Lengthy co-evolution of Homo sapiens and Mycobacterium tuberculosis, the main causative agent of tuberculosis, resulted in a dramatically successful pathogen species that presents considerable challenge for modern medicine. The continuous and ever increasing appearance of multi-drug resistant mycobacteria necessitates the identification of novel drug targets and drugs with new mechanisms of action. However, further insights are needed to establish automated protocols for target selection based on the available complete genome sequences. In the present study, we perform complete proteome level comparisons between M. tuberculosis, mycobacteria, other prokaryotes and available eukaryotes based on protein domains, local sequence similarities and protein disorder. We show that the enrichment of certain domains in the genome can indicate an important function specific to M. tuberculosis. We identified two families, termed pkn and PE/PPE that stand out in this respect. The common property of these two protein families is a complex domain organization that combines species-specific regions, commonly occurring domains and disordered segments. Besides highlighting promising novel drug target candidates in M. tuberculosis, the presented analysis can also be viewed as a general protocol to identify proteins involved in species-specific functions in a given organism. We conclude that target selection protocols should be extended to include proteins with complex domain architectures instead of focusing on sequentially unique and essential proteins only.
Tuberculosis (TB) remains a major world-wide health hazard, causing to roughly 2 million deaths per year. Approximately, one third of the world' s population is currently infected with Mycobacterium tuberculosis (MTB), the causative agent of TB [1], [2]. MTB is an intracellular parasite, an organism notoriously hard to fight. One of the major reasons for its persistence is the intricate network of host-pathogen interactions which is exploited by the bacterium and which creates a fine-tuned niche for its survival in macrophages [3]. This has been developed during lengthy periods of “co-habitation” and, consequently, co-evolution. The MTB genome has been molded to accommodate the circumstances of life within macrophages. In fact, the bacterium has been so successful in this process that it is notably hard to cultivate outside its physiological host. During the co-evolution process with humans (cf. archeological data presenting experimental evidence for the co-habitation of MTB and humans back to 9000 years [4]), the genome changes within the bacterium have been facilitated by its error-prone DNA polymerases [5]. As a result, the present MTB organism is very close to being an obligatory intracellular parasite. Mycobacteria are intrinsically resistant to most commonly used antibiotics and chemotherapeutic agents. Due to its specific structure and composition, the mycobacterial cell wall is an effective permeability barrier, generally considered to be a major factor in promoting the natural resistance of mycobacteria. Only a few drugs are active against mycobacterial pathogens, and current treatment strategies for TB consists of 3 or 4 drugs used in combination. However, the increasing emergence of multi-drug resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) necessitates the development of novel drugs [6]. Furthermore, novel drugs compatible with antiretroviral therapy are needed to treat co-infected AIDS patients [7] and new drugs are also required that can specifically be employed for children. Clearly, there is an urgent need for drug development projects that actually possess novel targets and novel mechanisms of action [8]. A significant step towards understanding the biology of MTB was provided by full genome sequencing of various strains of this microorganism, including the best characterized laboratory strain, H37Rv, that contains 3,984 genes [9]. The complete genome sequences of several other mycobacteria have also become available, showing various levels of divergence [10], [11]. While the genome size of M. bovis is largely similar to that of MTB, the genome of M. leprae is reduced to only 40% of that of MTB [12]. These genomes can also be compared to those of many other pathogenic and non-pathogenic bacteria, as the number of fully sequenced bacterial genomes is over 600 and is rapidly increasing. The genomes of several eukaryotic organisms have also been sequenced and are now largely annotated, including the human genome. Additionally, the Human Microbiome Project (HMP) has published the sequenced genomes of 178 microbes that exist within or on the surface of the human body [13], [14]. The plethora of genomic sequences offers a novel platform for comparative analyses and large-scale studies. This new source of data can help to identify proteins in the MTB proteome that perform essential functions ensuring the survival and virulence of the bacterium. These proteins present potential targets for drug design. Target selection is the crucial starting point of any drug development process. Traditionally, this procedure relied on established knowledge of individual proteins and their functions. The availability of complete genome sequences opened a