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Evidence for existence of thirty hypothetical proteins in rat brain.

Shin JH, Yang JW, Juranville JF, Fountoulakis M, Lubec G - Proteome Sci (2004)

Bottom Line: RESULTS: We constructed a two-dimensional protein map and searched for expression of hypothetical proteins in rat brain.A number of hypothetical gene products were detected (30 of 190, 15.8%) and are considered brain proteins.CONCLUSIONS: A major finding of this study is the demonstration of the existence of putative proteins that were so far only deduced from their nucleic acid structure by a protein chemical method independent of antibody availability and specificity and unambiguously identifying proteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pediatrics, University of Vienna, Vienna, Austria. gert.lubec@akh-wien.ac.at

ABSTRACT
BACKGROUND: The rapid completion of genome sequences has created an infrastructure of biological information and provided essential information to link genes to gene products, proteins, the building blocks for cellular functions. In addition, genome/cDNA sequences make it possible to predict proteins for which there is no experimental evidence. Clues for function of hypothetical proteins are provided by sequence similarity with proteins of known function in model organisms. RESULTS: We constructed a two-dimensional protein map and searched for expression of hypothetical proteins in rat brain. Two-dimensional electrophoresis (2-DE) with subsequent in-gel digestion of spots and matrix-assisted laser desorption/ionization (MALDI) spectrometric identification were applied. In total about 3700 spots were analysed, which resulted in the identification of about 1700 polypeptides, that were the products of 190 different genes. A number of hypothetical gene products were detected (30 of 190, 15.8%) and are considered brain proteins. CONCLUSIONS: A major finding of this study is the demonstration of the existence of putative proteins that were so far only deduced from their nucleic acid structure by a protein chemical method independent of antibody availability and specificity and unambiguously identifying proteins.

No MeSH data available.


Related in: MedlinePlus

Alignment of 1700082C19Rik protein (Q9D9F6) with homologs. Alignments were constructed using the CLUSTALW program . Multiple sequence alignment with CLUSTALW showed that 1700082C19Rik protein has 97.4% similarity to N-termial region of inner membrane, mitochondrial (IMMT_MOUSE, Q8CAQ8), 93.8% similarity to N-terminal region of IMMT_HUMAN (Q16891), and 34.9% similarity to N-terminal region of IMMT_DROME (Q91928).
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Figure 3: Alignment of 1700082C19Rik protein (Q9D9F6) with homologs. Alignments were constructed using the CLUSTALW program . Multiple sequence alignment with CLUSTALW showed that 1700082C19Rik protein has 97.4% similarity to N-termial region of inner membrane, mitochondrial (IMMT_MOUSE, Q8CAQ8), 93.8% similarity to N-terminal region of IMMT_HUMAN (Q16891), and 34.9% similarity to N-terminal region of IMMT_DROME (Q91928).

