BACKGROUND
control of gene expression at the transcriptional level is vital and several mechanisms exist that may regulate the dna binding of a transcription factor .
these include differential heterodimer formation, methylation of the dna target site  <cit> , phosphorylation in the tf dna-binding domain   <cit> , reduction/oxidation  of the dbd  <cit> , the concentration of cations  in the nuclear environment  <cit> .
a combination of differential heterodimer formation together with the phosphorylation and the redox mechanisms may yield complex behaviours that determine the expression or inhibition of downstream targets.
we are particularly interested in the complex behaviour that these  <dig> mechanisms create in the bzips, since these tfs are involved in cell proliferation and apoptosis.
bzips are eukaryotic tfs, found in fungi, plants and animals.
they are named for the highly conserved basic region  and leucine zipper  domains, found in all these proteins.
specifically, the bzip domain is responsible for dimerization mediated by the lz region and dna-binding is mediated by the br, which is n-terminal to the lz.
two mechanisms that control dna binding by bzip dimers are phosphorylation and redox.
this control is mediated by specific and conserved amino acids in the br of the protein.
serine and cysteine residues mediate phosphorylation and redox, respectively, at position  <dig> of the br domain .
we designate these residues as s <dig> and c <dig>  respectively.
crystallographic analysis of various bzip proteins, like jun-fos, gcn <dig>  pap <dig> and c/ebpα, has shown that the amino acids at this position make contacts with the dna  <cit> ,  <cit> .
phosphorylation of s <dig> in batf  <cit>  and c/ebp  <cit>  proteins has been shown to add a negative charge to the positive br and inhibit binding with the negatively charged dna.
phosphorylation of only one of the two s <dig> residues in a heterodimer is sufficient to block dna binding, thus having a dominant effect .
it has also been postulated that the corresponding tyrosine residue  in atf <dig> could potentially be phosphorylated  <cit> .
another mechanism of switching on or off dna binding is the reduction/oxidation of the cysteine residue in position  <dig> of the br of bzips   <cit> ,  <cit> .
oxidation of c <dig> blocks dna binding, and this mechanism has been shown to operate for the ap <dig> proteins.
several mechanisms have been proposed or predicted for the oxidation of c <dig>  such as reversible formation of sulphenic acid, a disulphide bond  <cit> , s-glutathiolation  <cit> , or s-cystenyl cystenylation  <cit> .
furthermore, c <dig> can either be protected from oxidation by the mbf <dig> co-activator  <cit> , or it can be switched back from its oxidised to its reduced state by the ref- <dig> protein  <cit> .
the importance of these two signalling mechanisms  is stressed by the conservation of the cysteine or serine at this position.
deppmann et al.
<cit>  report 55% and 35% occurrence of cysteine and serine, respectively, in position  <dig> in an alignment of human bzips.
here, we provide a more detailed phylogenetic analysis using several vertebrate and invertebrate species and highlight the level of conservation of these amino acids, strongly suggesting functional conservation.
in addition to conservation at the sequence level, the same cysteine residue and the redox mechanism have been demonstrated experimentally in both human and drosophila ap <dig> proteins  <cit> ,  <cit> ,  <cit> .
for the phosphorylation mechanism, the importance of s <dig> has been shown experimentally for batf and c/ebp proteins  <cit> ,  <cit> ,  <cit> .
in addition, mutation of the cysteine or serine in position  <dig> does not affect heterodimerization properties or dna-binding recognition  <cit> ,  <cit> ,  <cit> .
this mutation appears to affect the selection of the signal  that turns on or off the dna-binding ability of the dimer.
therefore, the conservation of the amino acids in position  <dig>  and the report of functional conservation across different families, strongly indicates that the same mechanism is preserved from drosophila to humans across many divergent evolutionary lineages.
in this work, we provide a visualization of the bzip dimerization network and show the level of conservation of c <dig> and s <dig> residues across different phylogenetic lineages.