new era and lead to the development of various bioinformatics methods which can prioritize targets in an automated cost-effective way. These approaches can take various criteria into account with the aim to minimize the interactions with the host environment yet specifically attack the pathogen' s growth and survival. Several such studies focused on metabolic enzymes. In their work, Anishetty and co-workers collected enzymes from the biochemical pathways of MTB using the KEGG metabolic pathway database [15]. As a result, 186 proteins were suggested as potential drug targets based on the lack of similarity to proteins from the host H. sapiens. Hasan and co-workers proposed a ranking system by targeting metabolic checkpoints based on the uniqueness of their role in the pathogen' s metabolome [16]. Additionally, targets were penalized for having high sequence similarity to proteins of the host and of the host flora. The targetTB database was created based on similar principles [17]. Using flux balance analysis and network analysis, proteins critical for the survival of MTB were first identified, and then subjected to comparative genomics analysis with the host. Finally, a novel structural analysis of potential binding sites was carried out to assess the validity of a protein as a target. The selection also incorporated data about the essentiality of proteins using the results of experiments carried out under nutrition rich conditions. A recent analysis constructed a proteome-wide drug target network by linking the structural proteome of MTB with structurally characterized approved drugs [18]. In most drug target selection protocols, the existence of a protein structure or a structural homologue is treated as an advantage for rational drug design. Breaking with this tradition, Anurag and Dash suggested a list of intrinsically disordered proteins in the MTB genome as potential drug targets [19]. This is in accordance with the recent finding that these proteins can also serve as promising drug targets [20], exemplified by the successful blocking of the p53-MDM2 interaction by a small molecule [21]. Fueled by this observation, a list of proteins with disordered protein segments were compiled and filtered for essentiality, uniqueness and involvement in protein-protein interactions. This resulted in 13 proposed drug targets. These proteins have a probable role in signaling, regulation and translation, instead of metabolisms [19]. The success of the target selection procedure critically depends on identifying distinctive features of the pathogen that are essential for its survival. The protein repertoire encoded by the genome provides the initial starting set from which potential targets can be selected based on various hypotheses. However, the optimal target selection criteria are still a matter of considerable debate [22], [23]. The prime criteria of current target selection protocols are essentiality, lack of sequence homologues at least in the host, and the presence of functional characterization. These criteria, however, can lead to the overlook of several important candidates. In the case of MTB, there are several proteins that do not meet the aforementioned criteria but should not be disregarded as potential targets due to their eminent biological importance. For example, the genome sequence of MTB revealed that about 10% of the coding of the genome is devoted to two largely unrelated families of acidic, glycine-rich proteins, the PE and PPE families [9]. These proteins are largely sequence specific to mycobacteria and have been implicated in host-pathogen interactions and antigenic variations [24]. However, most of these proteins are not essential and their function is largely uncharacterized. An additional new class of promising targets in MTB corresponds to signaling elements, in particular to the pkn family of Ser/Thr protein kinases [25], [26]. These MTB proteins play essential roles in both bacterial physiology and virulence [26], but are evolutionary related to eukaryotic protein kinases. These protein families are cases that challenge current target selection protocols and indicate that different approaches for target selection are needed. In this work, we propose a novel computational strategy based on phylogenetic profiling and comparative proteomic analysis that can highlight proteins involved in specifies-specific functions. This approach takes into account the complex evolutionary scenarios that can lead to the emergence of novel species-specific functions. Novel function can arise from de-novo protein creation but also from more ancient proteins by the combination of divergence, duplication and recombination events [27]. In order to gain insights into the contribution of the various processes, we carried out a comparative proteomic analysis. By focusing on the causative agent of tuberculosis, we analyzed the protein domain and disorder content of its proteome and carried out large-scale local sequence similarity searches to identify basic evolutionary patterns in MTB. We show that the enrichment of certain protein families in the genome can automatically indicate an important function specific to this pathogen. The implications of these findings for target selection are also discussed.