Mentions: Most nucleic acid sequences of hypothetical proteins were directly submitted to the GenBank/EMBL/DDBJ database. Based on the assumption that sequence-domain similarities reflect functional relationship, it may be predicted how hypothetical proteins play a role in biological mechanism. The sequences of hypothetical proteins were submitted to BLAST search. Putative conserved domains and identity to know protein were obtained by sequence similarity (Conserved Domain Database, ) (Table 1 – see additional file 1). A hypothetical protein showing one or more significant structural homologs, is predicted to have molecular properties similar to the homologs. Putative cellular localisations of hypothetical proteins were investigated by PSORT II using of k-nearest neighbour (k-NN) algorithm for assessing the probability of localising at each candidate sites. Hypothetical proteins may be localised in cytoplasm (16 of 30, 53.3 %), mitochondria (9 of 30, 30 %) and nuclear (5 of 30, 16.7 %) (data not shown). Hypothetical proteins were divided into several groups by putative function (Table 1 – see additional file 1). For five hypothetical proteins ("Unknown" in Table 1), poor information on predicted domains and function was available in data banks including SWISS-PROT database. Therefore, we performed BLAST search (NCBI, ) that predicted domains of two proteins, Homo sapiens sequence 42 from patent wo0222660 and Homo sapiens sequence 33 from patent wo0218424 (Fig 2). Homo sapiens sequence 42 from patent wo0222660 (CAD34734) was detected in 2-DE gels as two spots with different pI, probably reflecting PTMs or isoforms (Fig. 1). This protein has 455 amino acid residues according to patent cDNA sequence (HYSEQ. INC, USA) and belongs to TufB family (Fig 2). Homo sapiens sequence 33 from patent wo0218424 (CAD33306) was resolved as four spot (Fig. 1) and consists of 429 amino acid residues. The protein has never been described in literature and is categorised as GTP/CDC (guanosine triphosphate/cell division control) family including CDC 3, CDC 10, CDC 11, CDC 12/Septin and some uncharacterised proteins involved in cytokinesis (Fig 2). Although members of this family are involved in cell division and bind GTP, biological roles of these proteins are unclear. To predict the function of 5730568A12Rik protein, 1700082C19Rik protein, and 1700021B03Rik protein, we searched for homologs of these proteins through bioinformatic tools (ProteinPredict, ) and performed the CLUSTALW multiple sequence alignments. The homologs of 5730568A12Rik protein (Q9CXS1) were identified from C. elegans (Q23344, hypothetical 34.0 kDa protein, putative serine/threonine protein phosphatase) to H. sapiens (Q96ER9, similar to 5730568A12Rik protein) and this finding suggests that 5730568A12Rik protein may play an important role in cell biology (data not shown). However, the putative function of 5730568A12Rik protein is still unknown. According to BLAST searching results, 1700082C19Rik protein (Q9D9F6) shows high homology with mitochondrial inner membrane protein (Fig 3) and 1700021B03Rik protein (Q9DA45) belongs to DUF 737 family containing uncharacterised protein.


Evidence for existence of thirty hypothetical proteins in rat brain.

Shin JH, Yang JW, Juranville JF, Fountoulakis M, Lubec G - Proteome Sci (2004)

Alignment of 1700082C19Rik protein (Q9D9F6) with homologs. Alignments were constructed using the CLUSTALW program . Multiple sequence alignment with CLUSTALW showed that 1700082C19Rik protein has 97.4% similarity to N-termial region of inner membrane, mitochondrial (IMMT_MOUSE, Q8CAQ8), 93.8% similarity to N-terminal region of IMMT_HUMAN (Q16891), and 34.9% similarity to N-terminal region of IMMT_DROME (Q91928).
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Related In: Results  -  Collection