it has yet to be established experimentally, for all bzip proteins, whether they are under redox or phosphorylation control.
however, given that all bzip dna-binding regions around the c <dig> and s <dig> residues have fundamentally similar properties, and extrapolating from experiments on jun, fos, c/ebp and batf proteins, we predict the bzip proteins in which the redox and phosphorylation mechanisms are utilised.
based on these predictions, we propose that the control mechanism is linked to the evolutionary history of the bzip families.
interestingly, certain dimerization types are over-represented, while others are under-represented – suggesting strong preference for particular interaction patterns.
specifically, c <dig> monomers tend to dimerize with other c <dig> monomers, probably in order to retain redox control and rarely interact with other monomers.
while dimerization with other monomer types can occur, such dimers usually have a repression function, so as to avoid inappropriate gene expression.
RESULTS
the c <dig> residue of the br alignment  is strikingly conserved in all vertebrates and invertebrates in the atf <dig>  atf <dig>  nfe <dig>  bach, creb, fos, jun, l-maf, s-maf families .
s <dig> is also strikingly conserved in the atf <dig>  batf, c/ebp, c/ebp-γ, e4bp <dig>  oasis, oasis-b and par families.
y <dig>  which could potentially be phosphorylated, is conserved in the atf <dig> family.
the xbp <dig> family is the only family that has a serine residue in the arthropods; this has been mutated to an alanine residue in chordates, suggesting loss of phosphorylation control in the br.
interestingly, we see the presence of serine and cysteine residues in fungal bzips as well as the presence of phenylalanine , which is restricted to the fungal lineage .
this phenylalanine is necessary for recognition of the yap dna-binding motif by the yap proteins in fungi  <cit> .
nevertheless, the dna-recognition property of this phenylalanine does not necessarily extend to the serine and cysteine residues, since they have no aromatic ring that can get stuck in the dna.
the presence of these particular serine and cysteine residues in both metazoan and fungal proteins emphasises the ancient nature of phosphorylation and redox control in bzips.
it appears that the highly conserved nature of these amino acids is due to functional reasons  and not due to size restrictions at the protein-dna interface.
while cysteine, serine and alanine are all very small amino acids, the presence of tyrosine and phenylalanine in the same position shows clearly that residue size is not a major constraint.
cysteine and serine are only one point mutation apart in the genetic code and so, if size was the only constraint, we might expect these two amino acids to occur with equal frequency at this site, even within families.
thus, the conservation of the same amino acid across all the family members, from vertebrates to invertebrates  strongly suggests that biochemical function is involved.
phylogenetic analysis of the br  indicates that the use of phosphorylation or redox control has emerged several times, as the various bzip families emerged in early metazoan evolution.
therefore, it is impossible to determine conclusively whether phosphorylation or redox control is the ancestral state at position  <dig>
the bzip network is visualised in figure  <dig>  the bzip dimerization network does not have the same statistical properties as all the other protein interaction networks studied to date  <cit> .
unlike them, it is not described by a power-law distribution , where the number of genes with k interactions should decay exponentially.
we have previously described a network  <cit>  of similar magnitude  that followed a power-law distribution and which seems to work as a multi-switch  <cit> .
in the case of the bhlh network, the majority of the proteins need to heterodimerize with one of the ubiquitously expressed hub proteins  in order to form functional dimers.
in contrast, in the bzip network, a large number of proteins can form homodimers.
therefore, if the bzip network is different, what are its purposes and functions?
integration of protein interaction data with sequence analysis reveals the different types of dimers and how many of them are formed in humans .
dna binding of all dimers that contain at least one s <dig> is probably controlled by phosphorylation.
the same may also happen for dimers that contain y <dig>  since this tyrosine can potentially be phosphorylated  <cit> .
all the dimers that contain at least two c <dig> residues are probably controlled by the redox mechanism.
dimers that contain only one c <dig> should be deficient in redox control, according to  <cit> .