In this work we carried out a comparative genomic study based on the content of domains and disordered regions and the result of large-scale sequence similarity searches. This approach is completely general and could be applied to any kind of organism with an annotated genome. Here, we focused on MTB, the causative agent of tuberculosis. Our analyses revealed two protein families in the proteome of MTB that stand out in several aspects. These proteins were also shown to have a functional importance essential for the survival of this pathogen. Next, we will examine them as potential targets for drug design. The common properties of both the pkn and PE/PPE families include unusual domain accretions specific to this organism. This is combined with an increase in their disorder content. Both families carry out important functions in the MTB and are involved in the interactions with the host cell. Various members were shown to be essential for the organism and according to a recent analysis using guinea pig model, representatives of these families are significantly enriched in the early and chronic stages of infections [76]. Furthermore, many of them are either located in the surface of the bacteria or are exported into the host cell. The properties of these protein families underscore their biological importance and suggest that they would be ideal candidates for drug design. However, conventional drug design procedures generally overlooked such proteins as targets by largely focusing on metabolic processes. The need for novel drugs for the treatment of MTB forces researchers to explore new directions for target selection. The pkn and PE/PPE families, through their complex architectures offer several options in this regard. One of the most active areas of therapeutic research involves developing protein kinase inhibitors. With recent advances, protein kinases have now become the second most important group of drug targets after G-protein-coupled receptors [77]. Currently, three protein-kinase inhibitors are already in clinical use, and several other protein-kinase inhibitors are undergoing human clinical trials, mostly targeting cancer [77]. However, kinases may also be exploited in the development of novel antibiotics against mycobacteria. Mycobacterium tuberculosis contains 11 eukaryotic-like Ser/Thr protein kinases (STPKs). All of these proteins accommodate the common catalytic domain and the 12 conserved motifs that define the signature of eukaryotic protein kinases. Despite these similarities, the sequence identity to the human SPTK genes is around 30%, low enough to allow the promising search for species-specific inhibitors [26]. Recently, a high-resolution 3D structure of the pknG kinase in complex with a potent antimycobacterial compound was published [55]. This structure revealed that despite similarities in the overall fold of the conserved kinase domain, the species-specific structural characteristics of the protein still allows highly specific interaction patterns with the promising drug-like compound. The structure of the catalytic domain of pknB in complex with different ATP analogues was also published [78], [79] and revealed that in contrast to the similar kinase structures from eukaryotes, an important regulatory loop shows high degree of flexibility in the mycobacterial kinase preventing its localization in the crystal structure. Dimerization of signaling kinases is a frequently observed phenomenon, and within the architecture of the dimer interfaces, species-specific and conserved elements are both found [80], [81]. Specifically, the dimerization of the mycobacterial STPK proteins seems to be universal and functionally relevant [82], therefore the identified intermolecular interfaces may present a further target surface to perturb protein function. The additional sequence regions tethered to the common kinase domain are specific for each of the pkn proteins. As most of these domains are located outside of MTB cells, they could be more accessible for potential drugs. Although there is detailed structural information available for pknB, pknD and pknG proteins, they offer very few clues about potential “druggable” sites. According to their disorder profiles (Figure 5), pknE, pknK and to some extent pknJ are likely to contain additional ordered domains. The future structural characterization of these regions could offer further drug target sites. Concluding on the question whether mycobacterial kinases may present useful targets against MTB, we wish to emphasize that due the fact that many critical cellular processes in human are regulated by kinases, cross-reactivity could have dramatic consequences [83], [84]. In order to alleviate such effects, we propose to focus on a combined approach which allows targeting different elements of a mycobacterial kinase (eg dimerization domain). In such an approach, targeting the MTB-specific active site components of a kinase (eg. pknG), may be coupled to designing potentially inhibitory small molecular compounds that bind to MTB-specific sequence elements outside the active site. The PE/PPE proteins