Biology subjects

Puri, A. W.

Publications and source records attributed to Puri, A. W..

4 recordsLinked to original sources

bioRxiv2022

A widespread methylotroph acyl-homoserine lactone synthase produces an atypical quorum sensing signal

Pink pigmented facultative methylotrophs of the genera Methylorubrum and Methylobacterium are omnipresent bacteria often found associated with plants. Despite their widespread occurrence, the molecular details of how these organisms interact with each other and their environment remain understudied. We analyzed genes encoding N-acylhomoserine lactone quorum sensing signal synthases in published genomes of these bacteria and determined that the product of the largest group of signal synthases had not been characterized. We subsequently identified this N-acylhomoserine lactone product using inverse stable isotopic labeling (InverSIL), which revealed an atypical signal. We then demonstrate in one representative strain that this signal activates its cognate LuxR-family transcription factor and is produced in a positive feedback loop. These results reveal a previously undescribed yet widespread signal used by pink pigmented facultative methylotrophs, which helps us understand the chemical ecology of these important bacteria.

microbiology↗

bioRxiv2022

A conserved biosynthetic gene cluster is regulated by quorum sensing in a shipworm symbiont

Bacterial symbionts often provide critical functions for their hosts. For example, wood-boring bivalves called shipworms rely on cellulolytic endosymbionts for wood digestion. However, how the relationship between shipworms and their bacterial symbionts is formed and maintained remains unknown. Quorum sensing (QS) often plays an important role in regulating symbiotic relationships. We identified and characterized a QS system found in Teredinibacter sp. strain 2052S, a gill isolate of the wood-boring shipworm Bactronophorus cf. thoracites. We determined that 2052S produces the signal N-decanoyl-L-homoserine lactone (C10-HSL), and that this signal controls activation of a biosynthetic gene cluster co-located in the symbiont genome that is conserved among all symbiotic Teredinibacter isolates. We subsequently identified extracellular metabolites associated with the QS regulon, including ones linked to the conserved biosynthetic gene cluster, using mass spectrometry-based molecular networking. Our results demonstrate that QS plays an important role in regulating secondary metabolism in this shipworm symbiont. This information provides a step towards deciphering the molecular details of the relationship between these symbionts and their hosts. Furthermore, because shipworm symbionts harbor vast yet underexplored biosynthetic potential, understanding how their secondary metabolism is regulated may aid future drug discovery efforts using these organisms. IMPORTANCEBacteria play important roles as symbionts in animals ranging from invertebrates to humans. Despite this recognized importance, much is still unknown about the molecular details of how these relationships are formed and maintained. One of the proposed roles of shipworm symbionts is the production of bioactive secondary metabolites due to the immense biosynthetic potential found in shipworm symbiont genomes. Here, we report that a shipworm symbiont uses quorum sensing to coordinate activation of its extracellular secondary metabolism, including the transcriptional activation of a biosynthetic gene cluster that is conserved among many shipworm symbionts. This work is a first step towards linking quorum sensing, secondary metabolism, and symbiosis in wood-boring shipworms.

microbiology↗

bioRxiv2021

Methylotroph Natural Product Identification by Inverse Stable Isotopic Labeling

Natural products are an essential source of bioactive compounds. Isotopic labeling is an effective way to identify natural products that incorporate a specific precursor; however, this approach is limited by the availability of isotopically-enriched precursors. We used an inverse stable isotopic labeling approach to identify natural products by growing bacteria on a 13C-carbon source and then identifying 12C-precursor incorporation by mass spectrometry. We applied this approach to methylotrophs, ecologically important bacteria predicted to have significant yet underexplored biosynthetic potential. We demonstrate this method identifies N-acyl homoserine lactone quorum sensing signals produced by diverse methylotrophs grown on three different one-carbon compounds. We then apply this approach to simultaneously identify five uncharacterized signals produced by a methylotroph, and link these compounds to their synthases. We envision that this method can be used to identify other natural product classes synthesized by methylotrophs and other organisms that grow on relatively inexpensive 13C-carbon sources.

biochemistry↗

bioRxiv2021

GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser

Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.

bioinformatics↗