the immediate question is whether there is a pattern to the dimerization partners that is related to the phosphorylation and redox mechanisms.
to test whether the distribution of different types of dimers is significantly different from random , a chi-squared test was used .
according to the null hypothesis, the same number of proteins with the same frequency of serine and cysteine residues could dimerize randomly.
note, this statistical analysis must be treated with caution since differential gene expression and protein expression could distort the null hypothesis.
by using the frequency of each amino acid in the  <dig> human bzips for which interaction data are available  <cit> , we looked for all the types of bzip dimers that could potentially form if all potential pairs were co-expressed.
we were particularly interested in the redox control and therefore focused on the presence of c19-bearing dimers.
we observed biases, particularly an over-representation of c-c type dimers that also resulted in an under-representation of c-x dimers  and vice versa .
it is conceivable that this under-representation of c-x dimers is an artefact and this could have arisen in two different ways.
firstly, we explored the possibility that c19-bearing proteins tend to homodimerize more than the others.
secondly, we explored the possibility that c19-bearing proteins tend to dimerize more with their closest homologues, that is proteins of the same family that also have a cysteine at position  <dig>  in order to exclude biases created by these two options, we also performed the chi-squared test for heterodimers only, and for heterodimers that are not close paralogues .
in both cases, the over-representation of c-c and under-representation of c-x dimers is statistically significant.
in the above statistical tests, we used all the paralogues of each family.
nevertheless, most paralogues have similar dimerization patterns.
if position  <dig> is not actually linked to the dimerization pattern, but is only responsible for family-specific dna core-site recognition, then gene duplication  could have caused an artefactual connection.
in order to exclude this possibility, all the paralogues of each family were collapsed into one such that the network was then composed of interacting families.
we retained the structure of the network among the families, but we shuffled the amino acids of position  <dig> across the various families  <dig>  times.
this model showed clearly that, in less than 2% of the shuffled networks, did we obtain an under-representation of c-x family dimers similar to that observed in the data  .
furthermore, we performed the same analysis in other positions of the br alignment  that are also strongly conserved within each family, but we did not observe any under/over-representation of amino acid combinations at a cut-off level of 5% , in contrast to what we observed for position  <dig>  it should also be stressed that the experimental evidence from  <cit>  shows that mutation of c <dig> did not affect dna binding, dna element recognition, or dimerization of the zta bzip protein.
interestingly, it is apparent that the c-x heterodimer type is not favoured.
this can be explained by the dominant nature of phosphorylation over redox control.
the presence of only one s <dig> residue would be sufficient to place the dna-binding properties of the dimer under phosphorylation control.
the loss or decrease of the redox mechanism in the br is known to increase the transforming activity of the jun-fos heterodimer  <cit> ,  <cit> .
thus, it is presumably important to retain the redox mechanism and avoid heterodimerizing with other types .
what is the function of the c-type bzips that actually dimerize with other types , thus forming c-x type dimers and exhibiting insufficient redox control?
by examining the activation/inhibition activity of the x-type partners in general, it appears that e4bp <dig>  <cit> , p21-sntf  <cit>  and batf  <cit>  have an inhibitory effect when dimerizing with other factors.
in the case of e4bp <dig>  this is due to the active repression domain that it possesses.
the cases of atf <dig>  c/ebp-β and c/ebp-γ are more complex because they can exhibit activating or inhibiting effects, depending on post-translational modification  <cit> , alternative splicing  <cit> , or the cell type in which they are expressed  <cit> .
nevertheless, they do have the ability to function as inhibitors.
it is reasonable to assume that, for c-type molecules, it is generally acceptable to escape from the redox control, as long as they dimerize with an inhibitor, or if the new heterodimer cannot recognise and bind to promoters of downstream targets that need to be controlled by the redox mechanism – thus preventing uncontrolled activation of downstream targets.
dimerization is an important mechanism for generating complex behaviour with a limited number of protein "building blocks".
