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The Mining of Toxin-Like Polypeptides from EST Database by Single Residue Distribution Analysis Sergey Kozlov, Eugene Grishin*

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The Mining of Toxin-Like Polypeptides from EST Database by Single Residue Distribution Analysis Sergey Kozlov, Eugene Grishin* Kozlov and Grishin BMC Genomics 2011, 12:88 http://www.biomedcentral.com/1471-2164/12/88 RESEARCHARTICLE Open Access The mining of toxin-like polypeptides from EST database by single residue distribution analysis Sergey Kozlov, Eugene Grishin* Abstract Background: Novel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening. Results: Using the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined. Conclusions: The suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed. Background modules facilitating different stages of analysis, such as Expressed sequence tag (EST) analysis is widely used in those for preprocessing of data [8-10] and software for molecular biology. This analysis comprises the transcrip- combining sequences in contigs and their annotation, tome of a given tissue at a given time. These data are have been developed [11-13]. To improve the quality of deposited in a specialized resource at the National Cen- initial data processing, the results of different scanning ter for Biotechnology Information (NCBI) - dbEST [1]. methods can be combined from homology search of a The EST databases are used to address different pro- nucleotide consensus sequence, homology search of blems [2-6]. deduced protein sequences and involvement of reference The EST database analysis requires the development databases of known organisms [14-17]. of novel methods and software for data processing. The The strategy of bioinformatics to database analysis standard procedure includes processing of the biological remains the same, variety of diverse crude sequences material, production of clones, construction of libraries, combined by cluster analysis in contigs should be sub- and data analysis, from grouping in contigs to gene jected to alignment search tools and function classifica- annotation and microarray design [7]. Special program tion by gene ontologies. It gives good results although is not always optimum. Earlier, analysis of the EST data- * Correspondence: [email protected] base from spider venomous glands showed [18] that the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy conventional approach including the preprocessing of of Sciences ul. Miklukho-Maklaya, 16/10, 117997, Moscow, Russia © 2011 Kozlov and Grishin; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Kozlov and Grishin BMC Genomics 2011, 12:88 Page 2 of 12 http://www.biomedcentral.com/1471-2164/12/88 theoriginaldataandformationofcontigsdecreasedthe Methods efficiency of identification of rare polypeptide toxins. The SRDA recommended search procedure of scanning translated In many proteins the position of certain (key) amino acid sequences against characteristic toxin structural motifs residues in the polypeptide chain is conserved. The proved more effective. Another alternative consists in the arrangement of these residues may be described by a poly- use of search queries created from the alignment of peptide pattern, in which the key residues are separated by known proteins families for database screening. Thus, numbers corresponding to the number of nonconserved 83 new peptides were found, which were not earlier dis- amino acids between the key amino acids (see Figure 1). covered in the EST databases of different aphid species For successful analysis, the choice of the key amino [19]. A family of new proteins from corals with a Cys- acid is of crucial importance. In polypeptide toxins, the rich beta-defensin motif was identified as well [20]. structure-forming cysteine residues play this role, for Identification of short polypeptides in EST datasets is other proteins, some other residues, e.g. lysine, may be especially challenging since they may be aligned only as much important (see Figure 1). Sometimes it is with highly homologous proteins. They are synthesized necessary to find a specific residues distribution not in as precursors, which are consequently processed into the whole protein sequences, but in the most conserved mature polypeptides. The enzymes involved in matura- or other interesting sequence fragments. It is advised to tion recognize specific regulatory amino acid motifs, start key residue mining in training data sets of limited which help to identify precursor proteins in EST size. Several amino acids in the polypeptide sequence databases [18,19,21]. may be selected for polypeptide pattern construction; Polypeptide toxins from natural venoms are of consid- however, in this case, the polypeptide pattern will be erable scientific and practical interest. They may be more complicated. If more than three key amino acid used for designing drugs of new generation [22]. Venom residues are chosen, analysis of their arrangement of a single spider contains hundreds of polypeptides of becomes too complicated. It is necessary to know the similar three-dimensional structure but divergent biolo- position of breaks in the amino acid sequences corre- gical activity. In toxins, the mature peptide domain is sponding to stop codons in protein-coding genes. highly variable, while the signal peptide and the propep- Figure 1 clearly demonstrates that the distribution of tide domain are conserved [23,24]. The specificity of Cys residues in the sequence analyzed by SRDA ("C”) action on different cellular receptors depends on the differs considerably from that of SRDA ("C.”) taking into unique combination of variable amino acid residues in account termination symbols. For scanning A. viridis the toxin molecule. Using a common scaffold, venomous EST database, the position of termination codons was animals actively change amino acid residues in the spa- always taken into consideration. tial loops of toxins thus adjusting the structure of a The flowchart of the analysis is presented in Figure 2. novel toxin molecule to novel receptor types. This array The EST database sequences were translated in six of polypeptide toxins in venoms is called a natural com- frames prior to search, whereupon the deduced amino binatorial library [25-27]. acid sequences were converted into polypeptide pattern. Homologous polypeptides in a combinatorial library The SRDA procedure with key cysteine residues and the may differ by point mutations or deletions of single termination codons was used. The converted database, amino acid residues. During contig formation such which contained only identifiers and six associated sim- mutations may be considered as sequencing errors and plified structure variants (polypeptide patterns), formed can be ignored. Our method is devoid of such limita- the basis for retrieval of novel polypeptide toxins. tions. Instead of the whole EST dataset annotation and To search for sequences of interest, a correctly formu- search for all possible homologous sequences, we sug- lated query is necessary. Queries also in pattern format gest to consider the bank as a “black box”,fromwhich (screening line in Figure 2) were based on amino acid the necessary information may be recovered. The criter- sequences of anemone toxins after analysis of homology ion for selection of necessary sequences in each particu- between their simplified structures. lar case depends on the aim of the research and the At subsequent stages, from the converted database, structural characteristics of the proteins of interest. amino acid sequences that satisfy each query were To make queries in the EST database and to search selected. Using the identifier, the necessary clones and for structural homology, we suggest to use single residue open reading frames in the original EST database were distribution analysis (SRDA) earlier developed
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