BACKGROUND
the growth rate of cells represents their physiological status, and cellular physiology largely relies on gene expression.
consequently, gene expression is believed to be related to growth rate  <cit> .
in bacterial cells, growth rate-associated gene expression is known to be related to ribosome biosynthesis  <cit>  and the level of rna polymerase  <cit> , and growth rate-related gene expression has been reported in relation to carbon, nitrogen and sulfur utilization  <cit> .
in yeast cells, growth rate-coordinated gene expression has been reported to be affected by the interplay between the stress signal of sapk  and the growth signal of tor   <cit> , which both antagonistically regulate the expression of growth- and stress-related genes  <cit> .
in addition, yeast cell transcriptome analyses identified genes that are correlated with growth rate, with both positive and negative associations  <cit> .
despite intensive study, the conclusions reached thus far have been limited to describing a number of genes with particular functions, and the studies have been restricted to examining experimental conditions under which cells were grown with depleted resources.
nevertheless, a correlation between growth rate and gene expression has been assumed universal across the genome regardless of environmental variations.
that is, the patterns of global transcriptional changes could be independent of the types of environmental stresses.
this assumption was partially supported not only by the observation of negative epistasis in bacterial transcriptome reorganization in response to environmental and genetic perturbations  <cit> , but also the finding of hundreds of overlapped genes with core stress responses in yeast  <cit> .
however, global transcriptional changes have been investigated to establish the rules of stress responses , and the results have provided fruitful insights into the specific patterns of gene expression that occur in response to particular external perturbations  <cit> , but without any linkage to the growth rate.
thus, it remains necessary to determine the general relationships between growth rate and global gene expression .
to correlate the transcriptome with the growth rate, it is crucial to analyze the gene expression in cells that are growing exponentially at a constant growth rate rather than in responsive cells during stress response.
intermediate changes in gene expression in response to stress were accompanied by decreased growth, and this response might differ from the changes in gene expression that correspond to constant growth at a reduced rate .
transcriptional changes in response to pulse-like perturbations, such as heat shock, osmotic shock, and peroxide, did not show any significant correlation to growth rate  <cit> .
the dissimilarity among these studies is believed to be caused by divergent time scales; in particular, differences in the time exposure to changed environments , the speed of gene regulation in response to stressors, and the lag time between changes in transcription and growth .
differences in environmental controls and/or experimental design  could lead to contradictory results.
to investigate the potential relationship between gene expression and growth rate, exponentially growing escherichia coli cells were cultured in multiple types of defined environments and examined.
the regulatory mechanisms corresponding to gene expression and stress conditions are generally highly related, such as the heat shock activated rpoh regulation  <cit> , the general stress response induced rpos <cit> , and the stringent response mediated by ppgpp  <cit> .
because these mechanisms generally involved different genes and varied regulatory network sizes, the following environmental controls were varied osmotic pressure, temperature and starvation.
these environmental conditions contribute to cell growth and proliferation, and accordingly affect global gene expression greatly.
investigating the gene expression pattern responsible for constant growth rate rather than changes in response to stress would further promote strategies for achieving cell sustainability under changing environments.
in brief, our analyses successfully linked the global architectures involved in transcriptional changes and exponential growth rate , and presented an evident correlation between changes in gene expression and positive or negative growth rates.
the results emphasize not only the reorganized gene expression patterns that are responsible for sustainable growth under varied environments but also offer valuable hints to understanding how the cell transcriptome is adjusted in a universal manner when organisms expand their ecological niche.
RESULTS
constant exponential growth under diverse environments
to experimentally link constant growth and gene expression patterns, the growth rates of exponentially growing cells were determined under varied conditions.
because the present study focused on the exponential growth phase , the unpredictable delay and/or time lags related to changes in both gene expression and growth could be neglected .
cell growth took place under defined conditions.
three types of environmental controls were applied, that is, osmotic variety , temperature diversity  and starvation .
cell growth within the exponential phase under precisely controlled culture conditions was repeatedly tested to find quantitative relationships between growth rates and external conditions .
finally, ten conditions comprising three culture conditions for each environmental control and the standard condition  were analyzed.
the cells experienced comparable growth rates under even the most diverse culture conditions, for instance, cell growth in the presence of  <dig>  m nacl  was approximately equivalent to growth at  <dig> °c .
these results clearly reconfirmed that the cells could attain equivalent growth rates in different types of environments.