are similar to pkn proteins in the sense that they also contain a well-conserved N-terminal domain that defines these families and C-terminal parts that show large variations in terms of their length, domain composition and disorder content. Despite the obvious biological importance of these proteins, very little structural and functional information is available for them. In a large-scale structural genomics approach it was found that individual members of both PE and PPE families did not express well or expressed in insoluble or unfolded forms [73]. To explain the failure of structure determination efforts it was suggested that these proteins need partners to fold. Indeed, via a genomic analysis one specific pair of PE and PPE proteins was predicted to interact, and their structure was successfully determined [73]. The extensive interface formed between the PE and PPE domains, that also contain the conserved N-terminal motifs, can also be considered from the viewpoint of drug design. This is supported by the growing number of examples of small molecules successfully blocking protein-protein interactions [85]. PE/PPE proteins also contain several additional ordered domains (Figure 6), however, they lack detailed structural information. In most cases, functional and structural information cannot be inferred from sequence homologs, as the family itself is highly specific to Corynebacterineae with the vast majority of PE/PPE members being present in mycobacteria only. There are, however, some exceptions, like the α/β hydrolase 3 domain, that is a catalytic domain found in a very wide range of enzymes [86], or the phosphoglycerate mutase (PGAM) domain that catalyses reactions involving the transfer of phospho groups between the three carbon atoms of phosphoglycerate [87]. Another common property of several members of both families is the presence of long disordered segments. Until recently, the feasibility of targeting proteins without a well-defined structure was unclear for the purpose of drug development. There is now, however, a newly sparked interest in intrinsically disordered proteins as potential drug targets [88], [89]. This originates partly from recognizing the biological importance of disordered proteins, especially in signaling and regulatory processes, but also from realizing the specific mode of their binding [32], [90]. Disordered proteins usually interact via a coupled folding and binding process that involves a transition from a largely flexible state to a more ordered state [34]. This transition is associated with a large entropy cost that can make the overall binding quite weak while maintaining specificity. The low binding free energy of these interactions indicates that they would be relatively easy to block by small molecules [20]. In one example, a promising small, drug-like molecule was found to bind into the groove of MDM2. This molecule inhibits the association of the ordered protein MDM2 with the disordered segment of p53 by mimicking the short alpha helical structure of p53 adopted upon binding. In another example, dimerization of two disordered proteins, c-Myc and Max, was blocked by specific inhibitors [89]. Generally, the analysis of known examples of the druggable regions of disordered proteins indicated that these segments overlapped with the binding regions predicted by ANCHOR [91]. Therefore, ANCHOR [41] and other disordered binding region prediction algorithms that will be hopefully developed in the years to come can be extremely useful to highlight potential druggable sites directly from the amino acid sequence, especially in combination with other methods. According to our results, both pkn and PE/PPE protein families contain putative druggable sites located in disordered segments. For example, the region in the C-terminal part of pknA (residues 419–431) can be of special interest, as here a high-confidence disordered binding region is predicted by ANCHOR that coincides with a high confidence predicted α helical region predicted by PSIPRED [92] (Figure S1). This is indicative of a special class of disordered binding regions that form an α helix upon binding to their partner, similarly to the binding of p53 to MDM2. The large number of disordered binding regions predicted in the PE/PPE families indicates that there can be many other druggable sites awaiting further characterization. The two families highlighted in this study offer various options for drug design. However, most members would be omitted from traditional target selection procedures due the lack of essentiality. In the pkn families, only pknA, pknB and pknG were shown to be essential, while essentiality was showed for only 9 members of the PE/PPE family. Since MTB is an obligate parasitic pathogen, it is extremely difficult to identify genes that are required for the optimal growth of mycobacteria under in-vivo conditions. Depiction of the MTB proteome during infection is usually based on a hypothesized environment that simulates the conditions within the infected lung and defined on the basis of bacterial response to pH, starvation and hypoxia [93]–[96]. Recently, the guinea pig model was used to examine the bacterial proteome in vivo during the early and chronic stages of the disease [76]. According to this study, various members of the PE/PPE families and pknA were observed among the most dominant proteins in the infected lung samples, giving further support for the importance of these protein families. Interestingly, there were major differences between the results of these in vitro and in vivo studies, suggesting that none of the simulated in vitro model environments accurately reflects the protein profile within the lung [76]. A further limitation of studying the essentiality of individual proteins arises from the functional overlap among members of various protein families. Each member of the pkn group contains the kinase domain, and they share many of their substrates despite the differences in their sensor domains [97]. Although PE/PPE proteins are much less well-characterized, several members of them can also exhibit significant similarities with each other and this phenomenon is also reflected in their domain composition. The similarity often goes beyond the common N-terminal domain, as many members of the PE/PPE protein family share the same domain architecture (see Figure 6). There is a high likelihood of functional overlap in these cases. Protein families with overlapping functions challenge the notion of essentiality as target selection criteria. However, by targeting the common domain of protein families, several proteins of the pathogen can be attacked using the same drug molecule. Relying on such multi-target drugs can be a more efficient avenue in drug design [98]. In this respect, relatively conserved domains that occur multiple times can be of potential interest. Such examples include the PE and PPE domains, the kinase domain of pkn proteins, the NHL domain that occurs twice in the PE-PGRS groups as well as in pknD. There are several other currently uncharacterized domains occur multiple times in the genome of MTB (Figure 6). These proteins can provide interesting targets for polypharmacological drugs [18]. The increasing number of complete genome sequences has enabled comparative genomic analyses which can be used to understand the distinctive properties of various pathogens and to specifically target them based on this knowledge. In this work we analyzed the proteins encoded by the genome of MTB from this viewpoint. We identified two protein families, the pkn and PE/PPE, that showed unusual species-specific enrichment of domains. These proteins can be considered as potential targets for drug design as they are involved in vital functions that are specific to this pathogen. Members of both families have complex domain architectures that combine family-specific domains with other domains and disordered segments. The analysis presented in this study predicts that drug design against members of these two families may lead to promising hits; verification of this prediction awaits further studies. It is important to emphasize that members of these two families represent novel potentials since the compounds that are either currently used in the clinics against tuberculosis or are under clinical trials are directed against other target proteins. Although some of our findings are specific to MTB, there are several more general implications of this study. The exclusivity of certain proteins to a given pathogen is often one of prime criteria used in various target selection protocols. However, our results indicate that species-specific functions are not necessarily brought about by species-specific proteins. In contrast, many novel functions developed from already existing proteins. In the case of eukaryotes, there are several notable examples, such as the development of olfaction, reproduction, and immunity [27], where the combination of gene duplication, divergence and recombination led to the expansion of protein families and provided jumping points in evolution. The example of MTB shows that such complex evolutionary scenarios play important roles in prokaryotes as well and can be detected by species-specific enrichment of certain protein domains or families. Protein families emerging as a result of such processes often have complex domain architectures. Consequently, these proteins can be approached from multiple directions for the purpose of drug development. Besides traditional strategies that aim to inhibit enzymatic functions, less well-established approaches should also be considered, such as developing compounds against protein-protein interaction sites or disordered binding regions. Due the potential overlap within these protein families, individual members might not comply with essentiality. In these cases, however, a single drug can be effective against more than one protein. These cases of functional overlap arising from direct similarity, unlike indirect effects [99], may be predicted based on target similarity. Taking the various factors of our findings into account can help to improve the success rate of target selection protocols and drug development process.
