US 6,507,788 B1Grant

Rational selection of putative peptides from identified nucleotide, or peptide sequences, of unknown function

Issue Date:2003-01-14

•11 Claims

Abstract

A method for identifying putative peptides of a given function from among nucleotide or peptide sequences of unknown function comprising the steps of:

(i) obtaining a polynucleotide or polypeptide database;

(ii) screening the database for the presence of a combination of nucleotides or amino acids indicative of the peptide of given function;

(ii) identifying the polynucleotide or polypeptide sequences which comprise the combination of nucleotides or amino acids indicative of the peptide of given function.

Metadata

Assignees

Société de Conseils de Recherches et d'Applications Scientifiques (S.C.R.A.S.)
Centre National de la Recherche Scientifique (C.N.R.S)

Inventors

Jose Antonio Camara y Ferrer
Christophe Alain Thurieau
Jean Martinez
Gilbert Bergé
Catherine Gozé

Application Information

Application Number:US 09/257,525

Filing Date:1999-02-25

Priority Date:1999-02-25

Art Unit:7

Classifications

IPC:

C12Q 168A01N 6100A61K 3800C07H 2100G01N 3348

Field of Search:

435 6536 231536 241

Patent Drawings

This patent does not have any drawings.

Description

Background of the Invention

[0005] (i) Field of the Invention

[0006] The present invention relates to a method for identifying putative peptides from nucleotide or peptide sequences of unknown function such as both nucleic acid and peptide precursors of a peptide comprising an amidated C-terminal end and, more particularly, to a method wherein putative precursor peptides are identified from a genetic database.

[0007] (ii) Description of Related Art

[0008] Certain combinations of nucleotides, when present in a polynucleotide, are known to give rise to certain properties in the polypeptide translated therefrom. One example includes those nucleotides which encode polypeptide hormone precursors which undergo a post-translation amidation reaction. Another example, as set forth in U.S. Pat. No. 4,917,999, relates to certain nucleotides which are characteristic of polypeptides exhibiting α-amylase enzymatic activity.

[0009] Amidated polypeptide hormones are synthesized in the form of a precursor which undergoes maturation. This maturation consists of an amidation reaction. The amidation reaction of the C-terminal end is a characteristic reaction of amidated polypeptide hormones. This reaction, which occurs on the precursor of one or more hormones, allows maturation of the hormone and also ensures its biostability in the physiological medium: the amide group formed is less vulnerable than the free acid function. The hormone is therefore more resistant to carboxypeptidases, it remains active in the cell for longer and retains an optimum affinity for its receptor site.

[0010] Amidation has been widely described (“Peptide amidation”, Alan F. Bradbury and DerekG. Smyth, TIBS 16:112-115, March 1991 and “Functional and structural characterization of peptidylamidoglycolate lyase, the enzyme catalysing the second step in peptide amidation”, A. G. Katopodis, D. S. Ping, C. E. Smith and S. W. May, Biochemistry, 30(25): 6189-6194, June 1991), and its mechanism is as follows:

[0011] 1—Cleavage of the precursor polypeptide chain of the hormone by an endoprotease at the two basic amino acids, that is to say arginine and/or lysine,

[0012] 2—Subsequently two cleavages by carboxypeptidase result, which lead to the extended glycine intermediate,

[0013] 3—The enzyme PAM (peptidyl-glycine-amidating monooxygenase) comprises two distinct enzymatic activities: firstly, it converts the extended glycine intermediate into an α-hydroxyglycine derivative, the subunit of the enzyme PAM involved is PHM (peptidyl-glycine-hydrolylating monooxygenase). The derivative obtained serves as the substrate for the second subunit of PAM (called PAL: peptidyl-hydroxyglycine-amidating lyase), which fixes the amine function of the glycine on to the amino acid immediately adjacent to the N-terminal side and liberates glyoxylate.

[0014] This reaction involves the presence of a recognition site on the precursor of the hormone or hormones, a site which always comprises the sequence: glycine and two basic amino acids (arginine or lysine). The amidated polypeptide hormones which are to be secreted outside the endoplasmic reticulum are known to comprise a consensus signal sequence of about fifteen to thirty amino acids, this sequence being present at the N-terminal end of the polypeptide chain. It is cut later by a signal peptidase enzyme such that it is no longer found in the protein once secreted.

[0015] Given the importance of known amidated polypeptides in the context of numerous biological systems, methods have been sought for the identification of additional amidated polypeptides. Unfortunately, at the present time, the discovery of a new protein is not easy.

[0016] To date, the art has developed certain approaches in an attempt to identify novel proteins of potential biological interest.

[0017] In one approach, potentially new proteins of interest are isolated from a source by selecting a specific property which the researcher believes will be possessed by one or more potential proteins of interest in a sample. According to this approach, proteins can be isolated and purified by various techniques: precipitation at the isoelectric point, selective extraction by certain solvents and then purification by crystallization, counter-current distribution, adsorption, partition or ion exchange chromatography, electrophoresis.

