BACKGROUND
the availability of complete genome sequences opened up a new era in biology, providing a global and systems view of the range of genome sizes in different organisms, the presence or absence of genes involved in various cellular functions, the genes involved in particular cellular functions, and the relative abundance of different gene families.
this new global view is creating major new areas of research such as functional genomics  <cit> .
at the time of this writing, over  <dig> prokaryotic genomes and over  <dig> complete eukaryotic genomes have been sequenced  <cit> .
just as the field of sequence genomics has yielded complete genome sequences for a variety of organisms, the field of structural genomics aims to provide structures for the complete array of biological macromolecules found in nature,  <cit> .
the first phase of structural genomics focused only on proteins , and has proven to be an efficient means of providing structural information for new protein families  <cit> .
after the first sequencing of a complete genome of haemophilus influenzae  <cit> , some of the earliest subsequent genomes sequenced were from the "minimal organisms" mycoplasma genitalium and m. pneumoniae  <cit> .
minimal organisms have been the subject of numerous experimental and computational genomic studies because of the possibility of identifying the minimal complement of genes necessary for sustaining life  <cit> .
because of their small size, organisms with minimal genomes have also been popular for structure and function prediction  <cit> .
the minimal organisms m. genitalium  and m. pneumoniae  have also been the focus of structural genomics research at the berkeley structural genomics center  <cit> .
other minimal organisms that have been sequenced more recently include the aphid symbiont buchnera aphidicola   <cit> , the ant symbiont candidatus blochmannia floridanus   <cit> , the tsetse fly symbiont wigglesworthia glossinidia brevipalpis   <cit> , and the whipple's disease parasite tropheryma whipplei   <cit> .
comparative analysis of the first three symbiont genomes and m. genitalium has demonstrated that the symbionts are closely related, sharing  <dig> orthologous genes , and that they share  <dig> genes with m. genitalium  <cit> .
however, a broader comparison of all five species, including t. whipplei, indicated significant variability in the functional repertoire of proteins in these organisms, suggesting that minimal genomes are not the result of a unique reductive evolutionary pathway, but the products of reductive evolution in specific environments  <cit> .
a recent survey of proteins from  <dig> complete genomes revealed that fold assignments  can be made for the majority of non-membrane proteins of minimal organisms  <cit> .
statistically significant sequence similarity to a protein of known structure allows homology  to be inferred, thus enabling the fold of the homologous proteins to be assigned even in cases where the degree of sequence similarity is insufficiently high to allow accurate modeling  <cit> .
fold assignment of a protein has implications for functional annotation, because the link between molecular function and structure is well known.
todd and colleagues showed that while the majority of superfamilies display variation in enzyme function , the biochemical mechanisms  are almost always conserved between proteins with 40% sequence identity or above  <cit> .
more recent work has shown that conserved domain combinations, or supradomains, are more likely to maintain a conserved molecular function even at lower sequence identity  <cit> .
a study in two proteomes  found clear tendencies for fold-function association across a broad range of molecular functions  <cit> .
the latter study also found the fold distributions in the two proteomes surveyed did not vary significantly from the average across all sequenced proteomes, although the study was based on fold assignments for less than 10% of the total number of proteins.
we now report that recent efforts in structural biology and structural genomics have succeeded in enabling fold assignments for over ~90% of soluble, globular proteins in the five minimal organisms described above.
in this report, we survey the classes of protein folds found in each organism, and examine the conservation in fold usage of proteins in several broad categories of cellular function.
we find that the degree of conservation of fold usage varies among cellular functional categories, with the most conserved categories of proteins performing essential cellular functions closely related to transcription and translation.
finally, we compare the degree of conservation in cellular functions and fold usage among the five minimal organisms and e. coli, a non-minimal organism.
RESULTS
near-complete coverage of soluble, globular proteomes of "minimal" organisms
in table  <dig>  we show the percentage of proteomes that may be assigned folds for five minimal organisms and for e. coli, an example of a well-studied organism that is not "minimal."
for the minimal organisms considered in this study, nearly all proteins annotated as soluble and globular may be assigned to a known fold.
the aphid symbiont b. floridanus has the highest coverage, at 96% of soluble, globular proteins .
<dig> of the remaining proteins in the proteome  have unknown structure, but are predicted to have at least one transmembrane helix.