work on other dimerizing tf families, like the bhlh, has revealed a dimerization network with a hub-based structure  <cit>  that seems to work as a multi-switch  <cit> , especially in development and the cell cycle.
a very different network structure was found for the bzip proteins, despite the fact that they share a similar crystal structure with the bhlh proteins.
interestingly, there seems to be a pattern in the formation of dimers in the bzips .
these results indicate that environmental signals  could have imposed some selective pressure on the dimerizing properties of these proteins.
alternatively, the dimerizing properties of each monomer could have imposed some pressure on the presence of cysteine or serine in position  <dig> of the br.
the redox mechanism has been implicated in the regulation of dna binding in other tf proteins: p <dig>  sp <dig>  nfi, nf-κb, pebp2/cbf, the nuclear receptor proteins  and the bhlh protein, usf .
when cells undergo oxidative stress, the cell cycle is affected and it seems that the redox control of cysteine residues in the dna-binding domain of various tfs is a simple  mechanism of transducing environmental signals to the transcriptional machinery.
in addition, oxidative stress has been implicated in the aetiology of several human diseases, like cancer, ischemia, atherosclerosis, neurodegenerative disorders and ageing .
it will be of great interest to further enhance our understanding of how this mechanism works and affects other dimerizing tf families, like the bhlh and nuclear receptors, determining whether this pattern is global or restricted to the bzips.
CONCLUSIONS
the integration of genomic, phylogenetic and functional data reveals a preference in the interaction partners of bzip proteins that is linked to oxidative stress.
specifically, bzip proteins whose dna binding is controlled by redox tend to dimerize, with a frequency more than that expected by chance, with other bzip proteins that are also controlled by redox.
these results demonstrate that abiotic factors may play a major role in shaping regulatory networks.
while the dimerization networks of bhlh proteins and nuclear receptors are hub-based, that of the bzip proteins is not.
nevertheless we have demonstrated that this network is not random.
it follows a logic which strongly links its structure with the network's functional role in environmental sensing.

 control of gene expression at the transcriptional level is vital and several mechanisms exist that may regulate the dna binding of a transcription factor. these include differential heterodimer formation, methylation of the dna target site, phosphorylation in the tf dna-binding domain, reduction/oxidation of the dbd, the concentration of cations in the nuclear environment. a combination of differential heterodimer formation together with the phosphorylation and the redox mechanisms may yield complex behaviours that determine the expression or inhibition of downstream targets. we are particularly interested in the complex behaviour that these mechanisms create in the bzips, since these tfs are involved in cell proliferation and apoptosis. bzips are eukaryotic tfs, found in fungi, plants and animals. they are named for the highly conserved basic region and leucine zipper domains, found in all these proteins. specifically, the bzip domain is responsible for dimerization mediated by the lz region and dna-binding is mediated by the br, which is n-terminal to the lz. two mechanisms that control dna binding by bzip dimers are phosphorylation and redox. this control is mediated by specific and conserved amino acids in the br of the protein. serine and cysteine residues mediate phosphorylation and redox, respectively, at position of the br domain. we designate these residues as s and c respectively. crystallographic analysis of various bzip proteins, like jun-fos, gcn pap and c/ebpα, has shown that the amino acids at this position make contacts with the dna,. phosphorylation of s in batf and c/ebp proteins has been shown to add a negative charge to the positive br and inhibit binding with the negatively charged dna. phosphorylation of only one of the two s residues in a heterodimer is sufficient to block dna binding, thus having a dominant effect. it has also been postulated that the corresponding tyrosine residue in atf could potentially be phosphorylated. another mechanism of switching on or off dna binding is the reduction/oxidation of the cysteine residue in position of the br of bzips,. oxidation of c blocks dna binding, and this mechanism has been shown to operate for the ap proteins. several mechanisms have been proposed or predicted for the oxidation of c such as reversible formation of sulphenic acid, a disulphide bond, s-glutathiolation, or s-cystenyl cystenylation. furthermore, c can either be protected from oxidation by the mbf co-activator, or it can be switched back from its oxidised to its reduced state by the ref- protein. the importance of these two signalling mechanisms is stressed