[0018] The conventional protein isolation techniques described above provide only limited success in the isolation and identification of new biological molecules of interest. This approach implies knowledge of the properties of the protein to be isolated. Typically, one of two situations arises based on isolation of proteins using a common property. In the first situation, the common property will be for the most part unrelated or only marginally related to the biological function of the molecules being isolated. One could envision, for example, two proteins sharing identical isoelectric points but having completely unrelated biological functions. In the second situation, separation might be achieved based on common property which is very closely related to the biological function of the molecule being isolated. In this category, for example, one might envision molecules which bind to the same receptor molecule. In the former situation, the isolation of potentially new polypeptides is quite unfocussed given its likelihood of isolating compounds of completely unrelated biological function. By complete contrast, the latter situation suffers the exact opposite deficiency in that it enables isolation of only a very limited number of new biologically interesting molecules.

[0019] Thus, a person skilled in the art seeking to isolate potentially new polypeptides of interest by conventional protein separation techniques was confronted with the dilemma of obtaining a hodgepodge of biologically unrelated polypeptides or, alternatively, only a very specific set of polypeptides.

[0020] Another serious shortcoming of conventional techniques for isolation of new polypeptides from a sample relates to the nature of the sample itself. Obviously, there will be a limited number of available polypeptides for isolation and identification in any given biological sample. Furthermore, great care must be taken with such samples to ensure the continued integrity of the biologically active molecules therein.

[0021] Not surprisingly, previous attempts to isolate and characterize new peptides comprising an amidated C-terminal end have followed the conventional approach of starting with a biological sample and choosing from the arsenal of known separation techniques for isolating and identifying the peptides. For example, in U.S. Pat. No. 5,360,727 in the name of Matsuo et al., there was isolated a C-terminal alpha-amidating enzyme of porcine origin by extracting and purifying the enzyme from porcine atrium cords exhibiting the enzyme activity. In U.S. Pat. No. 5,871,995 issued in the name of lida et al., purified enzymes participating in C-terminal amidation were purified from a biological material such as horse serum by affinity chromatography using a peptide C-terminal glycine adduct as a ligand. In U.S. Pat. No. 4,708,934 in the name of Gilligan et al., peptidyl-glycine alpha.-amidating monooxygenase enzyme was extracted from medullary thyroid carcinoma cell lines and tissue samples. Where identification of substantial numbers of new polypeptides capable of amidation is the goal, conventional isolation techniques such as these are completely unsuitable, as they typically permit isolation of only a single polypeptide of interest from a source suspected to contain that polypeptide.

[0022] In PCT/FR98/01767, the assignee of the present application has recently developed a method which overcomes many of disadvantages discussed above in that it enables the rapid identification of a large number of putative peptides which comprise an amidated C-terminal end. In particular, unlike earlier techniques which relied on a particular physical property of the polypeptide to isolate it from a source suspected or known to contain it, the method developed by the assignee relies on a characteristic of the peptide sequence of the precursor of all amidated hormones known to date, thereby allowing simultaneous detection of several new hormones of this category. More particularly, this technique relies on the direct identification of the nucleotide sequence which codes for the precursors in cDNA banks prepared from tissues in which the precursors of these hormones can be synthesized.

[0023] The method of PCT/FR98/01767 permits identification of the precursor of a peptide having an amidated C-terminal end, by the following successive stages:

[0024] 1—Obtaining of a DNA bank;

[0025] 2—Hybridization of one or more oligonucleotides OX with the DNA bank;

[0026] 3—Identification of the DNA sequence or sequences of the bank which hybridizes with an oligonucleotide OX;

[0027] 4—Identification in this sequence or sequences of one or more peptides with a possible amidated C-terminal end.

[0028] OX is a single-stranded oligonucleotide which can hybridize under mild conditions with an oligonucleotide OY of the sequence Y1-Y2-Y3-Y4-Y5, in which Y1 represents a nucleotide sequence of 1 to 12 nucleotides or Y1 is suppressed, Y2 represents a trinucleotide which codes for Gly, Y3 and Y4 independently represent a trinucleotide which codes for Arg or Lys and Y5 represents a nucleotide sequence of 1 to 21 nucleotides or Y5 is suppressed.

[0029] Preferably, the DNA bank is a cDNA bank. A cDNA bank contains the cDNA corresponding to the cytoplasmic mRNA extracted from a given cell. The bank is called complete if it comprises at least one bacterial clone for each starting mRNA. Hybridization takes place if two oligonucleotides have substantially complementary nucleotide sequences, and they can combine over their length by establishing hydrogen bonds between complementary bases.

[0030] The search by this method of PCT/FR98/01767 has been found to be much less restricting than the abovementioned conventional techniques of biochemistry, since:

[0031] it can lead to the isolation of several distinct precursors present in the same tissue by the same principle;

[0032] it allows detection, under the same technical conditions, of precursors corresponding to hormones which have very different biochemical and biological properties;

[0033] it allows concomitant identification of all the peptide hormones which can be contained in the same precursor.

[0034] As a result, the screening technique set forth in PCT/FR98/01767 allows a not insignificant saving in time and money in a sector where the costs of research and development represent a very high proportion of turnover.

