Genomic Analysis and Molecular Biology of Predatory Prokaryotes

Tudor, John; McCann, Michael P.

doi:10.1007/7171_056

Cited by 6 publications

(3 citation statements)

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“…Among the haves, an extended complement of hydrolytic enzymes stood out, along with a large number of transporters, while sensors and regulators were present in average numbers (Rendulic et al, 2004;Tudor and McCann, 2007). On the missing side, biosynthesis pathways for many amino acids as well as for vitamins were absent, and quorum sensing systems were also apparently absent.…”

Section: Discussionmentioning

confidence: 99%

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

Pasternak

Pietrokovski

Rotem

et al. 2012

ISME J

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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.

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Section: Discussionmentioning

confidence: 99%

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

Pasternak

Pietrokovski

Rotem

et al. 2012

ISME J

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“…They also hold a plethora of genes encoding outer membrane proteins and transport proteins, which may be required for enzyme secretion and prey‐derived nutrient uptake. On the other hand, the pathways for the synthesis of many amino acids and vitamins, and quorum‐sensing systems are apparently absent (Rendulic et al ., ; Tudor and McCann, ; Sockett, ; Pasternak et al ., ). The use of microarrays to study the B. bacteriovorus predatosome during the switch from the attack phase to the growth phase has revealed that almost 7% of all the B. bacteriovorus genes were significantly upregulated in this transition, suggesting a role for these genes in digestion of the prey (Lambert et al ., ).…”

Section: Genomes Transcriptomes and Comparative Genomics Of Predatorsmentioning

confidence: 99%

Bacterial predation: 75 years and counting!

Pérez

Moraleda‐Muñoz

Marcos‐Torres

et al. 2016

Environmental Microbiology

207

193

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SummaryThe first documented study on bacterial predation was carried out using myxobacteria three quarters of a century ago. Since then, many predatory strains, diverse hunting strategies, environmental consequences and potential applications have been reported by groups all over the world. Now we know that predatory bacteria are distributed in a wide variety of environments and that interactions between predatory and non-predatory populations seem to be the most important factor in bacterial selection and mortality in some ecosystems. Bacterial predation has now been proposed as an evolutionary driving force. The structure and diversity of the predatory bacterial community is beginning to be recognized as an important factor in biodiversity due to its potential role in controlling and modelling bacterial populations in the environment. In this paper, we review the current understanding of bacterial predation, going over the strategies used by the main predatory bacteria to kill their prey. We have also reviewed and integrated the accumulated advances of the last 75 years with the interesting new insights that are provided by the analyses of genomes, predatomes, predatosomes and other comparative genomics studies, focusing on potential applications that derive from all of these areas of study.

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“…Biochemical and microbiological studies carried out in several laboratories and analyses of the genomes and transcriptomes during predation (predatosomes) of obligate epibiotic predators such as Micavibrio aeruginosavorus , Vampirovibrio chlorellavorus , and B. exovorus [56] , [57] , [58] , and endobiotic B. bacteriovorus and other BALOs ( Bdellovibrio and like organisms), have revealed that they are able to synthesize and secrete an unusual number of hydrolytic proteins, such as lipases, glycanases, peptidases and proteases, which are probably involved in damaging and digesting prey cell structures [53] , [58] , [59] , [60] , [61] . They are, however, non-competent antibiotic producers [62] , since their killing strategies are based on the active search and recognition of the prey, the specific binding to the external structures, and its degradation.…”

Section: Predatory Bacteria: What Are They? How Do They Kill?mentioning

confidence: 99%