<dig> additional proteins have unknown structure and no predicted transmembrane helices, but 20% or more of their residues are in predicted low complexity or coiled coil regions, and thus not easily tractable in experimental structural studies.
overall, the folds of  <dig> of  <dig> b. floridanus proteins  may be annotated by sequence similarity to a protein of known structure.
other minimal organisms also have high structural coverage: 95% of soluble, globular w. glossinidia proteins, 94% of soluble, globular b. aphidicola proteins, 87% of soluble, globular m. genitalium proteins, and 87% of soluble, globular t. whipplei proteins can reliably be assigned folds.
in contrast, only 78% of soluble, globular e. coli proteins can reliably be assigned folds.
the low numbers of predicted transmembrane proteins in several of the minimal organisms  is also notable; previous analyses suggest that some transmembrane proteins  are less important to intracellular symbiotes than to free-living bacteria  <cit> .
α/β fold class is the most common category of fold
for the proteins that could be reliably assigned folds, we examined their structural classification in the scop database  <cit> .
scop is a widely used, manually curated database in which protein structures are divided into domains, which are classified in a hierarchy indicating different types of structural and evolutionary relationships between the domains.
domains classified together in a single "family" or "superfamily" are hypothesized to have a common evolutionary origin on the basis of sequence or structural evidence.
superfamilies that share similar secondary structural features and topology, but for which there is little or no evidence to suggest a common evolutionary origin, are classified together at the "fold" level.
scop folds are grouped together in seven major "classes" , based on common physical characteristics such as the predominant type of secondary structure or the order of connection of the different secondary structures .
note that the scop "multi-domain" class encompasses folds that are comprised of multiple domains that individually would belong to different classes; individual domains from multi-domain proteins are not classified in the "multi-domain" class.
although we use the term "fold" to refer to a protein's overall 3d backbone structure, we use the term "scop fold" to refer to a specific fold classification within the scop database.
the fraction of proteins found in each organism belonging to each of these scop classes is shown in figure  <dig>  those proteins that could not reliably be assigned folds, and those that were assigned a fold based on homology to a protein not yet classified in scop, are described as "unsolved" and "unclassified," respectively.
for all organisms, the highest proportion of scop folds are in the α/β class, and those in the α/β and α+β classes together comprise over half of the assigned scop folds.
this reflects the observation that the α/β class contains some of the most functionally diverse "superfolds" that act as scaffolds for a wide array of molecular or chemical functions  <cit> .
usage of protein fold classes are conserved for key cellular processes
in order to analyze how the annotated cellular function of each protein correlates with its structure, we examined the "functional role" annotation for each protein as provided in the tigr database  <cit> .
we found that the distribution of proteins among scop fold classes was highly conserved within some roles and showed much more variability in others.
in contrast, figure  <dig> shows the fold class distribution of proteins in the "cell envelope" functional category across all  <dig> proteomes.
this functional category is also highly represented in each proteome , but the proteins show a much higher degree of variation in fold usage.
this category contains the highest proportion of unassigned folds, as well as a diverse array of assigned scop folds: for example, 6% and 4% of domains from w. glossinidia and e. coli cell envelope proteins belong to the all-α structural class, while cell envelope proteins from the other proteomes contain few or no all-α structures.
e. coli also contains a number of solved transmembrane structures, while other proteomes contain significant numbers of proteins predicted to be transmembrane proteins not detectably homologous to any protein with a known 3d structure.
m. genitalium and t. whipplei contain the largest fractions of cell envelope proteins that could not be reliably assigned a fold at this time, although most of these m. genitalium proteins are expected to be soluble and globular, while the majority of such proteins from t. whipplei are predicted to contain at least one transmembrane helix.
the high amount of variability suggests that proteins in the "cell envelope" category evolve rapidly in response to specific pressures in an organism's environment, and different sets of these proteins remain after reductive evolution in the different environments occupied by the different species of minimal organisms.
cellular functions with most conserved scop fold usage
previous comparative sequence genomic analyses of symbionts have shown that the number of proteins in most cellular function categories varies little between symbiont proteomes, and that many of the most highly conserved proteins have cellular functions related to information storage and processing, particularly translation and ribosomal structure  <cit> .
