Cross-species characterisation of abundantly expressedOchrobactrum anthropi gene products

Wasinger, Valerie C.; Urquhart, Brooke L.; Humphery‐Smith, Ian

doi:10.1002/(sici)1522-2683(19990801)20:11<2196::aid-elps2196>3.0.co;2-v

Cited by 14 publications

(9 citation statements)

References 45 publications

(24 reference statements)

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“…Since the genome of the investigated yeast is not yet available, the protein sequences of this organism are still unknown. Consequently, cross-species identifications are imperative as it has been already suggested and accomplished for other organisms [15,29,30]. As S. cerevisiae is considered as the model yeast, we used the protein sequences from this yeast to identify proteins extracted from industrial strain.…”

Section: Resultsmentioning

confidence: 99%

“…Cross-species identifications of proteins with MS (MALDI-TOF) or protein sequence comparisons have already been carried out to study other organisms [29,30,[41][42][43][44]. A theoretical approach of protein cross-species identifications has been previously published [45].…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, better results have been obtained by combining these both methods (60%). This combined approach has been successfully used to identify 45 2-D gel-separated proteins extracted from Ochrobacterium anthropi [29]. Nevertheless, protein identifications based on either the first or either the second analytical technique have been also reported [30,43,44].…”

Section: Discussionmentioning

confidence: 99%

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Identification by mass spectrometry of two-dimensional gel electrophoresis-separated proteins extracted from lager brewing yeast

Jouber¹,

Strub

Zugmeyer³

et al. 2001

Electrophoresis

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As two-dimensional (2-D) electrophoresis allows the separation of several hundred proteins in a single gel, this technique has become an important tool for proteome studies and for investigating the cellular physiology. In order to take advantage of information provided by the comparison of proteome pictures, the mass spectrometry technique is the way chosen for a rapid and an accurate identification of proteins of interest. Unfortunately, in the case of industrial yeasts, due to the high level of complexity of their genome, the whole DNA sequence is not yet available and all encoded protein sequences are still unknown. Nevertheless, this study presents here 30 lager brewing yeast proteins newly identified with matrix assisted laser desorption/ionization-time of flight (MALDI-TOF), tandem mass spectrometry (MS/MS) and database searching against the protein sequences of Saccharomyces cerevisiae. The identified proteins of the industrial strain correspond to proteins which do not comigrate with known proteins of S. cerevisiae separated on 2-D gels. This study presents an application of the MS technique for the identification of industrial yeast proteins which are only homologous to the corresponding S. cerevisiae proteins.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Identification by mass spectrometry of two-dimensional gel electrophoresis-separated proteins extracted from lager brewing yeast

Jouber¹,

Strub

Zugmeyer³

et al. 2001

Electrophoresis

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show abstract

“…It was suggested that this observation reflected the larger size of the S. melliferum genome [24]. A similar approach employing combined amino acid composition analysis and peptide mass mapping was used to characterise the proteome of Ochrabacterum anthropi [25]. Although only 45 of the resolved proteins from O. anthropi were identified, a large percentage of the orthologues were related to genes previously characterised in the related Rhizobiaceae.…”

Section: Linking the Proteome And Genomementioning

confidence: 99%

Proteomics in medical microbiology

Cash

2000

Electrophoresis

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“…This approach can be successfully applied for organisms the genomes of which are fully sequenced and annotated, or for proteins having sequences well-conserved for cross-species identification. Otherwise, additional information such as amino acid sequences is often needed for an unambiguous identification [1,3,10,17-19]. Therefore, systematic identification of protein expressions of an organism can be greatly enhanced with genome sequence data.…”

Section: Introductionmentioning

confidence: 99%

Untitled

et al. 2003

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Separation of proteins by two-dimensional gel electrophoresis (2-DE) coupled with identification of proteins through peptide mass fingerprinting (PMF) by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is the widely used technique for proteomic analysis. This approach relies, however, on the presence of the proteins studied in public-accessible protein databases or the availability of annotated genome sequences of an organism. In this work, we investigated the reliability of using raw genome sequences for identifying proteins by PMF without the need of additional information such as amino acid sequences. The method is demonstrated for proteomic analysis of Klebsiella pneumoniae grown anaerobically on glycerol. For 197 spots excised from 2-DE gels and submitted for mass spectrometric analysis 164 spots were clearly identified as 122 individual proteins. 95% of the 164 spots can be successfully identified merely by using peptide mass fingerprints and a strain-specific protein database (ProtKpn) constructed from the raw genome sequences of K. pneumoniae. Cross-species protein searching in the public databases mainly resulted in the identification of 57% of the 66 high expressed protein spots in comparison to 97% by using the ProtKpn database. 10 dha regulon related proteins that are essential for the initial enzymatic steps of anaerobic glycerol metabolism were successfully identified using the ProtKpn database, whereas none of them could be identified by cross-species searching. In conclusion, the use of strain-specific protein database constructed from raw genome sequences makes it possible to reliably identify most of the proteins from 2-DE analysis simply through peptide mass fingerprinting.

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Cross-species characterisation of abundantly expressedOchrobactrum anthropi gene products

Cited by 14 publications

References 45 publications

Identification by mass spectrometry of two-dimensional gel electrophoresis-separated proteins extracted from lager brewing yeast

Identification by mass spectrometry of two-dimensional gel electrophoresis-separated proteins extracted from lager brewing yeast

Proteomics in medical microbiology

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