by the conservation of the cysteine or serine at this position. deppmann et al. report 55% and 35% occurrence of cysteine and serine, respectively, in position in an alignment of human bzips. here, we provide a more detailed phylogenetic analysis using several vertebrate and invertebrate species and highlight the level of conservation of these amino acids, strongly suggesting functional conservation. in addition to conservation at the sequence level, the same cysteine residue and the redox mechanism have been demonstrated experimentally in both human and drosophila ap proteins,,. for the phosphorylation mechanism, the importance of s has been shown experimentally for batf and c/ebp proteins,,. in addition, mutation of the cysteine or serine in position does not affect heterodimerization properties or dna-binding recognition,,. this mutation appears to affect the selection of the signal that turns on or off the dna-binding ability of the dimer. therefore, the conservation of the amino acids in position and the report of functional conservation across different families, strongly indicates that the same mechanism is preserved from drosophila to humans across many divergent evolutionary lineages. in this work, we provide a visualization of the bzip dimerization network and show the level of conservation of c and s residues across different phylogenetic lineages. it has yet to be established experimentally, for all bzip proteins, whether they are under redox or phosphorylation control. however, given that all bzip dna-binding regions around the c and s residues have fundamentally similar properties, and extrapolating from experiments on jun, fos, c/ebp and batf proteins, we predict the bzip proteins in which the redox and phosphorylation mechanisms are utilised. based on these predictions, we propose that the control mechanism is linked to the evolutionary history of the bzip families. interestingly, certain dimerization types are over-represented, while others are under-represented – suggesting strong preference for particular interaction patterns. specifically, c monomers tend to dimerize with other c monomers, probably in order to retain redox control and rarely interact with other monomers. while dimerization with other monomer types can occur, such dimers usually have a repression function, so as to avoid inappropriate gene expression.  the c residue of the br alignment is strikingly conserved in all vertebrates and invertebrates in the atf atf nfe bach, creb, fos, jun, l-maf, s-maf families. s is also strikingly conserved in the atf batf, c/ebp, c/ebp-γ, e4bp oasis, oasis-b and par families. y which could potentially be phosphorylated, is conserved in the atf family. the xbp family is the only family that has a serine residue in the arthropods; this has been mutated to an alanine residue in chordates, suggesting loss of phosphorylation control in the br. interestingly, we see the presence of serine and cysteine residues in fungal bzips as well as the presence of phenylalanine, which is restricted to the fungal lineage. this phenylalanine is necessary for recognition of the yap dna-binding motif by the yap proteins in fungi. nevertheless, the dna-recognition property of this phenylalanine does not necessarily extend to the serine and cysteine residues, since they have no aromatic ring that can get stuck in the dna. the presence of these particular serine and cysteine residues in both metazoan and fungal proteins emphasises the ancient nature of phosphorylation and redox control in bzips. it appears that the highly conserved nature of these amino acids is due to functional reasons and not due to size restrictions at the protein-dna interface. while cysteine, serine and alanine are all very small amino acids, the presence of tyrosine and phenylalanine in the same position shows clearly that residue size is not a major constraint. cysteine and serine are only one point mutation apart in the genetic code and so, if size was the only constraint, we might expect these two amino acids to occur with equal frequency at this site, even within families. thus, the conservation of the same amino acid across all the family members, from vertebrates to invertebrates strongly suggests that biochemical function is involved. phylogenetic analysis of the br indicates that the use of phosphorylation or redox control has emerged several times, as the various bzip families emerged in early metazoan evolution. therefore, it is impossible to determine conclusively whether phosphorylation or redox control is the ancestral state at position the bzip network is visualised in figure the bzip dimerization network does not have the same statistical properties as all the other protein interaction networks studied to date. unlike them, it is not described by a power-law distribution, where the number of genes with k interactions should decay exponentially. we have previously described a network of similar magnitude that followed a power-law distribution and which seems to