Document Detail


By their genes ye shall know them: genomic signatures of predatory bacteria.
MedLine Citation:
PMID:  23190728     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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 full-genome proteomic comparisons are applicable to other ecological interactions between microbes, and provide a convenient and rational tool for the functional classification of bacteria.
Authors:
Zohar Pasternak; Shmuel Pietrokovski; Or Rotem; Uri Gophna; Mor N Lurie-Weinberger; Edouard Jurkevitch
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2012-11-29
Journal Detail:
Title:  The ISME journal     Volume:  7     ISSN:  1751-7370     ISO Abbreviation:  ISME J     Publication Date:  2013 Apr 
Date Detail:
Created Date:  2013-03-19     Completed Date:  2013-09-30     Revised Date:  2014-04-01    
Medline Journal Info:
Nlm Unique ID:  101301086     Medline TA:  ISME J     Country:  England    
Other Details:
Languages:  eng     Pagination:  756-69     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Bacteria / classification,  genetics*,  metabolism
Bacterial Physiological Phenomena*
Bacterial Proteins / genetics
Food Chain*
Genomics*
Phylogeny
Chemical
Reg. No./Substance:
0/Bacterial Proteins
Comments/Corrections

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