PMID:18304323 - Revision history

imported>Wikientrybot: change PMID template to TableEdit version

2013-09-15T04:34:05Z

change PMID template to TableEdit version

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	'''~~No author listed~~''' (2008) Protein abundance profiling of the Escherichia coli cytosol. ''BMC Genomics'' '''9''':102		'''Ishihama, Y, Schmidt, T, Rappsilber, J, Mann, M, Hartl, FU, Kerner, MJ and Frishman, D''' (2008) Protein abundance profiling of the Escherichia coli cytosol. ''BMC Genomics'' '''9''':102
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imported>Wikientrybot: change PMID template to TableEdit version

2013-09-01T19:04:10Z

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← Older revision		Revision as of 19:04, 1 September 2013
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	<~~protect~~>		<!--box uid=d41d8cd98f00b204e9800998ecf8427e.166469.Y52238faa45bdc-->
	<~~span style = 'font~~-~~size: large'> ''~~'~~Ishihama, Y, Schmidt,~~ T~~, Rappsilber, J, Mann, M, Hartl, FU, Kerner, MJ and Frishman, D'''~~ ~~(2008) Protein abundance profiling of~~ the ~~Escherichia coli cytosol~~.~~''BMC Genomics'' '''9''':102</span~~>		<!--
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	\|~~{{TableHeadingColor}}~~ \|'''~~Abstract~~''' ~~\|\| <protect>BACKGROUND: Knowledge about the~~ abundance of molecular components is an important prerequisite for building quantitative predictive models of cellular behavior. Proteins are central components of these models, since they carry out most of the fundamental processes in the cell. Thus far, protein concentrations have been difficult to measure on a large scale, but proteomic technologies have now advanced to a stage where this information becomes readily accessible. RESULTS: Here, we describe an experimental scheme to maximize the coverage of proteins identified by mass spectrometry of a complex biological sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli ~~strain MC4100~~. A measure of abundance is presented for each of the identified proteins, based on the recently developed emPAI approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell.As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal proteins. Proteins involved in energy metabolism as well as those with binding function were also found in high copy number while proteins annotated with the terms metabolism, transcription, transport, and cellular organization were rare. The barrel-sandwich fold was found to be the structural fold with the highest abundance. Highly abundant proteins are predicted to be less prone to aggregation based on their length, pI values, and occurrence patterns of hydrophobic stretches. We also find that abundant proteins tend to be predominantly essential. Additionally we observe a significant correlation between protein and mRNA abundance in E. coli cells. CONCLUSION: Abundance measurements for more than 1000 E. coli proteins presented in this work represent the most complete study of protein abundance in a bacterial cell so far. We show significant associations between the abundance of a protein and its properties and functions in the cell. In this way, we provide both data and novel insights into the role of protein concentration in this model organism.</protect>		!align=left \|Citation
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			'''No author listed''' (2008) Protein abundance profiling of the Escherichia coli cytosol. ''BMC Genomics'' '''9''':102
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	\|~~{{TableHeadingColor}} nowrap~~ \|~~'''~~Links~~'''~~ \|\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18304323 PubMed]~~<br~~/>Online version:[http://dx.doi.org/10.1186/1471-2164-9-102 10.1186/1471-2164-9-102]		!align=left \|Abstract
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			Knowledge about the abundance of molecular components is an important prerequisite for building quantitative predictive models of cellular behavior. Proteins are central components of these models, since they carry out most of the fundamental processes in the cell. Thus far, protein concentrations have been difficult to measure on a large scale, but proteomic technologies have now advanced to a stage where this information becomes readily accessible.
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			[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18304323 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2292177 PMC2292177]
			Online version:[http://dx.doi.org/10.1186/1471-2164-9-102 10.1186/1471-2164-9-102]
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			!align=left \|Keywords
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			Chromatography, Liquid/methods; Cytosol/metabolism; Escherichia coli/metabolism; Escherichia coli Proteins/analysis; Mass Spectrometry/methods; Proteomics/methods

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	==Significance {{HelpIcon\|Help:Literature}} ==		==Significance {{HelpIcon\|Help:Literature}} ==
	{{LitSignificance}}		{{LitSignificance}}

127.0.0.1: /Volumes/r3/t3/ul/working/touchTables/touch_all_tables.php

2010-06-17T20:42:19Z

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127.0.0.1: Update TableEdit tables.

2010-01-09T04:33:51Z

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JimHu: /* References */

2009-10-12T23:59:47Z

References

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			[[Category:E. coli proteomics]]

JimHu: Fill PMID: Page!

2009-10-12T23:59:34Z

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		<span style = 'font-size: large'> '''Ishihama, Y, Schmidt, T, Rappsilber, J, Mann, M, Hartl, FU, Kerner, MJ and Frishman, D''' (2008) Protein abundance profiling of the Escherichia coli cytosol.''BMC Genomics'' '''9''':102</span>

		{\|{{Prettytable}} align = 'center' width= '70%'
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		\|{{TableHeadingColor}} \|'''Abstract''' \|\| <protect>BACKGROUND: Knowledge about the abundance of molecular components is an important prerequisite for building quantitative predictive models of cellular behavior. Proteins are central components of these models, since they carry out most of the fundamental processes in the cell. Thus far, protein concentrations have been difficult to measure on a large scale, but proteomic technologies have now advanced to a stage where this information becomes readily accessible. RESULTS: Here, we describe an experimental scheme to maximize the coverage of proteins identified by mass spectrometry of a complex biological sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins, based on the recently developed emPAI approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell.As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal proteins. Proteins involved in energy metabolism as well as those with binding function were also found in high copy number while proteins annotated with the terms metabolism, transcription, transport, and cellular organization were rare. The barrel-sandwich fold was found to be the structural fold with the highest abundance. Highly abundant proteins are predicted to be less prone to aggregation based on their length, pI values, and occurrence patterns of hydrophobic stretches. We also find that abundant proteins tend to be predominantly essential. Additionally we observe a significant correlation between protein and mRNA abundance in E. coli cells. CONCLUSION: Abundance measurements for more than 1000 E. coli proteins presented in this work represent the most complete study of protein abundance in a bacterial cell so far. We show significant associations between the abundance of a protein and its properties and functions in the cell. In this way, we provide both data and novel insights into the role of protein concentration in this model organism.</protect>
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		\|{{TableHeadingColor}} nowrap \|'''Links''' \|\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18304323 PubMed]<br/>Online version:[http://dx.doi.org/10.1186/1471-2164-9-102 10.1186/1471-2164-9-102]
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		</protect>
		==Significance {{HelpIcon\|Help:Literature}} ==
		{{LitSignificance}}

		== Useful Materials and Methods {{HelpIcon\|Help:Literature}}==
		{{LitMaterials}}

		==Annotations {{HelpIcon\|Help:Literature}}==
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		==EcoliWiki Links {{HelpIcon\|Help:Literature}} ==
		{{LitLinks}}

		==See also==

		==References==
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JimHu: New PMID: Page!

2009-10-12T23:59:34Z

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