Gene Flow and Molecular Innovation in Bacteria

Ruzzini, Antonio C.; Clardy, Jon

doi:10.1016/j.cub.2016.08.004

Cited by 24 publications

(22 citation statements)

References 44 publications

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“…Remarkable new insight is being gained into the evolutionary processes that drive natural product biosynthesis (Medema et al, 2014;Ruzzini and Clardy, 2016;Lind et al, 2017). These studies have helped reveal the dynamic processes of gene gain, loss and degradation in BGCs and how subtle changes in regulatory genes can have substantial effects on both gene expression and compound production .…”

Section: Discussionmentioning

confidence: 99%

Diversity and distribution of the bmp gene cluster and its Polybrominated products in the genus Pseudoalteromonas

Busch

Agarwal

Schorn

et al. 2019

Environmental Microbiology

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Summary The production of pentabromopseudilin and related brominated compounds by Pseudoalteromonas spp. has recently been linked to the bmp biosynthetic gene cluster. This study explored the distribution and evolutionary history of this gene cluster in the genus Pseudoalteromonas. A phylogeny of the genus revealed numerous clades that do not contain type strains, suggesting considerable species level diversity has yet to be described. Comparative genomics revealed four distinct versions of the gene cluster distributed among 19 of the 101 Pseudoalteromonas genomes examined. These were largely localized to the least inclusive clades containing the Pseudoalteromonas luteoviolacea and Pseudoalteromonas phenolica type strains and show clear evidence of gene and gene cluster loss in certain lineages. Bmp gene phylogeny is largely congruent with the Pseudoalteromonas species phylogeny, suggesting vertical inheritance within the genus. However, the gene cluster is found in three different genomic environments suggesting either chromosomal rearrangement or multiple acquisition events. Bmp conservation within certain lineages suggests the encoded products are highly relevant to the ecology of these bacteria.

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Section: Discussionmentioning

confidence: 99%

Diversity and distribution of the bmp gene cluster and its Polybrominated products in the genus Pseudoalteromonas

Busch

Agarwal

Schorn

et al. 2019

Environmental Microbiology

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“…However, in M. whittenburyi, this locus does not contain the predicted NRPS cluster, transposase fragments, or mbaI' pseudogene. These observations led us to speculate that this biosynthetic gene cluster is a potential genomic island (22) that was either inserted into the genome of M. tundripaludum or lost in other known members of the Methylobacter genus.…”

Section: Resultsmentioning

confidence: 99%

Quorum Sensing in a Methane-Oxidizing Bacterium

Puri

Schaefer

et al. 2017

J Bacteriol

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Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Dissecting the molecular details of how these organisms interact in the environment may increase our understanding of how they perform this important ecological role. Many bacterial species use quorum sensing (QS) systems to regulate gene expression in a cell density-dependent manner. We have identified a QS system in the genome of Methylobacter tundripaludum, a dominant methane oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA). We determined that M. tundripaludum produces primarily N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-C 10 -HSL) and that its production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by QS in this methane oxidizer using transcriptome sequencing (RNA-seq) and discovered that this system regulates the expression of a putative nonribosomal peptide synthetase biosynthetic gene cluster. Finally, we detected an extracellular factor that is produced by M. tundripaludum in a QS-dependent manner. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.IMPORTANCE Aerobic methanotrophs are critical for sequestering carbon from the potent greenhouse gas methane in the environment, yet the mechanistic details of chemical interactions in methane-oxidizing bacterial communities are not well understood. Understanding these interactions is important in order to maintain, and potentially optimize, the functional potential of the bacteria that perform this vital ecosystem function. In this work, we identify a quorum sensing system in the aerobic methanotroph Methylobacter tundripaludum and use both chemical and genetic methods to characterize this system at the molecular level.KEYWORDS methane, methanotroph, quorum sensing, sociomicrobiology, acyl-homoserine lactone, biosynthetic gene cluster A erobic methane-oxidizing bacteria (methanotrophs) are an important component of the carbon cycle that serve to sequester carbon from the potent greenhouse gas methane after it is produced by anaerobic microbial ecosystems (1, 2). Methanotrophs provide a carbon and energy source for communities of organisms that cannot oxidize methane themselves, thereby serving as key supporting species in the environment (3, 4). The methanotroph Methylobacter tundripaludum is a member of the Gammaproteobacteria (type I methanotroph), and it has been repeatedly identified as a dominant member of methane enrichment and stable isotope probing experiments of sediment from Lake Washington, Seattle, WA (3, 5-7). Methylobacter spp. have also been isolated from other geographically distinct regions, including the arctic (8), estuaries (9), and temperate wetlands (10), highlighting the diverse environments inhabited by this genus. We, therefore, use M. tundripaludum as part of a model system for ...

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“…Horizontal gene transfer is thought to play a central role in the diversification of natural product biosynthetic pathways . It is well established that entire biosynthetic gene clusters can spread through horizontal gene transfer where they confer a selective advantage upon the recipient organism .…”

Section: Horizontal Gene Transfer Facilitates the Distribution Of Natmentioning

confidence: 99%

A pharmaceutical model for the molecular evolution of microbial natural products

Fewer

Metsä‐Ketelä

2019

The FEBS Journal

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Microbes are talented chemists with the ability to generate tremendously complex and diverse natural products which harbor potent biological activities. Natural products are produced using sets of specialized biosynthetic enzymes encoded by secondary metabolism pathways. Here, we present a two‐step evolutionary model to explain the diversification of biosynthetic pathways that account for the proliferation of these molecules. We argue that the appearance of natural product families has been a slow and infrequent process. The first step led to the original emergence of bioactive molecules and different classes of natural products. However, much of the chemical diversity observed today has resulted from the endless modification of the ancestral biosynthetic pathways. The second step rapidly modulates the pre‐existing biological activities to increase their potency and to adapt to changing environmental conditions. We highlight the importance of enzyme promiscuity in this process, as it facilitates both the incorporation of horizontally transferred genes into secondary metabolic pathways and the functional differentiation of proteins to catalyze novel chemistry. We provide examples where single point mutations or recombination events have been sufficient for new enzymatic activities to emerge. A unique feature in the evolution of microbial secondary metabolism is that gene duplication is not essential but offers opportunities to synthesize more complex metabolites. Microbial natural products are highly important for the pharmaceutical industry due to their unique bioactivities. Therefore, understanding the natural mechanisms leading to the formation of diverse metabolic pathways is vital for future attempts to utilize synthetic biology for the generation of novel molecules.

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Gene Flow and Molecular Innovation in Bacteria

Cited by 24 publications

References 44 publications

Diversity and distribution of the bmp gene cluster and its Polybrominated products in the genus Pseudoalteromonas

Diversity and distribution of the bmp gene cluster and its Polybrominated products in the genus Pseudoalteromonas

Quorum Sensing in a Methane-Oxidizing Bacterium

A pharmaceutical model for the molecular evolution of microbial natural products

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