For the domain assignment the protein domains contained in the Pfam database were used (http: //pfam. sanger. ac. uk/) [30]. Pfam is composed of two parts, Pfam-A and Pfam-B. Pfam-A domains are manually curated and have a distinct name (e. g. Abhydrolase_3). On the other hand, Pfam-B domains are automatically assigned using sequence similarity searches and usually no additional annotation is supplied concerning them. Pfam-B domains are not given a separate name and can be identified by a unique numerical ID. For the proteome-scale comparative studies, a dataset containing 1,904,578 protein sequences from 467 known complete proteomes was assembled (20 eukaryotic and 447 bacterial proteomes containing 392,401 and 1,512,177 proteins respectively). These proteomes were taken from the UniProt ftp server (ftp: //ftp. uniprot. org/) [100]. For the similarity searches between MTB proteins and the proteins in the SDCP, PSI-BLAST was used [101]. First, a PSI-BLAST profile was calculated for each of the 3,948 proteins in the MTB proteome using the UniRef90 database, with three iterations. Next, these profiles were used to find hits from the proteins in SDCP, the database containing protein sequences from 467 known complete proteomes. A hit was considered significant (the MTB and the other protein was considered similar) and was used further on, if the e-value was below 10−4. Since the similarity between proteins is often restricted to shorter parts of the sequence, an explicit coverage threshold was not included in this work. This enabled the recognition of similar domains or other local protein regions between proteins, and was necessary for the successful clustering of related proteins, such as the PE/PPE families. The e-value cutoff ensured that these similarities are still significant. Based on the alignments, all locally similar sequences from the SDCP were collected for each protein in the MTB proteome. Next, for each MTB protein a similarity profile was built that contains the number of similar sequences for each of the 467 organism in the SDCP. In general, the locally similar segments identified by PSI-BLAST are larger than single domains. The aligned regions can also contain disordered regions that are not excluded by the low complexity filter. Furthermore, since the similarity searches were centered around the MTB proteins, this analysis could also find similarities between sequences in some cases, even if they do not share Pfam domains. For the functional categorization of MTB proteins, data were taken from the TubercuList server (http: //genolist. pasteur. fr/TubercuList/) [42]. According to this site, each MTB protein is unambiguously grouped into one of the following categories: virulence, detoxification, adaptation; lipid metabolism; information pathways; cell wall and cell processes; insertion sequences and phages; PE/PPE; intermediary metabolism and respiration; regulatory proteins; conserved hypotheticals. We omitted the unknown category that contained only 16 proteins and the category corresponding to RNAs. Therefore, nine functional categories were used in this study. For the prediction of protein disorder IUPred was used (http: //iupred. enzim. hu/) [39], [40]. The algorithm assigns a score between 0 and 1 for every residue in the protein. This score shows the tendency of that residue being disordered. For the binary categorization of residues we consider a residue disordered if it has a score greater than 0. 5, and ordered if its score is less than 0. 5. For the prediction of disordered binding regions we used ANCHOR (http: //anchor. enzim. hu/) [37], [41]. Similarly to IUPred, ANCHOR calculates the tendency of each residue being in a disordered binding region. For binary classification, a cutoff of 0. 5 was used here as well. The input for the clustering algorithm is based on the similarity profiles generated for each MTB sequence. Each profile consisted of 467 numbers that represent the number of sequences similar to the MTB sequence in the 467 studied proteomes. In the cluster analysis Euclidean distance was used together with Ward' s method. The result of clustering was largely insensitive to various parameters of the clustering, including the type of the clustering method, various types of normalizations, parameters of PSI-BLAST. The clustering was implemented in the R program package.
Mycobacterium tuberculosis (MTB), the causative agent of TB, is a dramatically successful pathogen that poses a considerable challenge for modern medicine. The increase in multi-drug resistant TB necessitates the identification of novel drug targets and drugs with new mechanisms of action. In this work, we developed a novel computational strategy based on comparative proteomic analysis that can highlight proteins involved in specifies-specific functions. Our analyses of the proteins encoded by the MTB genome identified two protein families that stand out in this respect. These proteins have complex architecture combining various domains and disordered segments. They are also involved in vital functions, especially in host-pathogen interactions. Although these proteins generally do not fit into traditional drug design paradigms, there are several new strategies emerging that can be used to target these proteins during drug development. Our results challenge current target selection protocols that largely rely on the uniqueness and the essentiality of proteins. Instead, these findings emphasize the importance of complex evolutionary scenarios that can lead to the emergence of species-specific functions from more ancient building blocks of proteins. The experiences gained from this work have important implications specifically for targeting MTB, and in broader terms, to improve current target selection protocols in drug development.
sequence analysis
systems biology
biochemistry
genomics
biology
computational biology
comparative genomics
proteomics
pharmacogenomics
Proteins with Complex Architecture as Potential Targets for Drug Design: A Case Study of Mycobacterium tuberculosis