the precisely evaluated growth rates quantitatively reflected both the physiological activity of the exponentially growing cells and the magnitude of the continued stress from these environments.
gene expression was evaluated using a high density tiling array as previously described  <cit> , and three replicates from each independent culture were performed for each growth condition.
mean values of the three replicates were used for the transcriptome analyses that followed .
the final expression data sets corresponded to  <dig>  genes and were analyzed by removing repeated gene names from all  <dig>  genes that were assigned to the e. coli strain used in the present study.
similarities in transcriptional changes regardless of environmental variation
gene set enrichment analysis   <cit>  was performed to evaluate the significance of transcriptional changes at the gene group level.
two categories of gene groups were employed: the gene category  <cit> , which was clustered according to gene function and the transcriptional network  category  <cit> , which is based on modes of gene regulation.
gene categories showing significant transcriptional changes were identified by comparing gene expression under regular conditions with expression under the other nine conditions.
the statistical significance of transcriptional changes at the gene category level is represented using a heat map .
similar gene expression changes were identified independent of environmental diversity.
for instance, genes in the unknown function, cell process and regulator categories exhibited upregulated expression, whereas genes in the transporter and structural component categories exhibited downregulated expression .
a consistent analytical result was acquired with respect to the tfs, and this result was based on the same comparison.
for example, the transcriptional networks regulated by lexa and rpos appeared to be induced whereas those controlled by fur and glng appeared to be suppressed, regardless of the external conditions .
the two relevant heat maps provide a global view of transcriptional changes taking place in both gene category and gene regulation and capture the overlapped transcriptional changes in common, regardless of the environmental specificity.
this finding was supported by data sets relating to the stress response of e. coli cells under an assortment of environmental perturbations  <cit>  .
genes categorized according to correlated transcriptional change dynamics
a k-means clustering analysis  <cit>  was subsequently performed to categorize genes with similar dynamics in transcriptional changes among all conditions.
all  <dig>  genes were manually divided into three clusters , as other cases of varied k values, i.e., k =  <dig>  provided the equivalent conclusion .
genes classified within the same cluster exhibited similar patterns  in transcriptional changes under the nine culturing conditions.
in sum,  <dig> ,  <dig>  and  <dig>  genes were clustered in c <dig>  c <dig>  and c <dig>  respectively , without considering the environmental specificity or the growth rate.
cluster c <dig> included significant numbers of essential genes .
a three-dimensional space could be formed by considering groups c <dig>  c <dig>  and c <dig> as the x, y, and z axes, respectively .
transcriptional changes in genes from the same cluster under individual culture conditions were averaged to generate a mean value as the representative transcriptional change of the corresponding gene cluster under the defined conditions.
ten positions  with three representative values of c <dig>  c <dig>  and c <dig> were acquired.
the representative transcriptional changes for c <dig>  c <dig>  and c <dig> under the regular condition were all zero  because they provided the base values for the transcriptional change calculations.
the positions of these nine culture conditions appeared to be occupied within a limited space; that is, the range of decrease c <dig>  and increased c <dig>  across all nine environments .
furthermore, these condensed localizations on the c <dig> and c <dig> axes somehow exhibited reversed directions to one another; that is, increase on the c <dig> axis was always correlated with decrease on the c <dig> axis.
this reverse relationship between c <dig> and c <dig> must have triggered restrictive localization in the three-dimensional transcriptional change space.
differentiation in gene function and regulation among the three clusters
significantly  enriched gene functions and regulations in the three clusters were examined.
the biological functions of the genes that were significantly concentrated in clusters c <dig>  c <dig> and c <dig> were identified according to their annotations in go terms  <cit> , gene categories  <cit> , and multifun  <cit> , respectively.
multiple analyses of gene functions showed that the enriched gene functions did not overlap among the three clusters .
c <dig>  c <dig>  and c <dig> were highly enriched in genes related to transport , cell processes, and translation, respectively.
this differentiation in gene function among the three clusters was commonly observed in all three annotation types.
additionally, the genes that were largely concentrated in c <dig> displayed structural component functions ) and were consistent with the essential nature of c <dig> genes .
additionally, no overlap was detected in the enriched regulations  between the three clusters .
both regulators and sigma factors were separately responsible for the three clusters.
for instance, the genes regulated by rpon, rpod, and rpos largely appeared in the c <dig>  c <dig>  and c <dig> clusters, respectively.
