By their genes ye shall know them: genomic signatures of predatory bacteria

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.

In and out: an analysis of epibiotic vs periplasmic bacterial predators

“…Complete gene pathways for riboflavin and vitamin B6 were found in the periplasmic but not in the epibiotic predators, while the nicotinate pathway is complete in the three Bdellovibrionales but not in Micavibrio. As shown earlier (Pasternak et al, 2013), B. exovorus JSS, like almost all bacterial predators, possess a mevalonate pathway for isoprenoid biosynthesis while Micavibrio encodes the DOXP pathway. None of the predators are able to synthesize the reserve compounds glycogen and polyhydroxyalkanoate; yet, the periplasmic predators but not the epibiotic predators possess a polyhydroxyalkanoate depolymerase.…”

“…The genomes of predatory bacteria were shown to possess characteristic proteins and pathways, clearly distinguishing them from non-predatory bacterial genomes (Pasternak et al, 2013). However, how and why predators differ from each other is still very much an open question.…”

Cell-cycle progress in obligate predatory bacteria is dependent upon sequential sensing of prey recognition and prey quality cues

“…However, predation between bacteria, the most abundant cellular living entities on Earth, is poorly understood. The known diversity of predatory bacteria is low (4), and few studies have addressed predation dynamics in natural or man-made environments (5)(6)(7). An important aspect of predatory interactions is prey choice.…”

Bdellovibrioet organismes apparentés

“…La durée du cycle de vie, de l'attachement du prédateur à la proie jusqu'à la libération de nouvelles cellules en PA, dure entre 2,5 et 4 h. Durant leur croissance, les BALO sont en mesure de synthétiser tous les nucléotides mais comme de nombreux symbiontes et pathogènes bactériens, ils ne peuvent pas synthétiser et dégrader certains acides aminés, ainsi que la riboflavine [23]. Pour des raisons encore inconnues, chez la plupart des BALO et chez des pré-dateurs bactériens non-obligatoires, la production des isoprénoïdes 9 utilise la voie de biosynthèse du mévalo-nate et non la voie du méthylérythritol phosphate commune à la grande majorité des bactéries [24]. LPS) mais il est totalement dépourvu de groupes chargés négativement, en raison de la substitution des résidus phosphate (présents sur le LPS) par des résidus d'-D-mannopyranose [15].…”

“…Quelques souches HI ont aussi été isolées de l'environnement. Par contre, il n'a pas été possible d'obtenir de souches HI à partir de BALO épibiotiques 10 [24]. Les souches HI conservent le cycle de vie dimorphique des BALO et présentent un potentiel prédateur amoindri par rapport à celui de la souche parentale.…”