we calculated the coefficient of variation  in the number of proteins in each functional role category , as shown in equation  <dig>
cvsequence=stdevmean
mathtype@mtef@5@5@+=feaafiart1ev1aaatcvaufkttlearuwrp9mdh5mbpbiqv92aaexatlxbi9gbaebbnrfifhhdyfgasaach8aky=wiffydh8gipec8eeeu0xxdbba9frfj0=oqffea0dxdd9vqai=hguq8kuc9pgc9s8qqaq=dirpe0xb9q8qilsfr0=vr0=vr0dc8meaabaqaciaacagaaeqabaqabegadaaakeaacqwgdbwqcqwgwbgvdawgaawcbagaem4camnaemyzaumaemycaenaemydaunaemyzaumaemoba4maem4yammaemyzaugabeaakiabg2da9maalaaabagaem4uamlaemidaqnaemizaqmaemyzaumaemodaynaeiikagiaemota40aasbaasqaaiabigdaxaqabagccqwimayscqwgobgtdawgaawcbagaegonaydabeaakiabcmcapaqaaiabd2eanjabdwgaljabdggahjabd6gaujabcicaoiabd6eaonaabaaaleaacqaixaqmaeqaaogaesojgskaemota40aasbaasqaaiabiada2aqabagccqggpaqkaagaaczcaiaaxmaadaqadaqaaiabigdaxagaayjkaiaawmcaaaaa@59ba@
results are shown in table  <dig>  as expected, the category with the lowest variation in the number of proteins is "protein synthesis," and the top three categories are all closely related to transcription or translation.
we also calculated the coefficient of variation in the number of protein domains assigned to each scop class , then averaged that data across all  <dig> structural classes, as shown in equation  <dig>
cvstructure=∑class=17stdevmean7
mathtype@mtef@5@5@+=feaafiart1ev1aaatcvaufkttlearuwrp9mdh5mbpbiqv92aaexatlxbi9gbaebbnrfifhhdyfgasaach8aky=wiffydh8gipec8eeeu0xxdbba9frfj0=oqffea0dxdd9vqai=hguq8kuc9pgc9s8qqaq=dirpe0xb9q8qilsfr0=vr0=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@877c@
cvstructure was calculated separately for each functional role category, and these data are shown in table  <dig> and figure 5a.
the functional category with the lowest variation in the number of domains in each structural class is "protein synthesis," as would be expected from figure  <dig>  however, there are some interesting differences between the rankings based only on the cvsequence, and the rankings based on cvstructure.
for example, fold usage of proteins involved in biosynthesis of cofactors, carriers, and prosthetic groups varies to a higher degree than the variation in total numbers of these proteins in each proteome.
this implies that the repertoire of specific functions in this broad category is specialized to the particular needs of each organism, even though the overall number of such proteins varies little.
as expected, the distribution of structures in "catch-all" classes such as hypothetical and unclassified proteins are more varied than the distribution of structures found in more well-defined functional categories.
we also analyzed the degree of variation using data from only the five near-complete minimal organisms, excluding data from e. coli.
results are shown in table  <dig> and figure 5b.
as before, fold usage of proteins in the "protein synthesis" category shows the least variance of all functional categories.
the total genome size also slows relatively little variation among minimal organisms, as has been observed previously  <cit> .
however, some functional categories show relatively more variation between minimal organisms than between minimal organisms and e. coli.
for example, the cellular function categories "cell envelope," "central intermediary metabolism," and "amino acid biosynthesis" all drop in rank  by  <dig> positions relative to table  <dig>  indicating higher diversity of folds in these functional categories among minimal organisms.
in contrast, fold usage of proteins in the "regulatory functions" category shows relatively less variation among minimal organisms than between minimal organisms and e. coli.
this suggests that although the minimal organisms have lost many of the regulatory pathways unnecessary for survival in their relatively unchanging environments, they maintain a relatively conserved set of proteins responsible for common regulatory functions.
a more thorough phylogenetic analysis of these proteins would be necessary to test this hypothesis.
common and overrepresented folds in minimal organisms
we examined the most common protein folds  in minimal organisms.
results are shown in table  <dig>  four of the eleven most common scop folds  are among the nine superfolds originally described by orengo and colleagues as scaffolds that can support a wide array of molecular functions  <cit> .
however, all have fewer copies in minimal organisms than are found in e. coli.
interestingly, all  <dig> scop folds present in equal or greater numbers in all minimal organisms as in e. coli are also folds for which only a single superfamily is characterized in scop; i.e., all proteins sharing the fold are also annotated as evolutionarily related to each other.
the case of multiple superfamilies sharing one fold may arise from two alternative causes: convergent evolution of two or more families to one fold, or a single family that has diverged enough that homology between different branches of the family are no longer evident even from structure .
these data imply that proteins that play sufficiently important roles to avoid elimination during reductive evolution have also not diverged as much as other protein families due to this same evolutionary pressure.
an additional set of scop folds found only in minimal organisms and not in e. coli is given in table  <dig>  none of these folds are found in all five minimal organisms, and the proteins are not generally related to essential cellular functions such as transcription, translation, or replication.
some are presumably adaptations to the specific environment of the organism, and several  are not typically found in bacteria.
these may represent lateral gene transfers or erroneous annotations.