this finding indicates that tasks are divided among the regulators that contribute to c <dig>  c <dig>  and c <dig>  the regulator itself was not always clustered in the same cluster as the factors that it regulates .
for example, a considerable number of genes regulated by rcsb were clustered in c <dig>  but rcsb itself was clustered in c <dig>  supporting the negative transcriptional change relationship between c <dig> and c <dig> .
tf name, regulated cluster, and tf cluster represent the names of the regulators for the transcriptional networks , the clusters  of the genes under the control of the corresponding regulators, and the clusters of the assigned regulators.
correlations between growth rates and changes in gene expression
a correlation between gene expression changes and growth rates was evaluated on the basis of three gene clusters.
the representative values for the average transcriptional changes  were normalized as described in the methods section, and the growth rates were determined as shown in figure  <dig>  intriguingly, statistically significant correlations between the growth rate and changes in gene expression were clearly observed , despite the fact that the clustering analysis did not account for growth.
the transcriptional changes in genes from the c <dig> and c <dig> clusters exhibited negative and positive correlations with growth rate, respectively .
these correlations were commonly observed in all three types of environmental controls; that is, growth-related transcriptional changes were universal in the genes assigned to c <dig> and c <dig> and were independent of the types of environmental controls examined.
on the other hand, the genes clustered in c <dig> exhibited distinct correlation directions with growth rates, which were positive in the osmo and strv conditions but negative in the heat conditions .
note that even when the number of genes was reduced from  <dig>  to  <dig>  following the removal of the low expression data sets, the k-means clustering analysis provided the same conclusion .
additionally, the k-means analysis that clustered with a larger number of gene clusters  toward the current data sets exhibited the same correlation trend .
conc.
cor
p
the gene cluster  and the environment  represent the clusters divided as described in figure  <dig> and the three types of environmental controls, respectively.
the statistical significance of the correlations between the growth rates and the changes in gene expression are represented using the statistical significance  and the correlation coefficient  values.
the positive or negative correlations shared by clusters c <dig> and c <dig> indicate that the gene expression changes went in the same direction, independent of environmental diversity; this finding is consistent with the results shown in figure  <dig>  a common gene expression induction and repression occurred in c <dig> and c <dig> and was not biased by the initial expression under regular conditions .
the difference in slopes for both positive and negative correlations within clusters c <dig>  c <dig>  and c <dig> implies an environmental specificity derived from osmotic pressure, temperature, and starvation.
in addition, a principal component analysis  showed that pc <dig> and pc <dig> divided the expression patterns into three directions corresponding to the environmental types , which reflected the c <dig> cluster patterns .
pc <dig> was correlated with growth rate  with a contribution of approximately 5% .
therefore, the pca analysis partially supported the conclusions drawn from the k-means clustering analysis but failed to illustrate a global confirmation of the correlation between growth and expression.
discussion
this study reports that  <dig>  genes in an exponentially growing cell adjusted their expression levels in accordance with the cell division rate, either positively or negatively .
balanced transcriptional changes were observed among the gene clusters .
the direction of transcriptional changes in c <dig> was environment-specific ; that is, the amount of c <dig> expression  was altered depending on the environmental type .
changes in the c <dig>  and c <dig>  expression levels ran counter to one another, regardless of environmental variation.
increased c <dig> expression was accompanied by decreased c <dig> expression and was coordinated with a reduction in growth rate .
the coherent dynamics of the c <dig> gene upregulation and the c <dig> downregulation indicated co-operation between gene clusters.
no specialized mechanisms have been reported in bacterial cells to explain this phenomenon as yet, although the specific pathways initiated by sapk and tor are known in eukaryotic cells  <cit> .
the new finding of a balanced relationship in bacterial gene expression indicates the existence of an energy saving and/or resource conservation strategy in transcriptome reorganization, which may help to maintain the homeostatic framework in cellular physiology, as predicted by in silico biochemical networks  <cit> .
this balanced lifestyle  was largely attributed to differentiation in gene function among the three gene clusters .
the c <dig> genes were largely enriched in membrane proteins and transporters, suggesting that these genes are the first responsive sensors to all types of environments .
the c <dig> genes shared a common decrease with increased growth  and a general stress response function , which plays a central role in cellular processes.
the difference in negative correlation slopes may indicate a diversity of molecular mechanisms under the three environmental types; osmotic pressure might be regulated by two-component systems  <cit> , growth at high temperatures might induce heat shock proteins  <cit> , and growth under starved conditions might activate the stringent response  <cit> .
