R - Nucleic Acids Res. (2013)

Distribution of proteins: the proteins in Arabidopsis genome that were identified DNA-binding on performing searches using the structure-based families were studied for their distribution in structural groups and families. The highest populated group was helix-turn-helix.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3753632&req=5

gkt505-F2: Distribution of proteins: the proteins in Arabidopsis genome that were identified DNA-binding on performing searches using the structure-based families were studied for their distribution in structural groups and families. The highest populated group was helix-turn-helix.
Mentions: In the set of proteins in At-Dbome identified using structural families, 20% (376) were identified by all three sequence search methods. Forty-seven per cent of the proteins were identified as DBP by only one of the methods and were validated by performing HMMScan against the PFam HMM models to check whether they identify the DBP family (Table 1). In the At-Dbome, we studied the distribution of proteins in structural groups and families. They were observed to belong to the eight groups and 57 structural families (Figure 2). The three most populated groups were helix-turn-helix, enzymes and β-propeller.Figure 2.

Bottom Line: Performing a comprehensive survey of the sequenced genomes for DNA-binding proteins (DBPs) will help in understanding their distribution and the associated functions in a particular genome.This resulted in 4471 proteins, identified as DNA-binding in Arabidopsis genome, which are distributed across 300 different PFam families.The functions observed to be overrepresented in the plant genome harbour DNA-3-methyladenine glycosylase activity, alkylbase DNA N-glycosylase activity and DNA-(apurinic or apyrimidinic site) lyase activity, suggesting their role in specialized functions such as gene regulation and DNA repair.

View Article: PubMed Central - PubMed

Affiliation: National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India.

ABSTRACT
The interaction of proteins with their respective DNA targets is known to control many high-fidelity cellular processes. Performing a comprehensive survey of the sequenced genomes for DNA-binding proteins (DBPs) will help in understanding their distribution and the associated functions in a particular genome. Availability of fully sequenced genome of Arabidopsis thaliana enables the review of distribution of DBPs in this model plant genome. We used profiles of both structure and sequence-based DNA-binding families, derived from PDB and PFam databases, to perform the survey. This resulted in 4471 proteins, identified as DNA-binding in Arabidopsis genome, which are distributed across 300 different PFam families. Apart from several plant-specific DNA-binding families, certain RING fingers and leucine zippers also had high representation. Our search protocol helped to assign DNA-binding property to several proteins that were previously marked as unknown, putative or hypothetical in function. The distribution of Arabidopsis genes having a role in plant DNA repair were particularly studied and noted for their functional mapping. The functions observed to be overrepresented in the plant genome harbour DNA-3-methyladenine glycosylase activity, alkylbase DNA N-glycosylase activity and DNA-(apurinic or apyrimidinic site) lyase activity, suggesting their role in specialized functions such as gene regulation and DNA repair.

Show MeSH