CONCLUSIONS
after five years of progress in structural genomics, near-complete structural complements of the soluble proteins of several "minimal organisms" are now known.
a complete set of fold assignments for nearly all soluble, globular proteins in a proteome is providing a global view of how minimal organisms are using various protein fold classes for different cellular functions and how the fold usage in each class is conserved.
data from near-complete structural proteomes can yield hypotheses on protein evolution at a global level.
simple statistical analyses of the variation in numbers of structures in each structural and functional category can shed light on which functional categories are more or less conserved in minimal organisms.
for example, the functional categories that showed the least variability in both sequence- and structure-based analyses were involved in essential cellular functions such as transcription and translation.
furthermore, every scop fold identified in equal or greater numbers in minimal organisms as in e. coli was the product of a single protein family, indicating that the proteins retained during reductive evolution of minimal organisms also tend to be from slow-evolving families.
the latter observation was expected, as essential genes in other species have previously been shown to evolve more slowly than non-essential genes  <cit> .
such observations may be followed up with more detailed studies based on phylogenetic modeling of protein families  <cit>  or the construction of atomic models of proteins in those categories.
detailed atomic modeling of all proteins in a biochemical pathway will be useful to study the plasticity of these pathways in response to evolutionary pressures imposed by different organisms' environments  <cit> .

 the availability of complete genome sequences opened up a new era in biology, providing a global and systems view of the range of genome sizes in different organisms, the presence or absence of genes involved in various cellular functions, the genes involved in particular cellular functions, and the relative abundance of different gene families. this new global view is creating major new areas of research such as functional genomics. at the time of this writing, over prokaryotic genomes and over complete eukaryotic genomes have been sequenced. just as the field of sequence genomics has yielded complete genome sequences for a variety of organisms, the field of structural genomics aims to provide structures for the complete array of biological macromolecules found in nature,. the first phase of structural genomics focused only on proteins, and has proven to be an efficient means of providing structural information for new protein families. after the first sequencing of a complete genome of haemophilus influenzae, some of the earliest subsequent genomes sequenced were from the "minimal organisms" mycoplasma genitalium and m. pneumoniae. minimal organisms have been the subject of numerous experimental and computational genomic studies because of the possibility of identifying the minimal complement of genes necessary for sustaining life. because of their small size, organisms with minimal genomes have also been popular for structure and function prediction. the minimal organisms m. genitalium and m. pneumoniae have also been the focus of structural genomics research at the berkeley structural genomics center. other minimal organisms that have been sequenced more recently include the aphid symbiont buchnera aphidicola, the ant symbiont candidatus blochmannia floridanus, the tsetse fly symbiont wigglesworthia glossinidia brevipalpis, and the whipple's disease parasite tropheryma whipplei. comparative analysis of the first three symbiont genomes and m. genitalium has demonstrated that the symbionts are closely related, sharing orthologous genes, and that they share genes with m. genitalium. however, a broader comparison of all five species, including t. whipplei, indicated significant variability in the functional repertoire of proteins in these organisms, suggesting that minimal genomes are not the result of a unique reductive evolutionary pathway, but the products of reductive evolution in specific environments. a recent survey of proteins from complete genomes revealed that fold assignments can be made for the majority of non-membrane proteins of minimal organisms. statistically significant sequence similarity to a protein of known structure allows homology to be inferred, thus enabling the fold of the homologous proteins to be assigned even in cases where the degree of sequence similarity is insufficiently high to allow accurate modeling. fold assignment of a protein has implications for functional annotation, because the link between molecular function and structure is well known. todd and colleagues showed that while the majority of superfamilies display variation in enzyme function, the biochemical mechanisms are almost always conserved between proteins with 40% sequence identity or above. more recent work has shown that conserved domain combinations, or supradomains, are more likely to maintain a conserved molecular function even at lower sequence identity. a study in two proteomes found clear tendencies for fold-function association across a broad range of molecular functions. the latter study also found the fold distributions in the two proteomes surveyed did not vary significantly from the average across all sequenced