the genes clustered in c <dig> were positive correlated with growth rate  and were largely related to ribosome translation machineries .
a correlation between the growth rate and the quantity of ribosomes was previously reported in cells growing under starvation conditions  <cit> .
a global view of the coordination of growth rate with transcriptional changes as presented here illustrates a vivid picture of the differentiated gene expression balance in sustaining life under diverse habitats.
here, we focused on constant growth states  rather than the stress response phase .
despite the divergence in time scales between the two phases, both types of transcriptome reorganization presented relationships between transcriptional fluctuations and the degree or magnitude of stress.
some common results were found, such as similar changes in transcriptional networks .
a few highly sensitive tfs were found, including purr and rcsb .
because these tfs were also found to be sensitive to genome reduction  <cit> , it appeared that these tfs responded to all types of perturbations, both internal and external, and were highly sensitive to phases of stress response and exponential growth.
however, the direction of transcriptional changes in the three gene clusters exhibited weak similarity in terms of stress response and exponential growth.
using the reported data sets on the stress response  <cit> , we found that only c <dig> genes experienced a common decrease in expression under all four stress conditions ; this finding is consistent with the positive correlation of c <dig> with growth rates .
furthermore, applying the same k-means clustering did not yield a clear correlation between growth rates and changes in gene expression during periods of stress response , which is consistent with findings in yeast  <cit> .
taken together, survival strategies in bacteria faced with pulse-like perturbations and continuous growth in new environments were partially shared, but the coordination with growth rate was apparent only in exponentially growing cells and was not present in responsive cells during stress response.
CONCLUSIONS
here, we provided the first experimental evidence for coordination between constant growth rates and changes in gene expression, which is a general phenomenon that applies to many environments.
growth rate-associated gene function differentiation and gene regulation task division were defined.
this experiment was successful in categorizing  <dig>  genes across the genome into three clusters and in matching the changes in gene expression patterns with the growth rate.
this success resulted from using an experimental design that primarily targeted the exponential phase and from the use of a clean genome without any insertion sequences  <cit>  that could have masked transcriptional change patterns.

 the growth rate of cells represents their physiological status, and cellular physiology largely relies on gene expression. consequently, gene expression is believed to be related to growth rate. in bacterial cells, growth rate-associated gene expression is known to be related to ribosome biosynthesis and the level of rna polymerase, and growth rate-related gene expression has been reported in relation to carbon, nitrogen and sulfur utilization. in yeast cells, growth rate-coordinated gene expression has been reported to be affected by the interplay between the stress signal of sapk and the growth signal of tor, which both antagonistically regulate the expression of growth- and stress-related genes. in addition, yeast cell transcriptome analyses identified genes that are correlated with growth rate, with both positive and negative associations. despite intensive study, the conclusions reached thus far have been limited to describing a number of genes with particular functions, and the studies have been restricted to examining experimental conditions under which cells were grown with depleted resources. nevertheless, a correlation between growth rate and gene expression has been assumed universal across the genome regardless of environmental variations. that is, the patterns of global transcriptional changes could be independent of the types of environmental stresses. this assumption was partially supported not only by the observation of negative epistasis in bacterial transcriptome reorganization in response to environmental and genetic perturbations, but also the finding of hundreds of overlapped genes with core stress responses in yeast. however, global transcriptional changes have been investigated to establish the rules of stress responses, and the results have provided fruitful insights into the specific patterns of gene expression that occur in response to particular external perturbations, but without any linkage to the growth rate. thus, it remains necessary to determine the general relationships between growth rate and global gene expression. to correlate the transcriptome with the growth rate, it is crucial to analyze the gene expression in cells that are growing exponentially at a constant growth rate rather than in responsive cells during stress response. intermediate changes in gene expression in response to stress were accompanied by decreased growth, and this response might differ from the changes in gene expression that correspond to constant growth at a reduced rate. transcriptional changes in response to pulse-like perturbations, such as heat shock, osmotic shock, and peroxide, did not show any significant correlation to growth rate. the dissimilarity among these studies is believed to be caused by divergent time scales; in particular, differences in the time exposure to changed environments, the speed of gene regulation in response to stressors, and the lag time between changes in transcription and growth. differences in environmental controls and/or experimental design could lead to contradictory results. to investigate the potential relationship between gene expression and growth rate, exponentially growing escherichia coli cells were cultured in multiple types of defined environments and examined. the regulatory mechanisms corresponding to gene expression and stress conditions are generally highly related, such as the heat