[0035] By allowing the obtaining of a large number of potentially therapeutically useful polypeptides, the technique developed allows pharmacological study of active substances having a fundamental physiological roll in the mammalian organism: hormones and more particularly amidated polypeptide neurohormones. Having available for the first time cDNA corresponding to active substances, it is now possible to introduce the cloned vector by genetic engineering to lead to synthesis of hormones having a therapeutic use by means of microorganisms.

[0036] Although giving rise to numerous significant advantages in terms of the ability to rapidly obtain a large number of putative candidate peptide molecules which serve as precursors to peptides comprising an amidated C-terminal end, there are nonetheless still certain difficulties attendant with the use of a cDNA bank for carrying out the screening. As discussed earlier, the cDNA bank typically derives from a single cell and therefore will contain only those polypeptides which are expressed in that cell. This means that even if within the genome of the cell, the screening method will not detect a putative peptide if that peptide is not expressed in that cell. Furthermore, even to the extent that a polypeptide of interest is expressed in the cell, the screening technique is necessarily limited to polypeptides expressed by that particular cell and, indeed, by the particular species of life from which the cell is derived. This makes it difficult to screen for the vast numbers of putative peptides which are of interest.

[0037] Thus, the method of the PCT/FR98/01767 solved a very important restriction in the identification of putative peptides serving as precursors of peptides comprising an amidated C-terminal end. More specifically, while the method of PCT/FR98/01767 certainly provides the means through which to probe a cDNA bank for all possible sequences having the desired post-translational amidation property, it nonetheless was restricted to those cDNAs found in the cDNA bank.

[0038] Recently, there has been an interest in using available databases containing vast numbers of nucleotide sequences in order to, for example, compare a sequence of interest with known sequences.

[0039] For example, in U.S. Pat. No. 5,706,498, there is disclosed a gene database retrieval system for making a retrieval for a gene sequence having a sequence similar to a sequence data from a gene database. The gene database stores the sequence data of genes whose structures or sequences have already been analyzed and identified. The system includes a dynamic programming operation unit for determining the degree of similarity between target data and key data by utilizing the sequence data of the bases of the gene from the gene database as the target data and the sequence data of the bases as the key for retrieval, and a central processing device unit for executing the access process to make access to the gene database, in parallel to the operation process for determining the degree of similarity by transmitting the sequence data of the bases from the gene database continually one after another into the dynamic programming operation unit as the target data, by controlling the gene database and the dynamic programming operation unit.

[0040] U.S. Pat. No. 5,873,082 discloses a sequence database search wherein a homologous sequence of a given sequence is searched from the sequence database and the results outputted in order of higher homology. According to the patent, a plurality of lists having similarities and differences can be effectively compared. In the case of the sequence database search results, a large number of lists including a huge number of sequence names can be quickly compared.

[0041] In U.S. Pat. No. 5,577,249, there is disclosed a method for finding a reference sequence in a database. The most preferred embodiment has specific application to searching the genome of living organisms, in particular the human genome, to find locations and purposes of nucleotide sequences and other biological information that are found on strings of DNA. The method employs human genome databases commercially available which have substrings of the DNA chains broken down into nucleotide token sequences. A unique original index associated with the original DNA string is then created. A reference nucleotide sequence is selected. The reference indexes and original indexes are compared. The method was applied to match reference strings of nucleotides for the genome of E. coliwhich contains approximately 4 million nucleotides.

[0042] U.S. Pat. No. 5,701,256 discloses a method and apparatus for sequence comparisons wherein new proteins sequences are compared with known sequences, such as from a sequence database, typically with a view to determine what level of similarity is shared between the proteins in terms of structural and functional characteristics.

[0043] U.S. Pat. No. 5,523,208 discloses a method for scanning nucleotide or DNA sequence date banks to identify genetic regions or genes coding for biologically interacting proteins. In particular, the method provides a means of scanning data banks consisting of cloned genetic material, including but not limited to DNA, RNA, mRNA, tRNA and nucleotide fragments, to identify the function of genetic material of unknown function. The method, when used on DNA fragments of unknown coding potential will produce a list of gene fragments which code for proteins having the potential to form complexes or multimeric configurations with the unknown protein.

[0044] As the above discussion demonstrates, one of the major applications for computerized methods of searching databases of genetic information is the comparison of a newly found sequence of unknown function with a database of sequences of known function. The goal of such methods of course is to ascertain the function of the unknown protein by relating it to structurally similar proteins of known function. Another application of computerized methods is to find those sequences in a database which are structurally related. Still further methods try to find sequences which form complexes with a known sequence. The focus of all of these methods is generally on comparison of one sequence with another sequence with a view to determining which sequences are structurally similar, rather than determining which genes, from among a large database of genes, possesses a given biological property even where such genes are generally not structurally similar.

Summary and Objects of the Invention

[0045] The present invention has as its primary objective the overcoming of the disadvantages attendant with prior art techniques for identifying biologically interesting molecules from among a large group of candidate molecules. This objective is achieved by providing a method for identifying putative peptides of a given function from among nucleotide or peptide sequences of unknown function by screening a database for the presence of a particular combination of nucleotides or amino acids indicative of the peptides of given function.