proteomes, although the study was based on fold assignments for less than 10% of the total number of proteins. we now report that recent efforts in structural biology and structural genomics have succeeded in enabling fold assignments for over ~90% of soluble, globular proteins in the five minimal organisms described above. in this report, we survey the classes of protein folds found in each organism, and examine the conservation in fold usage of proteins in several broad categories of cellular function. we find that the degree of conservation of fold usage varies among cellular functional categories, with the most conserved categories of proteins performing essential cellular functions closely related to transcription and translation. finally, we compare the degree of conservation in cellular functions and fold usage among the five minimal organisms and e. coli, a non-minimal organism.  near-complete coverage of soluble, globular proteomes of "minimal" organisms in table we show the percentage of proteomes that may be assigned folds for five minimal organisms and for e. coli, an example of a well-studied organism that is not "minimal." for the minimal organisms considered in this study, nearly all proteins annotated as soluble and globular may be assigned to a known fold. the aphid symbiont b. floridanus has the highest coverage, at 96% of soluble, globular proteins. of the remaining proteins in the proteome have unknown structure, but are predicted to have at least one transmembrane helix. additional proteins have unknown structure and no predicted transmembrane helices, but 20% or more of their residues are in predicted low complexity or coiled coil regions, and thus not easily tractable in experimental structural studies. overall, the folds of of b. floridanus proteins may be annotated by sequence similarity to a protein of known structure. other minimal organisms also have high structural coverage: 95% of soluble, globular w. glossinidia proteins, 94% of soluble, globular b. aphidicola proteins, 87% of soluble, globular m. genitalium proteins, and 87% of soluble, globular t. whipplei proteins can reliably be assigned folds. in contrast, only 78% of soluble, globular e. coli proteins can reliably be assigned folds. the low numbers of predicted transmembrane proteins in several of the minimal organisms is also notable; previous analyses suggest that some transmembrane proteins are less important to intracellular symbiotes than to free-living bacteria. α/β fold class is the most common category of fold for the proteins that could be reliably assigned folds, we examined their structural classification in the scop database. scop is a widely used, manually curated database in which protein structures are divided into domains, which are classified in a hierarchy indicating different types of structural and evolutionary relationships between the domains. domains classified together in a single "family" or "superfamily" are hypothesized to have a common evolutionary origin on the basis of sequence or structural evidence. superfamilies that share similar secondary structural features and topology, but for which there is little or no evidence to suggest a common evolutionary origin, are classified together at the "fold" level. scop folds are grouped together in seven major "classes", based on common physical characteristics such as the predominant type of secondary structure or the order of connection of the different secondary structures. note that the scop "multi-domain" class encompasses folds that are comprised of multiple domains that individually would belong to different classes; individual domains from multi-domain proteins are not classified in the "multi-domain" class. although we use the term "fold" to refer to a protein's overall 3d backbone structure, we use the term "scop fold" to refer to a specific fold classification within the scop database. the fraction of proteins found in each organism belonging to each of these scop classes is shown in figure those proteins that could not reliably be assigned folds, and those that were assigned a fold based on homology to a protein not yet classified in scop, are described as "unsolved" and "unclassified," respectively. for all organisms, the highest proportion of scop folds are in the α/β class, and those in the α/β and α+β classes together comprise over half of the assigned scop folds. this reflects the observation that the α/β class contains some of the most functionally diverse "superfolds" that act as scaffolds for a wide array of molecular or chemical functions. usage of protein fold classes are conserved for key cellular processes in order to analyze how the annotated cellular function of each protein correlates with its structure, we examined the "functional role" annotation for each protein as provided in the tigr database. we found that the distribution of proteins among scop fold classes was highly conserved within some roles and showed much more variability in others. in contrast, figure shows the fold class distribution of proteins in the "cell envelope" functional category across all proteomes. this functional category is also highly represented in each proteome, but the proteins show a much higher degree of variation in fold usage. this category contains the highest proportion of unassigned folds, as well as a diverse array of assigned scop folds: for example, 6% and 4% of domains from w. glossinidia and e. coli cell envelope