shock activated rpoh regulation, the general stress response induced rpos, and the stringent response mediated by ppgpp. because these mechanisms generally involved different genes and varied regulatory network sizes, the following environmental controls were varied osmotic pressure, temperature and starvation. these environmental conditions contribute to cell growth and proliferation, and accordingly affect global gene expression greatly. investigating the gene expression pattern responsible for constant growth rate rather than changes in response to stress would further promote strategies for achieving cell sustainability under changing environments. in brief, our analyses successfully linked the global architectures involved in transcriptional changes and exponential growth rate, and presented an evident correlation between changes in gene expression and positive or negative growth rates. the results emphasize not only the reorganized gene expression patterns that are responsible for sustainable growth under varied environments but also offer valuable hints to understanding how the cell transcriptome is adjusted in a universal manner when organisms expand their ecological niche.  constant exponential growth under diverse environments to experimentally link constant growth and gene expression patterns, the growth rates of exponentially growing cells were determined under varied conditions. because the present study focused on the exponential growth phase, the unpredictable delay and/or time lags related to changes in both gene expression and growth could be neglected. cell growth took place under defined conditions. three types of environmental controls were applied, that is, osmotic variety, temperature diversity and starvation. cell growth within the exponential phase under precisely controlled culture conditions was repeatedly tested to find quantitative relationships between growth rates and external conditions. finally, ten conditions comprising three culture conditions for each environmental control and the standard condition were analyzed. the cells experienced comparable growth rates under even the most diverse culture conditions, for instance, cell growth in the presence of  m nacl was approximately equivalent to growth at °c. these results clearly reconfirmed that the cells could attain equivalent growth rates in different types of environments. the precisely evaluated growth rates quantitatively reflected both the physiological activity of the exponentially growing cells and the magnitude of the continued stress from these environments. gene expression was evaluated using a high density tiling array as previously described, and three replicates from each independent culture were performed for each growth condition. mean values of the three replicates were used for the transcriptome analyses that followed. the final expression data sets corresponded to genes and were analyzed by removing repeated gene names from all genes that were assigned to the e. coli strain used in the present study. similarities in transcriptional changes regardless of environmental variation gene set enrichment analysis was performed to evaluate the significance of transcriptional changes at the gene group level. two categories of gene groups were employed: the gene category, which was clustered according to gene function and the transcriptional network category, which is based on modes of gene regulation. gene categories showing significant transcriptional changes were identified by comparing gene expression under regular conditions with expression under the other nine conditions. the statistical significance of transcriptional changes at the gene category level is represented using a heat map. similar gene expression changes were identified independent of environmental diversity. for instance, genes in the unknown function, cell process and regulator categories exhibited upregulated expression, whereas genes in the transporter and structural component categories exhibited downregulated expression. a consistent analytical result was acquired with respect to the tfs, and this result was based on the same comparison. for example, the transcriptional networks regulated by lexa and rpos appeared to be induced whereas those controlled by fur and glng appeared to be suppressed, regardless of the external conditions. the two relevant heat maps provide a global view of transcriptional changes taking place in both gene category and gene regulation and capture the overlapped transcriptional changes in common, regardless of the environmental specificity. this finding was supported by data sets relating to the stress response of e. coli cells under an assortment of environmental perturbations. genes categorized according to correlated transcriptional change dynamics a k-means clustering analysis was subsequently performed to categorize genes with similar dynamics in transcriptional changes among all conditions. all genes were manually divided into three clusters, as other cases of varied k values, i.e., k =  provided the equivalent conclusion. genes classified within the same cluster exhibited similar patterns in transcriptional changes under the nine culturing conditions. in sum,, and genes were clustered in c c and c respectively, without considering the environmental specificity or the growth rate. cluster c included significant numbers of essential genes. a three-dimensional space could be formed by considering groups c c and c as the x, y, and z axes, respectively. transcriptional changes in genes from the same cluster under individual culture conditions were averaged to generate a mean value as the representative transcriptional change of the corresponding gene cluster under the defined conditions. ten positions with three representative values of c c and c were acquired. the representative transcriptional changes for c c and c under the regular condition were all zero because they provided the base values for the transcriptional change calculations. the positions of these nine culture conditions appeared to be occupied within a limited space; that is, the range of decrease c and increased c across all nine environments. furthermore, these condensed