Quantitative genome-scale analysis of protein localization in an asymmetric bacterium
Open Access
- 12 May 2009
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 106 (19), 7858-7863
- https://doi.org/10.1073/pnas.0901781106
Abstract
Despite the importance of subcellular localization for cellular activities, the lack of high-throughput, high-resolution imaging and quantitation methodologies has limited genomic localization analysis to a small number of archival studies focused on C-terminal fluorescent protein fusions. Here, we develop a high-throughput pipeline for generating, imaging, and quantitating fluorescent protein fusions that we use for the quantitative genomic assessment of the distributions of both N- and C-terminal fluorescent protein fusions. We identify nearly 300 localized Caulobacter crescentus proteins, up to 10-fold more than were previously characterized. The localized proteins tend to be involved in spatially or temporally dynamic processes and proteins that function together and often localize together as well. The distributions of the localized proteins were quantitated by using our recently described projected system of internal coordinates from interpolated contours (PSICIC) image analysis toolkit, leading to the identification of cellular regions that are over- or under-enriched in localized proteins and of potential differences in the mechanisms that target proteins to different subcellular destinations. The Caulobacter localizome data thus represent a resource for studying both global properties of protein localization and specific protein functions, whereas the localization analysis pipeline is a methodological resource that can be readily applied to other systems.Keywords
This publication has 23 references indexed in Scilit:
- PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel ResolutionPLoS Computational Biology, 2008
- ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-ListGenome Research, 2004
- An actin-like gene can determine cell polarity in bacteriaProceedings of the National Academy of Sciences, 2004
- Recruitment of a cytoplasmic response regulator to the cell pole is linked to its cell cycle-regulated proteolysisProceedings of the National Academy of Sciences, 2004
- MreB, the cell shape‐determining bacterial actin homologue, co‐ordinates cell wall morphogenesis in Caulobacter crescentusMolecular Microbiology, 2004
- The Gene Ontology (GO) database and informatics resourceNucleic Acids Research, 2004
- Global analysis of protein localization in budding yeastNature, 2003
- A moving DNA replication factory in Caulobacter crescentusThe EMBO Journal, 2001
- [34] GATEWAY recombinational cloning: Application to the cloning of large numbers of open reading frames or ORFeomesMethods in Enzymology, 2000
- Isolation and characterization of a xylose-dependent promoter from Caulobacter crescentusJournal of Bacteriology, 1997