Journal article
By their genes ye shall know them: genomic signatures of predatory bacteria
ISME Journal, Vol.7(4), pp.756-769
Apr/2013
Abstract
Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the 'predatome,' that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. Strikingly, predators and non-predators differ in isoprenoid biosynthesis: predators use the mevalonate pathway, whereas non-predators, like almost all bacteria, use the DOXP pathway. By defining predatory signatures in bacterial genomes, the predatory potential they encode can be uncovered, filling an essential gap for measuring bacterial predation in nature. Moreover, we suggest that fullgenome proteomic comparisons are applicable to other ecological interactions between microbes, and provide a convenient and rational tool for the functional classification of bacteria. The ISME Journal (2013) 7, 756-769; doi:10.1038/ismej.2012.149; published online 29 November 2012
Details
- Title
- By their genes ye shall know them; genomic signatures of predatory bacteria
- Creators
- Zohar Pasternak (null)Shmuel Pietrokovski (null) - 972WIS_INST___111Or Rotem (null)Uri Gophna (null)Mor N. Lurie-Weinberger (null)Edouard Jurkevitch (null)
- Resource Type
- Journal article
- Publication Details
- ISME Journal, Vol.7(4), pp.756-769; Apr/2013
- Number of pages
- 14
- Language
- English
- DOI
- https://doi.org/10.1038/ismej.2012.149
- Grant note
- Israel Science Foundation [1290/08]We thank Susan Koval at the University of Western Ontario and Albina Afinogenova (previously at the Russian Academy of Sciences, Pushchino, Russia) for kindly providing B. exovorus JSS and M. aeruginosavorus EPB, respectively. This work was supported by a grant of the Israel Science Foundation (Grant No1290/08)._ALMAME_DELIMITER_
- Record Identifier
- 993264239403596
Metrics
5 Record Views