Protein abundance profiling of the Escherichia coli cytosol

Ishihama, Yasushi; Schmidt, Thorsten; Rappsilber, Juri; Mann, Matthias; Hartl, F. Ulrich; Kerner, Michael; Frishman, Dmitrij

doi:10.1186/1471-2164-9-102

Cited by 436 publications

(502 citation statements)

References 70 publications

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“…However, many of the individual peaks that form a MALDI-TOF mass spectrum correspond to ribosomal proteins (RPs), which are encoded by more than 50 genes scattered in mostly chromosomal loci. RPs are ubiquitous and among the most abundant cytosolic proteins, regardless of the cell life stage or growth conditions (Ishihama et al 2008), and have masses mostly within the 4 to 30 kDa range that is examined with MALDI-TOF MS. Ribosomal multilocus sequence typing (rMLST) has been shown to be consistent with current bacterial nomenclature schemes and to provide accurate phylogenies for diverse taxonomic groups (Jolley et al 2012;Maiden et al 2013;Yutin et al 2012). These characteristics make RPs reliable biomarkers in MALDI-TOF MS analyses to obtain species and subspecies identification of diverse bacteria including bifidobacteria (Sato et al 2011), lactobacilli Teramoto et al 2007a), rhodococci (Teramoto et al 2009), members of the Sphingomonadaceae , and strains of Staphylococcus aureus (Josten et al 2013) and Neisseria meningitidis (Suarez et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Ziegler

Pothier

Ardley

et al. 2015

Appl Microbiol Biotechnol

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Accurate identification of soil bacteria that form nitrogen-fixing associations with legume crops is challenging given the phylogenetic diversity of root nodule bacteria (RNB). The labor-intensive and time-consuming 16S ribosomal RNA (rRNA) sequencing and/or multilocus sequence analysis (MLSA) of conserved genes so far remain the favored molecular tools to characterize symbiotic bacteria. With the development of mass spectrometry (MS) as an alternative method to rapidly identify bacterial isolates, we recently showed that matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) can accurately characterize RNB found inside plant nodules or grown in cultures. Here, we report on the development of a MALDI-TOF RNB-specific spectral database built on whole cell MS fingerprints of 116 strains representing the major rhizobial genera. In addition to this RNB-specific module, which was successfully tested on unknown field isolates, a subset of 13 ribosomal proteins extracted from genome data was found to be sufficient for the reliable identification of nodule isolates to rhizobial species as shown in the putatively ascribed ribosomal protein masses (PARPM) database. These results reveal that data gathered from genome sequences can be used to expand spectral libraries to aid the accurate identification of bacterial species by MALDI-TOF MS.

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Section: Introductionmentioning

confidence: 99%

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Ziegler

Pothier

Ardley

et al. 2015

Appl Microbiol Biotechnol

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“…Biochemical reactions proceed in sub-micron compartments where the total number of molecules is in the range of one to several thousand 3,4 , and intrinsic noise is hence expected to have an important functional role in biochemical circuits 5 . Biological systems are also subjected to extrinsic noise originating outside the immediate system of interest.…”

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confidence: 99%

Discreteness-induced concentration inversion in mesoscopic chemical systems

et al. 2012

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molecular discreteness is apparent in small-volume chemical systems, such as biological cells, leading to stochastic kinetics. Here we present a theoretical framework to understand the effects of discreteness on the steady state of a monostable chemical reaction network. We consider independent realizations of the same chemical system in compartments of different volumes. Rate equations ignore molecular discreteness and predict the same average steadystate concentrations in all compartments. However, our theory predicts that the average steady state of the system varies with volume: if a species is more abundant than another for large volumes, then the reverse occurs for volumes below a critical value, leading to a concentration inversion effect. The addition of extrinsic noise increases the size of the critical volume. We theoretically predict the critical volumes and verify, by exact stochastic simulations, that rate equations are qualitatively incorrect in sub-critical volumes.

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“…Les kits commerciaux permettent de produire 1 mg/ml de protéines dans un tube à essai en quelques heures, ce qui correspond à une concentration de 30 μm de protéine comme l'eGFP (enhanced green fluorescent protein). La concentration moyenne de protéines cytoplasmiques chez E. coli est d'environ 0,5 μm [45]. Par conséquent, une cinquantaine de gènes peuvent être exprimés avec ces kits à des concentrations pertinentes biologiquement.…”

Section: Les Systèmes Acellulaires D'expression Comme Plateforme Expéunclassified

Construction de cellules synthétiques

Noireaux

2015

Med Sci (Paris)

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Protein abundance profiling of the Escherichia coli cytosol

Cited by 436 publications

References 70 publications

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Discreteness-induced concentration inversion in mesoscopic chemical systems

Construction de cellules synthétiques

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