work as a multi-switch. in the case of the bhlh network, the majority of the proteins need to heterodimerize with one of the ubiquitously expressed hub proteins in order to form functional dimers. in contrast, in the bzip network, a large number of proteins can form homodimers. therefore, if the bzip network is different, what are its purposes and functions? integration of protein interaction data with sequence analysis reveals the different types of dimers and how many of them are formed in humans. dna binding of all dimers that contain at least one s is probably controlled by phosphorylation. the same may also happen for dimers that contain y since this tyrosine can potentially be phosphorylated. all the dimers that contain at least two c residues are probably controlled by the redox mechanism. dimers that contain only one c should be deficient in redox control, according to. the immediate question is whether there is a pattern to the dimerization partners that is related to the phosphorylation and redox mechanisms. to test whether the distribution of different types of dimers is significantly different from random, a chi-squared test was used. according to the null hypothesis, the same number of proteins with the same frequency of serine and cysteine residues could dimerize randomly. note, this statistical analysis must be treated with caution since differential gene expression and protein expression could distort the null hypothesis. by using the frequency of each amino acid in the human bzips for which interaction data are available, we looked for all the types of bzip dimers that could potentially form if all potential pairs were co-expressed. we were particularly interested in the redox control and therefore focused on the presence of c19-bearing dimers. we observed biases, particularly an over-representation of c-c type dimers that also resulted in an under-representation of c-x dimers and vice versa. it is conceivable that this under-representation of c-x dimers is an artefact and this could have arisen in two different ways. firstly, we explored the possibility that c19-bearing proteins tend to homodimerize more than the others. secondly, we explored the possibility that c19-bearing proteins tend to dimerize more with their closest homologues, that is proteins of the same family that also have a cysteine at position in order to exclude biases created by these two options, we also performed the chi-squared test for heterodimers only, and for heterodimers that are not close paralogues. in both cases, the over-representation of c-c and under-representation of c-x dimers is statistically significant. in the above statistical tests, we used all the paralogues of each family. nevertheless, most paralogues have similar dimerization patterns. if position is not actually linked to the dimerization pattern, but is only responsible for family-specific dna core-site recognition, then gene duplication could have caused an artefactual connection. in order to exclude this possibility, all the paralogues of each family were collapsed into one such that the network was then composed of interacting families. we retained the structure of the network among the families, but we shuffled the amino acids of position across the various families times. this model showed clearly that, in less than 2% of the shuffled networks, did we obtain an under-representation of c-x family dimers similar to that observed in the data. furthermore, we performed the same analysis in other positions of the br alignment that are also strongly conserved within each family, but we did not observe any under/over-representation of amino acid combinations at a cut-off level of 5%, in contrast to what we observed for position it should also be stressed that the experimental evidence from shows that mutation of c did not affect dna binding, dna element recognition, or dimerization of the zta bzip protein. interestingly, it is apparent that the c-x heterodimer type is not favoured. this can be explained by the dominant nature of phosphorylation over redox control. the presence of only one s residue would be sufficient to place the dna-binding properties of the dimer under phosphorylation control. the loss or decrease of the redox mechanism in the br is known to increase the transforming activity of the jun-fos heterodimer,. thus, it is presumably important to retain the redox mechanism and avoid heterodimerizing with other types. what is the function of the c-type bzips that actually dimerize with other types, thus forming c-x type dimers and exhibiting insufficient redox control? by examining the activation/inhibition activity of the x-type partners in general, it appears that e4bp, p21-sntf and batf have an inhibitory effect when dimerizing with other factors. in the case of e4bp this is due to the active repression domain that it possesses. the cases of atf c/ebp-β and c/ebp-γ are more complex because they can exhibit activating or inhibiting effects, depending on post-translational