Show All Figures
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Figure 3: Alignment of 1700082C19Rik protein (Q9D9F6) with homologs. Alignments were constructed using the CLUSTALW program . Multiple sequence alignment with CLUSTALW showed that 1700082C19Rik protein has 97.4% similarity to N-termial region of inner membrane, mitochondrial (IMMT_MOUSE, Q8CAQ8), 93.8% similarity to N-terminal region of IMMT_HUMAN (Q16891), and 34.9% similarity to N-terminal region of IMMT_DROME (Q91928).
Mentions: Most nucleic acid sequences of hypothetical proteins were directly submitted to the GenBank/EMBL/DDBJ database. Based on the assumption that sequence-domain similarities reflect functional relationship, it may be predicted how hypothetical proteins play a role in biological mechanism. The sequences of hypothetical proteins were submitted to BLAST search. Putative conserved domains and identity to know protein were obtained by sequence similarity (Conserved Domain Database, ) (Table 1 – see additional file 1). A hypothetical protein showing one or more significant structural homologs, is predicted to have molecular properties similar to the homologs. Putative cellular localisations of hypothetical proteins were investigated by PSORT II using of k-nearest neighbour (k-NN) algorithm for assessing the probability of localising at each candidate sites. Hypothetical proteins may be localised in cytoplasm (16 of 30, 53.3 %), mitochondria (9 of 30, 30 %) and nuclear (5 of 30, 16.7 %) (data not shown). Hypothetical proteins were divided into several groups by putative function (Table 1 – see additional file 1). For five hypothetical proteins ("Unknown" in Table 1), poor information on predicted domains and function was available in data banks including SWISS-PROT database. Therefore, we performed BLAST search (NCBI, ) that predicted domains of two proteins, Homo sapiens sequence 42 from patent wo0222660 and Homo sapiens sequence 33 from patent wo0218424 (Fig 2). Homo sapiens sequence 42 from patent wo0222660 (CAD34734) was detected in 2-DE gels as two spots with different pI, probably reflecting PTMs or isoforms (Fig. 1). This protein has 455 amino acid residues according to patent cDNA sequence (HYSEQ. INC, USA) and belongs to TufB family (Fig 2). Homo sapiens sequence 33 from patent wo0218424 (CAD33306) was resolved as four spot (Fig. 1) and consists of 429 amino acid residues. The protein has never been described in literature and is categorised as GTP/CDC (guanosine triphosphate/cell division control) family including CDC 3, CDC 10, CDC 11, CDC 12/Septin and some uncharacterised proteins involved in cytokinesis (Fig 2). Although members of this family are involved in cell division and bind GTP, biological roles of these proteins are unclear. To predict the function of 5730568A12Rik protein, 1700082C19Rik protein, and 1700021B03Rik protein, we searched for homologs of these proteins through bioinformatic tools (ProteinPredict, ) and performed the CLUSTALW multiple sequence alignments. The homologs of 5730568A12Rik protein (Q9CXS1) were identified from C. elegans (Q23344, hypothetical 34.0 kDa protein, putative serine/threonine protein phosphatase) to H. sapiens (Q96ER9, similar to 5730568A12Rik protein) and this finding suggests that 5730568A12Rik protein may play an important role in cell biology (data not shown). However, the putative function of 5730568A12Rik protein is still unknown. According to BLAST searching results, 1700082C19Rik protein (Q9D9F6) shows high homology with mitochondrial inner membrane protein (Fig 3) and 1700021B03Rik protein (Q9DA45) belongs to DUF 737 family containing uncharacterised protein.

Bottom Line: RESULTS: We constructed a two-dimensional protein map and searched for expression of hypothetical proteins in rat brain.A number of hypothetical gene products were detected (30 of 190, 15.8%) and are considered brain proteins.CONCLUSIONS: A major finding of this study is the demonstration of the existence of putative proteins that were so far only deduced from their nucleic acid structure by a protein chemical method independent of antibody availability and specificity and unambiguously identifying proteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pediatrics, University of Vienna, Vienna, Austria. gert.lubec@akh-wien.ac.at

ABSTRACT
BACKGROUND: The rapid completion of genome sequences has created an infrastructure of biological information and provided essential information to link genes to gene products, proteins, the building blocks for cellular functions. In addition, genome/cDNA sequences make it possible to predict proteins for which there is no experimental evidence. Clues for function of hypothetical proteins are provided by sequence similarity with proteins of known function in model organisms. RESULTS: We constructed a two-dimensional protein map and searched for expression of hypothetical proteins in rat brain. Two-dimensional electrophoresis (2-DE) with subsequent in-gel digestion of spots and matrix-assisted laser desorption/ionization (MALDI) spectrometric identification were applied. In total about 3700 spots were analysed, which resulted in the identification of about 1700 polypeptides, that were the products of 190 different genes. A number of hypothetical gene products were detected (30 of 190, 15.8%) and are considered brain proteins. CONCLUSIONS: A major finding of this study is the demonstration of the existence of putative proteins that were so far only deduced from their nucleic acid structure by a protein chemical method independent of antibody availability and specificity and unambiguously identifying proteins.

No MeSH data available.


Related in: MedlinePlus