ISSN: 0974-276X
Journal of Proteomics & Bioinformatics
Make the best use of Scientific Research and information from our 700+ peer reviewed, Open Access Journals that operates with the help of 50,000+ Editorial Board Members and esteemed reviewers and 1000+ Scientific associations in Medical, Clinical, Pharmaceutical, Engineering, Technology and Management Fields.
 
Meet Inspiring Speakers and Experts at our 3000+ Global Conferenceseries Events with over 600+ Conferences, 1200+ Symposiums and 1200+ Workshops on
Medical, Pharma, Engineering, Science, Technology and Business

Molecular Characterization and Phylogenetic Analysis of BZIP Protein in Plants

Dhivya Selvaraj1, Arul Loganathan2and Sathishkumar Ramalingam1*
1Molecular Biology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore -46, India
2Centre for Plant Molecular Biology, Tamilnadu Agriculture University, Coimbatore-46, India
Corresponding Author : Dr. Sathishkumar R
Molecular Biology Laboratory
Department of Biotechnology
Bharathiar University
Coimbatore-46, India
E-mail: rsathish@buc.edu.in
Received June 12, 2010; Accepted June 29, 2010; Published June 29, 2010
Citation: Selvaraj D, Loganathan A, Sathishkumar R (2010) Molecular Characterization and Phylogenetic Analysis of BZIP Protein in Plants. J Proteomics Bioinform 3:230-233. doi:10.4172/jpb.1000144
Copyright: © 2010 Selvaraj D, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Related article at
DownloadPubmed DownloadScholar Google

Visit for more related articles at Journal of Proteomics & Bioinformatics

Abstract

BZIP are a class of dimeric sequence specific DNA-binding proteins, is bipartite in structure containing region of enriched basic amino acids which is adjacent to leucine zippers. It is characterized by several leucine residues regularly spaced at seven amino acid intervals, basic region directly contacts with DNA. The leucine zipper mediates heterodimerization and homodimerization of protein monomers through parallel interactions which is unique to eukaryotes. The plant Arabidopsis thaliana genome shows 67 BZIP proteins. We have predicted dimeric properties of alpha helical leucine zipper and coiled coil structure of BZIP proteins in plants. In this analysis the length of leucine zippers, placement of asparagines in the hydrophobic interface and presence of interhelical electrostatic interactions were focused. Phylogenetic tree was also constructed by studying evolutionary relationship of BZIB existing among the plants.

