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A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus.

ABSTRACT: Ribosomes from the Gram-negative alpha-proteobacterium Caulobacter crescentus were isolated using standard methods. Proteins were separated using a two-dimensional liquid chromatographic system that allowed the analysis of whole proteins by direct coupling to an ESI-QTOF mass spectrometer and of proteolytic digests by a number of mass spectrometric methods. The masses of 53 of 54 ribosomal proteins were directly measured. Protein identifications and proposed post-translational modifications were supported by proteolysis with trypsin, endoprotease Glu-C, and exoproteases carboxypeptidases Y and P. Tryptic peptide mass maps show an average sequence coverage of 62%, and carboxypeptidase C-terminal sequence tagging provided unambiguous identification of the small, highly basic proteins of the large subunit. C. crescentus presents some post-translational modifications that are similar to those of Escherichia coli (e.g., N-terminal acetylation of S9 and S18) along with some unique variations, such as a near absence of L7 and extensive modification of L11. The comprehensive description of this organism's ribosomal proteome provides a foundation for the study of ribosome structure, dependence of post-translational modifications on growth conditions, and the evolution of subcellular organelles.

SUBMITTER: Running WE

PROVIDER: S-EPMC2536757 | biostudies-literature | 2007 Jan

REPOSITORIES: biostudies-literature

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A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus.

Running William E WE Ravipaty Shobha S Karty Jonathan A JA Reilly James P JP

Journal of proteome research 20070101 1

Ribosomes from the Gram-negative alpha-proteobacterium Caulobacter crescentus were isolated using standard methods. Proteins were separated using a two-dimensional liquid chromatographic system that allowed the analysis of whole proteins by direct coupling to an ESI-QTOF mass spectrometer and of proteolytic digests by a number of mass spectrometric methods. The masses of 53 of 54 ribosomal proteins were directly measured. Protein identifications and proposed post-translational modifications were ...[more]

PMID: 17203977

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Project description:Wetland habitats are changing under multiple anthropogenic pressures. Nutrient leakage and pollution modify physico-chemical state of wetlands and affect the ecosystem through bottom-up processes, while alien predators affect the ecosystems in a top-down manner. Boreal wetlands are important breeding areas for several waterbird species, the abundances of which potentially reflect both bottom-up and top-down ecosystem processes. Here, we use long-term national monitoring data gathered from c. 130 waterbird breeding sites in Finland from the 1980s to the 2020s. We hypothesised that the physico-chemical state of the waters and increasing alien predator abundance both play a role in steering the waterbird population trends. We set out to test this hypothesis by relating population changes of 17 waterbird species to changes in water chemistry and to regional alien predator indices while allowing species-specific effects to vary with foraging niche (dabblers, invertivore divers, piscivorous divers, herbivores), nesting site, female mass and habitat (oligotrophic, eutrophic). We found niche and nesting site-specific, habitat-dependent changes in waterbird numbers. While the associations with higher phosphorus levels and browning water were in overall positive at the oligotrophic lakes, the numbers of invertivore and piscivore diving ducks were most strongly negatively associated with higher phosphorus levels and browning water at the eutrophic lakes. Furthermore, increased pH levels benefitted piscivores. Invertivore diving duck species nesting on the wetlands had declined most on sites with high alien predator indices. Large herbivorous species and species preferring oligotrophic lakes seem to be successful. We conclude that the large-scale breeding waterbird decline in Finland is closely connected to both bottom-up and top-down processes, where negative associations are emphasised especially at eutrophic lakes. Niche-, nest site- and habitat-specific management actions are required to conserve declining waterbird populations. Managing wetlands on catchments level together with alien predator control may provide important approaches to future wetland management.

Dataset Information

A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus.

Publications

A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus.

Similar Datasets

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