[0046] It is a further object of the present invention to provide a method of identifying a putative peptide of a given function which is not limited to those peptides expressed in a particular biological source, for example because the protein is not expressed in that source.

[0047] It is another object of the present invention to provide a method of identifying a putative peptide of a given function which does not depend on physical properties of the peptide, such as isoelectric point or solubility, for the identification.

[0048] Yet another object of the present invention is to provide a method of identifying a putative peptide of a given function which is applicable to proteins which otherwise are biologically unrelated in their physical properties.

[0049] Still another object of the present invention is to provide a method of identifying a putative peptide of a given function from among candidate polypeptides which exhibit a very low degree of homology with each other.

[0050] Another object of the present invention is to provide a method of identifying a putative peptide of a given function which facilitates pharmacological study of active substances having a fundamental physiological role in an organism such as hormones and, more particularly, amidated polypeptide hormones.

[0051] Another object of the present invention is to provide a method of identifying a putative peptide of a given function which can be carried out with available genetic databases and available software.

[0052] Briefly described, these and other objects of the invention are achieved by providing a method for identifying putative peptides of a given function from among nucleotide or peptide sequences of unknown function comprising the steps of:

[0053] (i) obtaining a polynucleotide or polypeptide database;

[0054] (ii) screening said database for the presence of a combination of nucleotides or amino acids indicative of the peptide of given function;

[0055] (ii) identifying the polynucleotide or polypeptide sequences which comprise the combination of nucleotides or amino acids indicative of the peptide of given function.

[0056] In a preferred aspect, the present invention provides a method for identifying a precursor of a peptide comprising an amidated C-terminal end comprising the steps of:

[0057] (i) obtaining a polynucleotide or polypeptide database;

[0058] (ii) screening the database for the presence of a combination of nucleotides or amino acids indicative of the precursor of the peptide comprising the amidated C-terminal end;

[0059] (ii) identifying the polynucleotide or polypeptide sequences which comprise the combination of nucleotides or amino acids indicative of the precursor of the peptide comprising the amidated C-terminal end.

[0060] The database preferably comprises polynucleotide sequences and/or polypeptide sequences corresponding to the polynucleotide sequences and, optionally, accession numbers for the polynucleotide sequences. Where the polypeptide sequences are not available in the data base, they may be obtained by translating the polynucleotide sequences in said database. In a preferred embodiment, three different polypeptide sequences are obtained, corresponding to translation of three different reading frames of said polynucleotide sequences.

[0061] The database may further include annotational information relating to the polypeptide or polynucleotide sequences, such as at least one of origin, source, features and references for the sequences.

[0062] In screening the database, it is preferred to first locate the AUG start codon in a polynucleotide sequence and verify that no stop codon is present between the AUG start codon and the combination of nucleotides indicative of the precursor of the peptide comprising the amidated C-terminal end.

[0063] Once the step of identifying nucleotide or polypeptide sequences has been carried out, the identified sequences can be compared with sequences of known biological function and those identified sequences whose biological function is unknown selected. Alternatively, after the step of identifying nucleotide or polypeptide sequences has been carried out, the similarity of the selected sequences of unknown biological activity can be compared with sequences of known function and, if no similar sequence is found, the sequence of unknown biological activity selected for further investigation. If a similar sequence is found, the sequence of unknown biological activity can be selected as a candidate sequence exhibiting the putative function of the known similar sequence.

[0064] In one embodiment, the identified polypeptide sequence can be obtained and the properties of the polypeptide sequence evaluated.

[0065] The combination of nucleotides preferably comprises the sequence Y1-Y2-Y3-Y4-Y5, in which Y1 is a nucleotide sequence of 1 to 12 nucleotides or is suppressed, Y2 is a codon for Gly, Y3 and Y4 independently are codons for Arg or Lys and Y5 is a nucleotide sequence of 1 to 21 nucleotides or Y5 is suppressed.

[0066] With the foregoing as well as other objects, features and advantages of the invention that will become hereinafter apparent, the nature of the invention may be better understood by reference to the Detailed Description of the Preferred Embodiments and to the appended claims.

Detailed Description of Preferred Embodiments

[0067] By “putative peptides of a given function” is meant polypeptides which include a particular oligonucleotide sequence which is characteristic of a particular function shared by many proteins among a single species and/or among different species. In particular, certain oligonucleotide sequences have been found to be associated with certain types of proteins, such as C-terminal amindated hormones or amylases. The invention is applicable wherever there is an oligonucleotide sequence indicative of such a function.

[0068] By “precursor of a peptide comprising an amidated C-terminal end” is meant any of the precursor proteins which undergo an amidation reaction at the C-terminal end as described, for example, in Bradbury et al.

[0069] By “polynucleotide or polypeptide database” is meant any of the publicly available databases, such as FASTA, GENBANK, PROSITE or SWISS-PROT which typically include polynucleotide and/or polypeptide sequence data. The nucleotide sequence data is available, for example, at EMBL, GENBANK and at other places such as EXPASY. Such data often will also include ACCESSION numbers.