Keywords
BZIP; Transcription factor; Dimerization; Leucine zippers; Biophysical properties; Phylogenetic relationship
Introduction
Growth and development of all organisms depends on respective gene expression which is mainly controlled by transcription factors. Transcriptional regulators can be grouped into families of related proteins (Michel et al., 2001). The basic leucine zipper (BZIP) is one among the transcriptional regulatory factors that have been conserved in all eukaryotes. BZIP protein has DNA binding domain consisting of rich regions of basic amino acids that binds to DNA and so called leucine zippers. It consists of several heptad repeats of hydrophobic residues which cause dimerization. BZIP basic region shows a high degree of sequence similarity with Homo sapiens and Arabidopsis thaliana and contain two invariant residues of Asparagine and Arginine.
BZIP–DNA complex consists of two α helices lying perpendicular to the DNA, associated in a coiled coil structure with basic region contacting a half site in the DNA major groove. The previous study reveals that BZIP structures shows functional variability of conserved residues in DNA recognition (Maria et al., 2003). The genome of Arabidopsis thaliana have been sequenced and annotated. Findings suggest that BZIP proteins are important for pathogen defense, light- induced signaling, seed maturation and flower development in plants (Christopher et al., 2004). BZIP proteins form homodimers and heterodimers depending on the amino acid sequence of the leucine zipper (O’Shea et al., 1992). In the previous study of basic region of EmBp-1, eight or ten conserved residues were found in other leucine zipper proteins (Guiltinan et al., 1990).
Leucine zippers of monomeric BZIP have structural repeats of two α helical turns and the repeat is termed as heptad, with each seven positions assigned as a,b,c,d,e,f and g. The positions d, e and g are near to leucine zipper interface and shows dimerization specificity. Amino acids in a and d positions are hydrophobic that lies on same side of the helix. These hydrophobic amino acids interact interhelically with hydrophobic amino acids in the same a and d positions of the second α-helix of the leucine zipper that stabilize the dimerization property of the protein. The Amino acid leucine has better stabilizing property than other amino acids (Michel et al., 2001) Dimerization specificity is regulated by amino acids in the a, e and g positions. The charged amino acids present in g and e positions actively involve in the formation of attractive electrostatic interhelical interactions. These interactions are denoted as g<->e’ where the prime (‘) indicates a residue on the second α helix of the dimeric leucine zipper. Oppositely charged amino acid interactions promote dimerization specificity where as similarly charged amino acids shows repulsion and thereby inhibiting homodimerization. BZIP plays an important role in Abscisic Acid (ABA) signaling pathways in Arabidopsis. Through quantitative RT-PCR, it is analyzed that most of OsbZIPs were induced by ABA, ACC and abiotic stress. The RTPCR reveals that rice BZIP has a positive role in drought tolerance (Lu et al., 2009). Phylogenetic analysis of BZIP protein was done in algae, mosses, ferns, gymnosperms and angiosperms. The result suggests that the ancestor of green plants possess four bZIP genes that actively involved in oxidative stress and also in light-dependent regulations. (Luiz et al., 2008).
In this study, 109 motifs of BZIP in the genome of O.sativa japonica were analyzed by comparing with the model plant Arabidopsis thaliana and other plants. None of the proteins are homologous to animal BZIP proteins but they have similar amino acids to regulate dimerization specificity. BZIP protein sequences from different plant source like Phaseolus vulgaris, Capsicum annuum, Nicotiana tabacum, Antirrhinum majus, Hyacinthus orientalis, Malus x domestica, Phaseolus vulgaris, Triticum aestivum, Vitis vinifera, Glycine max, Lycopersicon esculentum, Catharanthus roseus, Spinacia oleracea and Psophocarpus tetragonolobus have been annotated. This analysis reveals that many O. sativa BZIP proteins have longer leucine zippers like A.thaliana and also shows similar dimerization property which is specified by attractive and repulsive g<->e’ interactions. Finally evolutionary relationship were analysed in plants by considering the BZIP protein.
Materials and Methods
Data collection
The data set of Indica Oryza sativa of BZIP factors were obtained from the database of rice transcription factors (DART), http://drtf.cbi.pku.edu.cn/. The different plant BZIP factors were obtained from protein sequence database of National centre for Biotechnology Information (NCBI), http://www.ncbi.nlm.nih.gov/.
Pattern matching
The Pattern matching program Motifscan 3Dinsight is an integrated database and search tool for structure, function and sequence patterns of biomolecules which is used to identify the BZIP patterns existing between different plant sources. Two types of query of regular expressions were used in this database. The basic region expression [KR]-x (1, 3)-[RKSAQ]-N-{VL}-x-[SAQ] (2)-{L}-[RKTAENQ]-x- R-{S}-[RK] was found to be same in different plants. The numbers of motifs observed in the above plants were presented in Table 1.
Secondary structure predcitions
Protein secondary structural elements were predicted using a new method called self optimized prediction method (SOPMA), which accurately predicts 69.5% of amino acid for the three state describing the secondary structure (α-helix, b-beta sheet and coil). This tool works on the basis of neural network method (PHD) (Geourjon and Deleage, 1995).
Multiple alignment and phylogenetic tree analysis
Protein sequences were aligned with Clustal X Program (Thompson et al., 1997). Phylogenetic relastionship of different Plant BZIP proteins were analyzed by the neighbour – joining method (Saitou and Nei, 1987) using Molecular evolutionary Genetic Analyis tool (MEGA).
Results and Discussion
Amino acid content and leucine zipper length
The interaction of g<->e position is characterized by charged amino acids like Arginine, serine, lysine, Proline and glycine. Pair of proline and glycine indicates the C- terminals. The plants like Antirrhinum majus, Capsicum annuum, Hyacinthus orientalis, Malus x domestica, Nicotiana tabacum, Phaseolus acutifolius, Phaseolus vulgaris, Triticum aestivum, Vitis vinifera shows triheptad repeats; Glycine max, Lycopersicon esculentum Nicotiana tabacum, Psophocarpus tetragonolobus contains tetra repeats; Catharanthus roseus and Hyacinthus orientalis contains penta heptads; Spinacia oleracea shows hepta heptads these were shown in the Table 1. The kind of amino acids found in the a, d, e and g regions of O.sativa are found to be coiled coil arrangements which are known to regulate dimerization stability and specificity , as shown in Figure 1. The number of leucine repeat distribution of BZIP in O.sativa was shown in the Figure 2. Allocation of Amino acid sequences of the Plants BZIP Domains were shown in Figure 4.
Biophysical analysis shows that how the positions of amino acids contribute to dimerization specificity. From the present data, serine(S) in the second position of the heptad interacts with I, N, K and S at the ‘a’ position. These data indicates that serine contributes less to dimerization specificity than aliphatic amino acids, polar asparagines or charged lysine residues.
Phylogenetic analysis
The evolutionary relationships between the plants were evaluated by phylogenetic analysis of the aligned amino acids sequence of their BZIP domain. From the analysis BZIP factor 4 of Nicotiana tabacum is closely related with BZIP of Antirrhinum majus and Lycopersicon esculentum. The factor ATB2 BZIP of Glycine max is highly similar with BZIP-2 of Nicotiana tabacum and Capsicum annum. BZIP factor 2 and 3 is found to be same in Phaseolus vulgaris. Factor 6 of Phaseolus vulgaris is closely related with taxon Triticum aestivum and Vitis vinifera putative ripening-related BZIP and Nicotiana tabacum. The plant Catharanthus roseus is not related with the above plants it has BZIP of G BoX Binding protein, shown in the tree Figure 3. Evolutionary relationships of 23 taxa were inferred using the Neighbor - Joining method. The optimal tree with the sum of branch length = 10.69915308 is shown. Phylogenetic analyses were conducted in MEGA4.
Future Perspectives
Experimental work should be done through in vivo and in vitro methods which show different binding activities of bHLH and bZIP protein motifs. Yeast one Hybrid provides a satisfactory technique for in vivo testing of Protein – DNA interactions like bHLHZ targets with E-box. Through in vitro fluorescence anisotropy titrations protein homodimer are to be measured: E-box dissociation constants and circular dichorisim can be used to demonstrate the leucine zipper significance.
Conclusions
In this analysis dimerization partners of different plant BZIP proteins were predicted and also observed for leucine zippers. The result reveals that plants Phaseolus vulgaris, Capsicum annuum, Lycopersicon esculentum and Hyacinthus orientalis, have three repeats where as Spinacia oleracea has seven repeats of leucine. BZIP proteins were identified based on the presence of α – helix breakers, proline, pair of glycines, presence of leucines in the d position, presence of charged amino acids in the g and e. Very few histidine residues are distributed in the plant source and suggest that such signaling system is absent. Phylogenetic analysis reveals that all BZIP proteins use the same amino acids to regulate dimerization specificity. Further experimental studies can be done to prove the dimerization property.
References