localizations on the c and c axes somehow exhibited reversed directions to one another; that is, increase on the c axis was always correlated with decrease on the c axis. this reverse relationship between c and c must have triggered restrictive localization in the three-dimensional transcriptional change space. differentiation in gene function and regulation among the three clusters significantly enriched gene functions and regulations in the three clusters were examined. the biological functions of the genes that were significantly concentrated in clusters c c and c were identified according to their annotations in go terms, gene categories, and multifun, respectively. multiple analyses of gene functions showed that the enriched gene functions did not overlap among the three clusters. c c and c were highly enriched in genes related to transport, cell processes, and translation, respectively. this differentiation in gene function among the three clusters was commonly observed in all three annotation types. additionally, the genes that were largely concentrated in c displayed structural component functions ) and were consistent with the essential nature of c genes. additionally, no overlap was detected in the enriched regulations between the three clusters. both regulators and sigma factors were separately responsible for the three clusters. for instance, the genes regulated by rpon, rpod, and rpos largely appeared in the c c and c clusters, respectively. this finding indicates that tasks are divided among the regulators that contribute to c c and c the regulator itself was not always clustered in the same cluster as the factors that it regulates. for example, a considerable number of genes regulated by rcsb were clustered in c but rcsb itself was clustered in c supporting the negative transcriptional change relationship between c and c. tf name, regulated cluster, and tf cluster represent the names of the regulators for the transcriptional networks, the clusters of the genes under the control of the corresponding regulators, and the clusters of the assigned regulators. correlations between growth rates and changes in gene expression a correlation between gene expression changes and growth rates was evaluated on the basis of three gene clusters. the representative values for the average transcriptional changes were normalized as described in the methods section, and the growth rates were determined as shown in figure  intriguingly, statistically significant correlations between the growth rate and changes in gene expression were clearly observed, despite the fact that the clustering analysis did not account for growth. the transcriptional changes in genes from the c and c clusters exhibited negative and positive correlations with growth rate, respectively. these correlations were commonly observed in all three types of environmental controls; that is, growth-related transcriptional changes were universal in the genes assigned to c and c and were independent of the types of environmental controls examined. on the other hand, the genes clustered in c exhibited distinct correlation directions with growth rates, which were positive in the osmo and strv conditions but negative in the heat conditions. note that even when the number of genes was reduced from to following the removal of the low expression data sets, the k-means clustering analysis provided the same conclusion. additionally, the k-means analysis that clustered with a larger number of gene clusters toward the current data sets exhibited the same correlation trend. conc. cor p the gene cluster and the environment represent the clusters divided as described in figure  and the three types of environmental controls, respectively. the statistical significance of the correlations between the growth rates and the changes in gene expression are represented using the statistical significance and the correlation coefficient values. the positive or negative correlations shared by clusters c and c indicate that the gene expression changes went in the same direction, independent of environmental diversity; this finding is consistent with the results shown in figure  a common gene expression induction and repression occurred in c and c and was not biased by the initial expression under regular conditions. the difference in slopes for both positive and negative correlations within clusters c c and c implies an environmental specificity derived from osmotic pressure, temperature, and starvation. in addition, a principal component analysis showed that pc and pc divided the expression patterns into three directions corresponding to the environmental types, which reflected the c cluster patterns. pc was correlated with growth rate with a contribution of approximately 5%. therefore, the pca analysis partially supported the conclusions drawn from the k-means clustering analysis but failed to illustrate a global confirmation of the correlation between growth and expression. discussion this study reports that genes in an exponentially growing cell adjusted their expression levels in accordance with the cell division rate, either positively or negatively. balanced transcriptional changes were observed among the gene clusters. the direction of transcriptional changes in c was environment-specific; that is, the amount of c expression was altered depending on the environmental type. changes in the c and c expression levels ran counter to one another, regardless of environmental variation. increased c expression was accompanied by decreased c expression and was coordinated with a reduction in growth rate. the coherent dynamics of the c gene upregulation and the c downregulation indicated co-operation between gene clusters. no specialized mechanisms have been reported in bacterial cells to explain this phenomenon as yet, although the specific pathways initiated by sapk and tor are known in eukaryotic cells. the new finding of a balanced relationship in bacterial gene expression indicates the existence of an energy saving and/or resource conservation strategy in transcriptome reorganization, which may help to maintain the homeostatic framework in cellular physiology, as predicted by in silico biochemical networks. this