[0070] If the peptide sequences corresponding to a given ACCESSION number are available (e.g., in SWISS-PROT), then this “validated” sequence is included in the database. Otherwise, the nucleotide sequence is preferably translated using programs available in the art such as Translate and/or Back-Translate. The translation is carried out using the data associated with the nucleotide sequence (3′ or 5′ end) and three different reading frames (N, N+1, N+2). If this information is not available, the translation is carried out using both the available nucleotide sequence and its complementary sequence (six putative peptides for a single nucleotide sequence).

[0071] Optionally, such database further includes annotations containing all of the information that is available for a particular sequence, such as ORIGIN, SOURCE, FEATURES, related REFERENCES and COMMENTS associated with the sequence. This facilitates further database mining. An example of the available for annotation is given below:


LOCUS HUMXT00347	239 bp mRNA EST 24-JUN-1992
DEFINITION	Human expressed sequence tag (EST00347 similar to Repeat: CT), mRNA
	sequence.
ACCESSION	M62275
NID	g340398
KEYWORDS	EST; expressed sequence tag.
SOURCE	(library: Stratagene catalog #936205) female 2 yr old
	Hippocampus cDNA to mRNA.
ORGANISM
	Eukaryotae;
	Vertebrata; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE	1 (bases 1 to 239)
AUTHORS	Adams, M. D., Kelley, J. M., Gocayne, J. D., Dubnick, M.,
	Polymeropoulos, M. H., Xiao, H., Wu, A., Olde, B., Moreno, R. F.,
	Kerlavage, A. R., McCombie, W. R. and Venter, J. C.
TITLE	Complementary DNA sequencing: Expressed sequence tags and human
	genome project
JOURNAL	Science 252, 1651-1656 (1991)
MEDLINE	91262645
FEATURES	Location/Qualifiers
source	1.239
	/organism=“
	/db_xref=“taxon:9606”
	/dev_stage=“2 yr old”
	/sex=“female”
	/tissue_type=“Hippocampus”
	/tissue_lib=“Stratagene catalog #936205”
BASE COUNT	36 a 72 c 33 g 97 t 1 others
ORIGIN

[0072] By “combination of nucleotides or amino acids indicative of the precursor of the peptide comprising the amidated C-terminal end” is preferably meant the sequence Y1-Y2-Y3-Y4-Y5, in which Y1 is a nucleotide sequence of 1 to 12 nucleotides or is suppressed, Y2 is a codon for Gly, Y3 and Y4 independently are codons for Arg or Lys and Y5 is a nucleotide sequence of 1 to 21 nucleotides or Y5 is suppressed. The particular combination is set forth in detail in PCT/FR98/01767, the disclosure of which is hereby incorporated by reference.

[0073] In the preferred embodiment, the database to be screened is obtained by running the sql/plus script follows:


-- ============================================================-- Nom de la
base : TGEN

[0074] Obviously, the size of the different ORACLE fields can be adjusted in order to fit the size of the data that is being imported in the tables.

[0075] The SOLOCUS, SODEFINITION, SOACCESSSION, SOORGANISM, SONID, SOKEYWORDS, SOSOURCE, SOREFERENCE, SOCOMMENT, SOFEATURES, SOBASECOUNT, SOSEQUENCE fields in oracle contains respectively the LOCUS, DEFINITION, ACCESSSION, ORGANISM, NID, KEYWORDS, SOURCE, REFERENCE, COMMENT, FEATURES, BASECOUNT , SEQUENCE entries of the genbank data files.

[0076] The SOPHASE contains the reading frame (0, +1, +2) if the peptide sequence is generated using IHB's DNA translator, SOPEPTIDE contains the peptide sequence corresponding to a given SOACCESSION, finally SOPEPTIDEORIGIN tells how the peptide sequence have been obtained (IHB's DNA Translator, GENBANK, SWISS-PROT, . . . ).

[0077] When a FASTA formatted file (see below) is used instead of a GENBANK formatted file, the header line is stored in the SODEFINITION field when we are dealing with a sequence of nucleotides and the nucleotidic sequence itself is stored in the SOSEQUENCE field. If the data being inserted in the database is a peptide sequence then the header line is stored in the SOPEPDEFINITION and the peptidic sequence is stored in the SOPEPTIDE field once again the SOPEPTIDEORIGIN will tell where the peptide sequence comes from (GENBANK, SWISS-PROT, . . . ).

[0078] .gi|402336 (M17352) dnaN protein [Salmonella typhimurium]

[0079] MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGALSLTGTDLEMEMVARVTLSQP SEQ ID NO:8

[0080] >gi|306148 (Li19604) core polypeptide [Heliobacillus mobilis]