modification, alternative splicing, or the cell type in which they are expressed. nevertheless, they do have the ability to function as inhibitors. it is reasonable to assume that, for c-type molecules, it is generally acceptable to escape from the redox control, as long as they dimerize with an inhibitor, or if the new heterodimer cannot recognise and bind to promoters of downstream targets that need to be controlled by the redox mechanism – thus preventing uncontrolled activation of downstream targets. dimerization is an important mechanism for generating complex behaviour with a limited number of protein "building blocks". work on other dimerizing tf families, like the bhlh, has revealed a dimerization network with a hub-based structure that seems to work as a multi-switch, especially in development and the cell cycle. a very different network structure was found for the bzip proteins, despite the fact that they share a similar crystal structure with the bhlh proteins. interestingly, there seems to be a pattern in the formation of dimers in the bzips. these results indicate that environmental signals could have imposed some selective pressure on the dimerizing properties of these proteins. alternatively, the dimerizing properties of each monomer could have imposed some pressure on the presence of cysteine or serine in position of the br. the redox mechanism has been implicated in the regulation of dna binding in other tf proteins: p sp nfi, nf-κb, pebp2/cbf, the nuclear receptor proteins and the bhlh protein, usf. when cells undergo oxidative stress, the cell cycle is affected and it seems that the redox control of cysteine residues in the dna-binding domain of various tfs is a simple mechanism of transducing environmental signals to the transcriptional machinery. in addition, oxidative stress has been implicated in the aetiology of several human diseases, like cancer, ischemia, atherosclerosis, neurodegenerative disorders and ageing. it will be of great interest to further enhance our understanding of how this mechanism works and affects other dimerizing tf families, like the bhlh and nuclear receptors, determining whether this pattern is global or restricted to the bzips.  the integration of genomic, phylogenetic and functional data reveals a preference in the interaction partners of bzip proteins that is linked to oxidative stress. specifically, bzip proteins whose dna binding is controlled by redox tend to dimerize, with a frequency more than that expected by chance, with other bzip proteins that are also controlled by redox. these results demonstrate that abiotic factors may play a major role in shaping regulatory networks. while the dimerization networks of bhlh proteins and nuclear receptors are hub-based, that of the bzip proteins is not. nevertheless we have demonstrated that this network is not random. it follows a logic which strongly links its structure with the network's functional role in environmental sensing. 
this analysis demonstrates the importance of abiotic factors in shaping regulatory networks. by integrating genomic, phylogenetic and functional data from the literature, we then propose a link between oxidative stress and the choice of interaction partners for the bzip proteins. they contain highly conserved basic region and leucine zipper domains and often function as environmental sensors. this integration permits the bzip dimerization network to be interpreted in functional terms, especially in the context of the role of bzip proteins in the response to environmental stress. specifically, bzips frequently have a role in mediating the response to oxidative stress, a crucial environmental signal that needs to be transduced to the gene regulatory network. based on sequence comparisons and experimental data on a number of important bzip transcription factors, we predict which bzips are under redox control and which are regulated via protein phosphorylation.
 bzips are transcription factors that are found throughout the eukarya from fungi to flowering plants and mammals. they contain highly conserved basic region and leucine zipper domains and often function as environmental sensors. specifically, bzips frequently have a role in mediating the response to oxidative stress, a crucial environmental signal that needs to be transduced to the gene regulatory network.  based on sequence comparisons and experimental data on a number of important bzip transcription factors, we predict which bzips are under redox control and which are regulated via protein phosphorylation. by integrating genomic, phylogenetic and functional data from the literature, we then propose a link between oxidative stress and the choice of interaction partners for the bzip proteins.  this integration permits the bzip dimerization network to be interpreted in functional terms, especially in the context of the role of bzip proteins in the response to environmental stress. this analysis demonstrates the importance of abiotic factors in shaping regulatory networks. 