balanced lifestyle was largely attributed to differentiation in gene function among the three gene clusters. the c genes were largely enriched in membrane proteins and transporters, suggesting that these genes are the first responsive sensors to all types of environments. the c genes shared a common decrease with increased growth and a general stress response function, which plays a central role in cellular processes. the difference in negative correlation slopes may indicate a diversity of molecular mechanisms under the three environmental types; osmotic pressure might be regulated by two-component systems, growth at high temperatures might induce heat shock proteins, and growth under starved conditions might activate the stringent response. the genes clustered in c were positive correlated with growth rate and were largely related to ribosome translation machineries. a correlation between the growth rate and the quantity of ribosomes was previously reported in cells growing under starvation conditions. a global view of the coordination of growth rate with transcriptional changes as presented here illustrates a vivid picture of the differentiated gene expression balance in sustaining life under diverse habitats. here, we focused on constant growth states rather than the stress response phase. despite the divergence in time scales between the two phases, both types of transcriptome reorganization presented relationships between transcriptional fluctuations and the degree or magnitude of stress. some common results were found, such as similar changes in transcriptional networks. a few highly sensitive tfs were found, including purr and rcsb. because these tfs were also found to be sensitive to genome reduction, it appeared that these tfs responded to all types of perturbations, both internal and external, and were highly sensitive to phases of stress response and exponential growth. however, the direction of transcriptional changes in the three gene clusters exhibited weak similarity in terms of stress response and exponential growth. using the reported data sets on the stress response, we found that only c genes experienced a common decrease in expression under all four stress conditions; this finding is consistent with the positive correlation of c with growth rates. furthermore, applying the same k-means clustering did not yield a clear correlation between growth rates and changes in gene expression during periods of stress response, which is consistent with findings in yeast. taken together, survival strategies in bacteria faced with pulse-like perturbations and continuous growth in new environments were partially shared, but the coordination with growth rate was apparent only in exponentially growing cells and was not present in responsive cells during stress response.  here, we provided the first experimental evidence for coordination between constant growth rates and changes in gene expression, which is a general phenomenon that applies to many environments. growth rate-associated gene function differentiation and gene regulation task division were defined. this experiment was successful in categorizing genes across the genome into three clusters and in matching the changes in gene expression patterns with the growth rate. this success resulted from using an experimental design that primarily targeted the exponential phase and from the use of a clean genome without any insertion sequences that could have masked transcriptional change patterns. 
the direction of transcriptional change in c indicated environmental specificity, whereas those in c and c were correlated negatively and positively with growth rates, respectively. we identified three gene clusters, exhibiting differential gene functions and distinct directions in their correlations with growth rates. growth rate-coordinated changes in gene expression were discovered by analyzing exponentially growing escherichia coli cells cultured under multiple defined environments, in which osmotic pressure, temperature and starvation status were varied. the three clusters exhibited differentiated gene functions and gene regulation task division. gene expression analyses showed that all genes in the genome could be simply divided into three clusters, which were accompanied by a generic trend in the growth rate that was coordinated with transcriptional changes. reverses in the direction of the growth rate correlated transcriptional changes and the distinguished duties of the three clusters indicated how transcriptome homeostasis is maintained to balance the total expression cost for sustaining life in new habitats. cell growth rate reflects an organism’s physiological state and largely relies on the ability of gene expression to respond to the environment. the relationship between cellular growth rate and gene expression remains unknown.
 cell growth rate reflects an organism’s physiological state and largely relies on the ability of gene expression to respond to the environment. the relationship between cellular growth rate and gene expression remains unknown.  growth rate-coordinated changes in gene expression were discovered by analyzing exponentially growing escherichia coli cells cultured under multiple defined environments, in which osmotic pressure, temperature and starvation status were varied. gene expression analyses showed that all genes in the genome could be simply divided into three clusters, which were accompanied by a generic trend in the growth rate that was coordinated with transcriptional changes. the direction of transcriptional change in c indicated environmental specificity, whereas those in c and c were correlated negatively and positively with growth rates, respectively. the three clusters exhibited differentiated gene functions and gene regulation task division.  we identified three gene clusters, exhibiting differential gene functions and distinct directions in their correlations with growth rates. reverses in the direction of the growth rate correlated transcriptional changes and the distinguished duties of the three clusters indicated how transcriptome homeostasis is maintained to balance the total expression cost for sustaining life in new habitats. 