[0081] MATADAAFNPRAQVFEWFKDKVPATRGAVLKAHINHLGMVAGFVSFVLVHHLSWLSDQVLFAPTPIFYARLYQLGLDASARSADALMVARLHLPAAIIFWIIGHIKTPREDEFLKNVTFGKTLVAQFHFLALVATLWGMHMAYIGVRGANGGIVPTGLSFDMFGPITGATLAGNHVAFGALLFLGGVFHHFAGFNTKRFAFFEKDWEAVLSVSAQVLAFHFATVVFAMIIWNRPDQPILSFYFMQDYALSNYAAPEIREIASQNPGFLIKQVILGHLVFGVMFWIGGVFHGASLHVRATNDPKLAEALKDFKMLKRCYDHDFQKKFLALIMFGAFLPIFVSYGIATHNTISDLHHLAKAGMFANMTYINIGTPLHDAIFGSHGTVSDFVAAHAIAGGLHFTMVPLWRMVFFSKVSPWTTKVGMKAKRDGEFPCLGPAYGGTCSISLVDQFYLAIFFSLQVIAPAWFYLDGCWMGSFVATSSEVYKQAAELFKANPTWFSLHAVSNFTSEVTSATSSLKPLVCSNTTMVTWFKPCWAAHFIWAFTFSMLFQYRGSRDEGAMVLKWAHEQVGLGFAGKVYNRALSLKEGKAIGTFLFFKMTVLCMWCLAMV SEQ ID NO:9

[0082] >gi|153320 (L05390) hydroxylase [Streptomyces haistedii]

[0083] MNARADRAGDTVHRVPVLVVGGSLVGLSTSVFLGRLGVRHMLVERHAGTSVHPRGRGNNVRTMEVYRAAGVEQGIX. SEQ ID NO:10

[0084] In compiling the database for screening, standard file formats used to store “High Throughput Sequencing” programs and other “Genome” programs (e.g., FASTA, GENBANK) are read and manipulated. Then, the portions of data which are relevant for the screening step, e.g., the annotation data, are identified. The resulting fields are inserted into oracle. If the nucleotide sequence is a 5′ end, the sequence is directly translated into a peptide sequence, if it is a 3′ end, the complementary sequence of the given sequence is generated and is used for translation (the translation phase takes into account the three possible reading frames to generate the peptide sequence). The last step involves the prediction of the secondary structure of the peptide, which is based on information theory and was developed by J. Garnier, D. Osguthorpe, and B. Robson. The software uses all possible pair frequencies within a window of 17 amino acid residues. After cross validation on a data base of 267 proteins, the predication has a mean accuracy of 64.4% for a three state prediction (helix, beta strand, and coil). The program produces two outputs, one giving the sequence and the predicted secondary structure, the other giving the probability values for each secondary structure at each amino acid position. The predicted secondary structure is the one of highest probability compatible with a helix segment of at least four residues and a extended segment (beta strand) of at least two residues.

[0085] Once the relevant data has been assembled in the database, such database can be screened for the presence of a combination of nucleotides or amino acids indicative of the precursor of the peptide comprising the amidated C-terminal end. The purpose of this step of course is to convert the huge amount of unsorted data to a limited set of putative peptides of pharmaceutical interest (potential hormones or hormone fragments, or endogene receptor ligands and the like). The general description of the process is followed by an application to a search of potential amidated peptides in the Expressed Sequence Tags database.

[0086] The general process proceeds as follows:

[0087] retrieve automated sequences from a public source, such as the internet (EMBL, GENBANK, SWISS-PROT, PDB, etc.)

[0088] Analyze file and import data into ORACLE

[0089] Select sequences from a subset (e.g. GENBANK EST) or the entire database

[0090] search for all of the sequences exhibiting a specific motif of interest, such as precursors of a peptide comprising an amidated C-terminal end

[0091] Check that no STOP codon is present in between the AUG codon indicating the beginning of the reading frame and the sought motif;

[0092] Select the sequences of unknown biological function

[0093] Verify that, when found, the motif is an Open Reading Frame (Kozak consensus sequence)

[0094] Compare the environment of the motif location to the one required (e.g., secondary structures required around a maturation site such as the proximity of alpha

[0095] helices or beta-sheets.

[0096] Check for similarity of the sequences and other known sequences (DEFINITION field)

[0097] use threading techniques to search sequences displaying similar secondary structure if no similar structures are defined in the database

[0098] If no similar sequence is found, select the sequence as a synthetic candidate whose function has to be determined

[0099] If similar sequences of known function are found, the sequences can be selected as a synthetic candidate hose putative function is the one of the similar sequence.

[0100] The following examples are given by way of illustration and should in no way be construed as limiting the subject matter disclosed and claimed.

Examples

[0101] Using the method described above, the following peptides were identified and tested:

[0102] (See Table on Following Page)

[0103] The experimental conditions employed are now discussed.

[0104] Binding Assay: Alternative protocol by Skatron

[0105] The experimental conditions are identical throughout the binding assay protocols except that:

[0106] the volume R in operation is 200 μl

[0107] the test is carried out in 96 well Falcon plaques

[0108] the reaction is directly stopped by filtration on filterMat (ref. 11734) Skatron and the radioactivity associated with the filtrate is evaluated:

[0109] either directly with a γ counter for the peptides labelled with iodine 124:

[0110] or with a counter in the presence of 5 mL of scintillating liquid.