Select your language of interest to view the total content in your interested language
 
Share This Article
   
 
   
 
Relevant Topics
Disc Applications of Bioinformatics
Disc Bacterial transcriptome
Disc Bioinformatics Algorithms
Disc Bioinformatics Databases
Disc Bioinformatics Tools
Disc Cancer Pharmacogenomics
Disc Cancer Proteomics
Disc Clinical Pharmacogenomics
Disc Clinical Proteomics
Disc Cluster analysis
Disc Comparative genomics
Disc Comparative proteomics
Disc Comparative transcriptomics
Disc Computational drug design
Disc Current Proteomics
Disc Data algorithms
Disc Data mining applications in genomics
Disc Data mining applications in proteomics
Disc Data mining in drug discovery
Disc Data mining tools
Disc Data modelling and intellegence
Disc Data warehousing
Disc Drug Dosage Formulations
Disc Drug Toxicity and Efficacy
Disc Epigenetics
Disc Epigenomic studies
Disc Gene Expression profiling
Disc Gene polymorphism
Disc Genome annotation
Disc Genomic Targets
Disc Genomic data mining
Disc Genomic data warehousing
Disc Glycome
Disc Human Proteome Project Applications
Disc Immune Disorders
Disc Individualized Medicine
Disc Mapping of genomes
Disc Mass Spectrometry in Proteomics
Disc Meta genomics
Disc Metabolome
Disc Microarray
Disc Microarray Proteomics
Disc Molecular and Cellular Proteomics
Disc Mouse transcriptome
Disc Non coding MRNA
Disc Personalized Medicine Studies
Disc Pharmacoeconomics in Drug Development
Disc Pharmacogenetics
Disc Pharmacogenomic Biomarker
Disc Pharmacogenomics Applications
Disc Pharmacogenomics Future Medicine
Disc Pharmacogenomics and Personalized Medicine
Disc Pharmacogenomics for Patient Care
Disc Pharmacoproteomics in Drug development
Disc Profiling
Disc Protein Sequence Analysis
Disc Protein engineering
Disc Proteogenomics
Disc Proteome
Disc Proteome Profiling
Disc Proteomic Analysis
Disc Proteomic Biomarkers
Disc Proteomics Clinical Applications
Disc Proteomics Research
Disc Proteomics Science
Disc Proteomics and Pharmacodynamics
Disc Proteomics data warehousing
Disc Python for Bioinformatics
Disc Quantitative Proteomics
Disc RNA sequencing
Disc RNA sequencing and analysis
Disc Sequencing
Disc Small RNA Sequencing
Disc Statistical data mining
Disc Transcripotme
Disc Transcriptional Attenuation
Disc Transcriptional Regulation
Disc Transcriptome analysis
Disc Translational Medicine
 
