Quantification of mRNA and protein and integration with protein turnover in a bacterium

Maier, Tobias; Schmidt, Alexander; Güell, Marc; Kühner, Sebastian; Gavin, Anne‐Claude; Aebersold, Ruedi; Serrano, Luís

doi:10.1038/msb.2011.38

Cited by 263 publications

(318 citation statements)

References 55 publications

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“…Both coefficients were used in previous studies to calculate mRNAprotein relationships (for review, see Maier et al, 2009;Vogel and Marcotte, 2012). In general, the relationship between mRNA and protein abundance is considered positive in a wide range of organisms but varies greatly between the studies (yeast [Lee et al, 2011], bacteria [Maier et al, 2011], maize endosperm and embryos [Walley et al, 2013], and maize leaf sections [Ponnala et al, 2014]). Variations in mRNAprotein correlation might be explained by many factors, such as bias in RNA and protein stability and movement, experimental measurement, and quantification methods (Ponnala et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes

et al. 2015

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A high-resolution proteome and phosphoproteome atlas of four maize (Zea mays) primary root tissues, the cortex, stele, meristematic zone, and elongation zone, was generated. High-performance liquid chromatography coupled with tandem mass spectrometry identified 11,552 distinct nonmodified and 2,852 phosphorylated proteins across the four root tissues. Two gradients reflecting the abundance of functional protein classes along the longitudinal root axis were observed. While the classes RNA, DNA, and protein peaked in the meristematic zone, cell wall, lipid metabolism, stress, transport, and secondary metabolism culminated in the differentiation zone. Functional specialization of tissues is underscored by six of 10 cortex-specific proteins involved in flavonoid biosynthesis. Comparison of this data set with high-resolution seed and leaf proteome studies revealed 13% (1,504/11,552) root-specific proteins. While only 23% of the 1,504 root-specific proteins accumulated in all four root tissues, 61% of all 11,552 identified proteins accumulated in all four root tissues. This suggests a much higher degree of tissue-specific functionalization of root-specific proteins. In summary, these data illustrate the remarkable plasticity of the proteomic landscape of maize primary roots and thus provide a starting point for gaining a better understanding of their tissue-specific functions.

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Section: Discussionmentioning

confidence: 99%

A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes

et al. 2015

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“…Proteomics studies from various organisms have shown a very poor, slightly positive correlation between mRNA levels and protein abundance (Taniguchi et al, 2010;Maier et al, 2011;Schwanhäusser et al, 2011;Vogel and Marcotte, 2012). Additionally, it is clear that many proteins are under posttranslational control, and we do not currently know to what extent posttranslational modifications (such as phosphorylation) play a role in UPS-mediated processes in plants.…”

Section: Future Directionsmentioning

confidence: 99%

Ubiquitin-Mediated Control of Plant Hormone Signaling

2012

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“…Transcriptomics and proteomics technologies both provide important and complementary insights: The former allow researchers to generate global quantitative gene expression profiles and to study gene regulatory aspects like the impact of short RNAs. However, due to the varying correlation of transcriptomics and proteomics data reported in the literature (de Godoy et al 2008;de Sousa Abreu et al 2009;Maier et al 2011;Marguerat et al 2012), the direct measurement of protein expression levels is often desirable. For certain aspects, proteomics data can provide more informative and accurate data, as it reflects the effects of other important regulatory processes like protein translation rates and protein stability (Schwanhausser et al 2011).…”

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confidence: 99%

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

et al. 2013

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Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant, and membrane localized, we could eliminate their initial underrepresentation compared to the estimated endpoint. A total of 1250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and 90% of the expressed protein-coding genes. Genes that were detected at the transcript but not protein level, were found to be highly enriched in several genomic islands. Furthermore, genes that lacked an ortholog and a functional annotation were not detected at the protein level; these may represent examples of overprediction in genome annotations. A dramatic membrane proteome reorganization was observed, including differential regulation of autotransporters, adhesins, and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage, which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.

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Quantification of mRNA and protein and integration with protein turnover in a bacterium

Abstract: Determination of the average cellular copy number of 400 proteins under different growth conditions and integration with protein turnover and absolute mRNA levels reveals the dynamics of protein expression in the genome-reduced bacterium Mycoplasma pneumoniae.

Cited by 263 publications

References 55 publications

A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes

A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes

Ubiquitin-Mediated Control of Plant Hormone Signaling

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

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