proteins belong to the all-α structural class, while cell envelope proteins from the other proteomes contain few or no all-α structures. e. coli also contains a number of solved transmembrane structures, while other proteomes contain significant numbers of proteins predicted to be transmembrane proteins not detectably homologous to any protein with a known 3d structure. m. genitalium and t. whipplei contain the largest fractions of cell envelope proteins that could not be reliably assigned a fold at this time, although most of these m. genitalium proteins are expected to be soluble and globular, while the majority of such proteins from t. whipplei are predicted to contain at least one transmembrane helix. the high amount of variability suggests that proteins in the "cell envelope" category evolve rapidly in response to specific pressures in an organism's environment, and different sets of these proteins remain after reductive evolution in the different environments occupied by the different species of minimal organisms. cellular functions with most conserved scop fold usage previous comparative sequence genomic analyses of symbionts have shown that the number of proteins in most cellular function categories varies little between symbiont proteomes, and that many of the most highly conserved proteins have cellular functions related to information storage and processing, particularly translation and ribosomal structure. we calculated the coefficient of variation in the number of proteins in each functional role category, as shown in equation cvsequence=stdevmean      mathtype@mtef@5@5@+=feaafiart1ev1aaatcvaufkttlearuwrp9mdh5mbpbiqv92aaexatlxbi9gbaebbnrfifhhdyfgasaach8aky=wiffydh8gipec8eeeu0xxdbba9frfj0=oqffea0dxdd9vqai=hguq8kuc9pgc9s8qqaq=dirpe0xb9q8qilsfr0=vr0=vr0dc8meaabaqaciaacagaaeqabaqabegadaaakeaacqwgdbwqcqwgwbgvdawgaawcbagaem4camnaemyzaumaemycaenaemydaunaemyzaumaemoba4maem4yammaemyzaugabeaakiabg2da9maalaaabagaem4uamlaemidaqnaemizaqmaemyzaumaemodaynaeiikagiaemota40aasbaasqaaiabigdaxaqabagccqwimayscqwgobgtdawgaawcbagaegonaydabeaakiabcmcapaqaaiabd2eanjabdwgaljabdggahjabd6gaujabcicaoiabd6eaonaabaaaleaacqaixaqmaeqaaogaesojgskaemota40aasbaasqaaiabiada2aqabagccqggpaqkaagaaczcaiaaxmaadaqadaqaaiabigdaxagaayjkaiaawmcaaaaa@59ba@ results are shown in table as expected, the category with the lowest variation in the number of proteins is "protein synthesis," and the top three categories are all closely related to transcription or translation. we also calculated the coefficient of variation in the number of protein domains assigned to each scop class, then averaged that data across all structural classes, as shown in equation cvstructure=∑class=17stdevmean7      mathtype@mtef@5@5@+=feaafiart1ev1aaatcvaufkttlearuwrp9mdh5mbpbiqv92aaexatlxbi9gbaebbnrfifhhdyfgasaach8aky=wiffydh8gipec8eeeu0xxdbba9frfj0=oqffea0dxdd9vqai=hguq8kuc9pgc9s8qqaq=dirpe0xb9q8qilsfr0=vr0=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@877c@ cvstructure was calculated separately for each functional role category, and these data are shown in table and figure 5a. the functional category with the lowest variation in the number of domains in each structural class is "protein synthesis," as would be expected from figure however, there are some interesting differences between the rankings based only on the cvsequence, and the rankings based on cvstructure. for example, fold usage of proteins involved in biosynthesis of cofactors, carriers, and prosthetic groups varies to a higher degree than the variation in total numbers of these proteins in each proteome. this implies that the repertoire of specific functions in this broad category is specialized to the particular needs of each organism, even though the overall number of such proteins varies little. as expected, the distribution of structures in "catch-all" classes such as hypothetical and unclassified proteins are more varied than the distribution of structures found in more well-defined functional categories. we also analyzed the degree of variation using data from only the five near-complete minimal organisms, excluding data from e. coli. results are shown in table and figure 5b. as before, fold usage of proteins in the "protein synthesis" category shows the least variance of all functional categories. the total genome size also slows relatively little variation among minimal organisms, as has been observed previously. however, some functional categories show relatively more variation between minimal organisms than between minimal organisms and e. coli. for example, the cellular function categories "cell envelope," "central intermediary metabolism," and "amino acid biosynthesis" all drop in rank by positions relative to table indicating higher diversity of folds in these functional categories among minimal organisms. in contrast, fold usage of proteins in the "regulatory functions" category shows relatively less variation among minimal organisms than between minimal organisms and e. coli. this suggests that although the minimal organisms have lost many of the regulatory pathways unnecessary for survival in their relatively unchanging environments, they maintain a relatively conserved set of proteins responsible for common regulatory functions. a more thorough phylogenetic analysis of these proteins would be necessary to test this hypothesis. common and overrepresented folds in minimal organisms we examined the most common protein folds in minimal organisms. results are shown in