Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities
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Abstract
Microbial communities are significant drivers of global biogeochemical cycles, yet accurate function prediction of their proteome and discerning their activity in situ for bioprospecting remains challenging. Here, we present environmental activity-based protein profiling (eABPP) as a novel proteomics-based approach bridging the gap between environmental genomics, correct function annotation and in situ enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases by combining genome-resolved metagenomics and mass spectrometry-based eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia. eABPP does not only advance current methodological approaches by providing evidence for enzyme and microbial activity in situ but also represents an alternative approach to sequence homology-guided biocatalyst discovery from environmental ecosystems.
Article activity feed
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two-step ABP aiming to target enzymes with the desired activity among the microbial enzyme repertoire directly at the site of sampling (eABPP)
Can you clarify if these enzymes are secreted enzymes that are stable in the environment, or if they are expected to be intracellular proteins that are exposed upon lysis conditions? Based on your methodology, it seems like you are mostly profiling extracellular serine hydrolases - can you explain the motivation for studying secreted proteins instead of the full proteome?
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extraction of eDNA
Can you clarify if the DNA is environmental in source - ie "eDNA" that is extracellular and released into the environment. Or, is the DNA from the microbial community? I'm guessing the latter since that is where you would get good assembly and bins. In that case, would you consider calling the DNA "community DNA" instead of "eDNA"? eDNA has a very specific definition as environmental DNA (ie extracellular), which I don't think what you mean here.
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This is really interesting work ! The approach of environmental ABPP is clever and has a lot of potential applications. It is a nice way improve our understanding functional potential of uncultivated microorganisms and their encoded proteins. This example of serine hydrolase discovery is a nice vignette applying the protocol, and I look forward to future developments in this area!
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This is really interesting work ! The approach of environmental ABPP is clever and has a lot of potential applications. It is a nice way improve our understanding functional potential of uncultivated microorganisms and their encoded proteins. This example of serine hydrolase discovery is a nice vignette applying the protocol, and I look forward to future developments in this area!
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extraction of eDNA
Can you clarify if the DNA is environmental in source - ie "eDNA" that is extracellular and released into the environment. Or, is the DNA from the microbial community? I'm guessing the latter since that is where you would get good assembly and bins. In that case, would you consider calling the DNA "community DNA" instead of "eDNA"? eDNA has a very specific definition as environmental DNA (ie extracellular), which I don't think what you mean here.
-
two-step ABP aiming to target enzymes with the desired activity among the microbial enzyme repertoire directly at the site of sampling (eABPP)
Can you clarify if these enzymes are secreted enzymes that are stable in the environment, or if they are expected to be intracellular proteins that are exposed upon lysis conditions? Based on your methodology, it seems like you are mostly profiling extracellular serine hydrolases - can you explain the motivation for studying secreted proteins instead of the full proteome?
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