[0111] Membrane Preparations of Guinea Pig Brains and Binding Assay

[0112] The guinea pigs are sacrificed by rupturing their cervical vertibrae, decapitated, and the brains are removed very rapidly into a sucrose-Tris-HCl buffer (5 mM, 0.32 M, Tris-HCl, 0.1 g/l bacitracine) at 4° C. (about 10 mL of buffer per brain). The brains are then homogenized with a Potter and the homogenate is placed in incubation 30 minutes at 37° C. under agitation, then centrifuged twice for 35 minutes at 100,000×g at 4° C. The bottoms are placed in suspension in a minimum buffer containing 50 mM Tris-HCl and 5 mM MgCl₂, then are aliquoted and stored in liquid nitrogen. The protein content of the membrane preparations is evaluated according to the method of Bradford (BioRad, according to the manufacturers protocol).

APPENDIX B

SUMMARY OF RESULTS OF COMBINATION

[0113] Bonding of Labelled Agonists to the Guinea Pig Brain Membrane Preparation

[0114] The membranes are placed in a buffer (50 mM Tris-HCl, 5 mM MgCl₂and 0.1 g/l bacitracine to the desired protein concentration (bond of iodized CCK), 0.1 mg of protein/ml; bond of iodized gastrine: 0.5 mg of proteins/ml). They are then incubated in the presence of a labelled ligand in a total volume of 500 μl (about 10 μM for the iodized CCK₈, 20 pM for the iodized gastrine,₃), 50-80 minutes at 25° C., and in the presence or absence of cold agonists. The reaction is stopped with 3 mL of additional BSA buffer (20 g/l) at 4° C., the tubes are centrifuged at 10,000×g, the supernatant is drawn off and the radioactivity associated with the precipitate is evaluated with a gamma counter.

[0115] Bonding of Radiolabelled Agonists to Jurkat T Cells

[0116] Culture Conditions of the Cells of the Jurkat T Human Lymphocytic Line

[0117] The Jurkat cells are cultivated in an RPMI 1640 supplement medium in a fetal veal (10% volume/volume) and antibiotic (50 U/mL of penicillin and 50 μm/mL of streptomycin) serum in a humid incubator at 37° C. under an atmosphere of 5% CO₂in the air.

[0118] Binding Assay

[0119] The cells are obtained by centrifugation (514 g, 5 minutes), then are washed twice in a standard medium containing: 98 mM NaCl; 6 mM Kcl; 2.5 mM NaH₂PO₄; 1.5 mM CaCl₂; 1 mM MgCl₂; 5 mM Na-pyruvate; 5 mM Na-fumarate; 5 mM Na-glutamate; 2 mM glutamine; 11.5 mM glucose; 24.5 mM Hepes (N-[2-hydroxyethyl]piperazine-N′-[2-ethane sulfonic acid]); 0.5 g/l bacitracine; 0.1 g/l Soybean Trypsin Inhibitor, pH 7.4.

[0120] The experiments of the bonds of agonists labelled with iodine 125 (about 50 picomolar) are carried out at 37° C. under agitation for 45-60 minutes in a final volume of 0.5 mL of standard medium containing 2×10⁶cells (4×10⁶cells/mL) and in the presence or absence of competitors. The reaction is stopped by addition of 2 mL of standard buffer at 4° C. supplemented with bovine serum albumin (BSA) (20 g/l), and 10 minutes of centrifugation at 10,000×g at 4° C. The radioactivity associated with the cellular precipitate is quantified with a gamma counter. The non-specific bond is evaluated in the presence of a micromolar concentration of cold homog peptide.

[0121] Membrane Preparations of different Rat Tissues and Organs

[0122] 1) Rats are sacrificed by rupturing their cervical vertebrae, and the different tissues removed and washed several times in a large volume of NaCl 9 per thousand.

[0123] The following steps are carried at 4° C.

[0124] 2) The tissues and organs are transferred, still separately, in a sucrose buffer containing:

[0125] 0.25 M sucrose

[0126] 25 mM TRIS-HCl, pH 7.4.

[0127] 0.2 mM PMSF

[0128] 0.1 mM, 1-10 phenantrolin

[0129] 100 μg/mL STI

[0130] They are then gently cut up with the aid of fine scissors and crushed using an ultraturax apparatus.

[0131] 3) The tissues and organs are finally ground using a Potter apparatus: minimum of ten times in each rotational direction at a minimum of 1000 rpm.

[0132] 4) The ground material is centrifuged at 500 g and for 10 minutes at 4° C. The supernatants are saved, the bottoms put again in the sucrose buffer and centrifuged again under the same conditions.

[0133] 5) The 2 supernatants are then mixed and centrifuged at 100,000×g for 30 minutes at 4° C.

[0134] 6) The supernatants are discarded and the bottoms placed again the the sucrose buffer for centrifuging a second time at 100,000×g for 30 minutes at 4° C.

[0135] 7) The supernatants are discarded, and the bottoms placed again in a binding buffer containing 50 mM TRIS-HCl at pH 7.4 and 5 mM MgCl₂.

[0136] 8) The content of proteins in the membrane suspensions is evaluated using a Bradford determination (Bradford, according to the protocol of the manufacturer). They are aliquoted and stocked in liquid nitrogen at −80° C.

[0137] The studies of the bonds are carried out according to a protocol identical to that used with the membranes of guinea pig brain.

[0138] Studies of the Labelled Agonists on the Hela Cell Line

[0139] The cells are cultivated in a DMEM medium supplemented with 10% fetal veal serum, 0.5% antibiotics (penicillin /streptomycin) and 0.5% glutamine.