table four of the eleven most common scop folds are among the nine superfolds originally described by orengo and colleagues as scaffolds that can support a wide array of molecular functions. however, all have fewer copies in minimal organisms than are found in e. coli. interestingly, all scop folds present in equal or greater numbers in all minimal organisms as in e. coli are also folds for which only a single superfamily is characterized in scop; i.e., all proteins sharing the fold are also annotated as evolutionarily related to each other. the case of multiple superfamilies sharing one fold may arise from two alternative causes: convergent evolution of two or more families to one fold, or a single family that has diverged enough that homology between different branches of the family are no longer evident even from structure. these data imply that proteins that play sufficiently important roles to avoid elimination during reductive evolution have also not diverged as much as other protein families due to this same evolutionary pressure. an additional set of scop folds found only in minimal organisms and not in e. coli is given in table none of these folds are found in all five minimal organisms, and the proteins are not generally related to essential cellular functions such as transcription, translation, or replication. some are presumably adaptations to the specific environment of the organism, and several are not typically found in bacteria. these may represent lateral gene transfers or erroneous annotations.  after five years of progress in structural genomics, near-complete structural complements of the soluble proteins of several "minimal organisms" are now known. a complete set of fold assignments for nearly all soluble, globular proteins in a proteome is providing a global view of how minimal organisms are using various protein fold classes for different cellular functions and how the fold usage in each class is conserved. data from near-complete structural proteomes can yield hypotheses on protein evolution at a global level. simple statistical analyses of the variation in numbers of structures in each structural and functional category can shed light on which functional categories are more or less conserved in minimal organisms. for example, the functional categories that showed the least variability in both sequence- and structure-based analyses were involved in essential cellular functions such as transcription and translation. furthermore, every scop fold identified in equal or greater numbers in minimal organisms as in e. coli was the product of a single protein family, indicating that the proteins retained during reductive evolution of minimal organisms also tend to be from slow-evolving families. the latter observation was expected, as essential genes in other species have previously been shown to evolve more slowly than non-essential genes. such observations may be followed up with more detailed studies based on phylogenetic modeling of protein families or the construction of atomic models of proteins in those categories. detailed atomic modeling of all proteins in a biochemical pathway will be useful to study the plasticity of these pathways in response to evolutionary pressures imposed by different organisms' environments. 
we find that proteins performing essential cellular functions closely related to transcription and translation exhibit a higher degree of conservation in fold usage than proteins in other functional categories. we report that this goal has nearly been reached for several "minimal organisms" – parasites or symbionts with reduced genomes – for which over 95% of the soluble, globular proteins may now be assigned folds, overall 3-d backbone structures. we also compare patterns in the conservation of folds among minimal organisms and those observed between minimal organisms and other bacteria. folds related to transcription and translation functional categories were also overrepresented in minimal organisms compared to other bacteria. determining the complete repertoire of protein structures for all soluble, globular proteins in a single organism has been one of the major goals of several structural genomics projects in recent years. we analyze the structures of these proteins as they relate to cellular functions, and compare conservation of fold usage between functional categories.
 determining the complete repertoire of protein structures for all soluble, globular proteins in a single organism has been one of the major goals of several structural genomics projects in recent years.  we report that this goal has nearly been reached for several "minimal organisms" – parasites or symbionts with reduced genomes – for which over 95% of the soluble, globular proteins may now be assigned folds, overall 3-d backbone structures. we analyze the structures of these proteins as they relate to cellular functions, and compare conservation of fold usage between functional categories. we also compare patterns in the conservation of folds among minimal organisms and those observed between minimal organisms and other bacteria.  we find that proteins performing essential cellular functions closely related to transcription and translation exhibit a higher degree of conservation in fold usage than proteins in other functional categories. folds related to transcription and translation functional categories were also overrepresented in minimal organisms compared to other bacteria. 