Recommended Journals
Disc Transcriptomics Journal
Disc Pharmacogenomics Journal
Disc Data Mining Journal
  View More»
 
Recommended Conferences
Disc 6th Bioinformatics Conference
August 22-23, 2016 Philadelphia, Pennsylvania, USA
Disc 7th International Conference and Expo on Proteomics
October 24-26, 2016 Rome, Italy
View More»
 
Article Tools
Disc Export citation
Disc Share/Blog this article
 
Article usage
  Total views: 11190
  [From(publication date):
July-2010 - May 30, 2016]
  Breakdown by view type
  HTML page views : 7457
  PDF downloads :3733
 
 

Post your comment

captcha   Reload  Can't read the image? click here to refresh

 
OMICS International Journals
 
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
 
 
OMICS International Conferences 2016-17
 
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings
 
 

Contact Us

Agri, Food, Aqua and Veterinary Science Journals

Dr. Krish

agrifoodaquavet@omicsinc.com

1-702-714-7001 Extn: 9040

Clinical and Biochemistry Journals

Datta A

clinical_biochem@omicsinc.com

1-702-714-7001Extn: 9037

Business & Management Journals

Ronald

business@omicsinc.com

1-702-714-7001Extn: 9042

Chemical Engineering and Chemistry Journals

Gabriel Shaw

chemicaleng_chemistry@omicsinc.com

1-702-714-7001 Extn: 9040

Earth & Environmental Sciences

Katie Wilson

environmentalsci@omicsinc.com

1-702-714-7001Extn: 9042

Engineering Journals

James Franklin

engineering@omicsinc.com

1-702-714-7001Extn: 9042

General Science and Health care Journals

Andrea Jason

generalsci_healthcare@omicsinc.com

1-702-714-7001Extn: 9043

Genetics and Molecular Biology Journals

Anna Melissa

genetics_molbio@omicsinc.com

1-702-714-7001 Extn: 9006

Immunology & Microbiology Journals

David Gorantl

immuno_microbio@omicsinc.com

1-702-714-7001Extn: 9014

Informatics Journals

Stephanie Skinner

omics@omicsinc.com

1-702-714-7001Extn: 9039

Material Sciences Journals

Rachle Green

materialsci@omicsinc.com

1-702-714-7001Extn: 9039

Mathematics and Physics Journals

Jim Willison

mathematics_physics@omicsinc.com

1-702-714-7001 Extn: 9042

Medical Journals

Nimmi Anna

medical@omicsinc.com

1-702-714-7001 Extn: 9038

Neuroscience & Psychology Journals

Nathan T

neuro_psychology@omicsinc.com

1-702-714-7001Extn: 9041

Pharmaceutical Sciences Journals

John Behannon

pharma@omicsinc.com

1-702-714-7001Extn: 9007

Social & Political Science Journals

Steve Harry

social_politicalsci@omicsinc.com

1-702-714-7001 Extn: 9042

 
© 2008-2016 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version