[0140] 24˜48 hours before experimentation, the cells are replicated in 24-well laques with approximately 100,000 cells per well and per mL.

[0141] The bonding studies are carried out with a BindH buffer


NaCl	98	mM	5.72 g/l
KCl	6	mM	0.45 g/l
NaH	2.5	mM	0.3 g/l
Na-pyruvate	5	mM	0.55 g/l
Na-fumarate	5	mM	0.58 g/l
Na-glutamate	5	mM	0.84 g/l
CaCl	1.5	mM	0.22 g/l
MgCl	1	mM	0.20 g/l
HEPES	25	mM	6.07 g/l
glucose	11.5	mM	2.07 g/l
glutamine	2	mM	0.22 g/l
STI			0.1 g/l

[0142] For the experiment, the medium is removed and the cells washed twice with 1 mL of buffer. The reaction medium (500 μL) containing the labelled agonist is added into each well in the presence or absence of the cold homolog agonist and the plaques are incubated one hour at 37° C.

[0143] The reaction is stopped by removal of the reaction volume and the wells are rinsed twice with 1 mL of BindH 20% BSA.

[0144] The cells are lysed with 500 μl of 1 N soda for 20 minutes at ambient temperature and the radioactivity associated with the lysate is evaluated with a gamma counter.

[0145] Although only preferred embodiments are specifically disclosed and claimed herein, it will be appreciated that modifications may be made to the preferred embodiments without departing from the spirit and intended scope of the invention.

Claims

What is claimed is:

1. A method for identifying a precursor of a peptide comprising an amidated C-terminal end comprising the steps of:

(i) screening a nucleotide database for the presence of a Y1-Y2-Y3-Y4-Y5 sequence, wherein Y1 is a nucleotide sequence of 1 to 12 nucleotides or is suppressed, Y2 is a codon for Gly, Y3 and Y4 independently are codons for Arg or Lys, and Y5 is a nucleotide sequence of 1 to 21 nucleotides or Y5 is suppressed;

(ii) identifying a polynucleotide sequence that comprises the Y1-Y2-Y3-Y4-Y5 sequence;

(iii) determining a polypeptide encoded by the polynucleotide sequence to identify said precursor of the peptide comprising the amidated C-terminal end.

2. The method of claim 1, wherein said database comprises polynucleotide sequences and accession numbers for said polynucleotide sequences.

3. The method of claim 1, wherein said database comprises both polynucleotide sequences and polypeptide sequences corresponding to said polynucleotide sequences.

4. The method of claim 1, wherein said database further comprises annotational information relating to said polynucleotide sequences.

5. The method of claim 3, wherein said annotational information comprises at least one of origin, source, features and references for said sequences.

6. The method of claim 1, wherein said step of screening said database further comprises the steps of locating the AUG start codon in a polynucleotide sequence and verifying that no stop codon is present between said AUG start codon and the combination of nucleotides indicative of the precursor of the peptide comprising the amidated C-terminal end.

7. The method of claim 1, further comprising the step, after the step of identifying nucleotide sequences, of comparing said identified sequences with sequences of known biological function and selecting those identified sequences whose biological function is unknown.

8. The method of claim 7, further comprising the step of comparing the similarity of the selected sequences of unknown biological activity with sequences of known function and, if no similar sequence is found, selecting said sequence of unknown biological activity for further investigation.

9. The method of claim 7, further comprising the step of comparing the similarity of the selected sequences of unknown biological activity with sequences of known function and, if a similar sequence is found, selecting said sequence of unknown biological activity as a candidate sequence exhibiting the putative function of the known similar sequence.

10. A method for identifying a precursor of a peptide comprising an amidated C-terminal end comprising the steps of:

(i) screening a polypeptide database for the presence of a polypeptide that is encoded by a nucleotide sequence comprising a Y1-Y2-Y3-Y4-Y5 sequence, wherein Y1 is a nucleotide sequence of 1 to 12 nucleotides or is suppressed, Y2 is a codon for Gly, Y3 and Y4 independently are codons for Arg or Lys and Y5 is a nucleotide sequence of 1 to 21 nucleotides or Y5 is suppressed;

(ii) identifying a polypeptide encoded by the nucleotide sequence to identify said precursor of the peptide comprising the amidated C-terminal end,

wherein said step of screening said database further comprises the steps of locating the AUG start codon in a polynucleotide sequence and verifying that no stop codon is present between said AUG start codon and the combination or nucleotides indicative of the precursor of the peptide comprising the amidated C-terminal end.

11. A method for identifying a precursor of a peptide comprising an amidated C-terminal end comprising the steps of:

(i) obtaining a polynucleotide or polypeptide database;

(ii) screening said database for the presence of a combination of nucleotide or amino acids indicative of the precursor of a peptide comprising an amidated C-terminal;

(iii) identifying the polynucleotide or polypeptide sequences which comprise the combination of nucleotides or amino acids indicative of the precursor of a peptide comprising an amidated C-terminal;

wherein said identified polypeptide sequence is SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, or SEQ ID NO: 6.

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Abstract