The power of the small: the underestimated role of small proteins in bacterial and archaeal physiology
Curr Opin Microbiol. 2023 Sep 28;76:102384. doi: 10.1016/j.mib.2023.102384. Online ahead of print.ABSTRACTSmall proteins encoded by small open-reading frames (sORFs) (≤70 aa) were overlooked for decades due to methodological reasons and are thus often missing in genome annotations. Novel detection methods such as ribosome profiling (Ribo-Seq) and mass spectrometry optimized for small proteins (peptidomics) have opened up a new field of interest and several catalogs of small proteins in bacteria and archaea have been recently reported. Many translated sORFs have been discovered in genomic locations previously thought to b...
Source: Current Opinion in Microbiology - September 30, 2023 Category: Microbiology Authors: Britta Jordan Katrin Weidenbach Ruth A Schmitz Source Type: research
The power of the small: the underestimated role of small proteins in bacterial and archaeal physiology
Curr Opin Microbiol. 2023 Sep 28;76:102384. doi: 10.1016/j.mib.2023.102384. Online ahead of print.ABSTRACTSmall proteins encoded by small open-reading frames (sORFs) (≤70 aa) were overlooked for decades due to methodological reasons and are thus often missing in genome annotations. Novel detection methods such as ribosome profiling (Ribo-Seq) and mass spectrometry optimized for small proteins (peptidomics) have opened up a new field of interest and several catalogs of small proteins in bacteria and archaea have been recently reported. Many translated sORFs have been discovered in genomic locations previously thought to b...
Source: Current Opinion in Microbiology - September 30, 2023 Category: Microbiology Authors: Britta Jordan Katrin Weidenbach Ruth A Schmitz Source Type: research
The power of the small: the underestimated role of small proteins in bacterial and archaeal physiology
Curr Opin Microbiol. 2023 Sep 28;76:102384. doi: 10.1016/j.mib.2023.102384. Online ahead of print.ABSTRACTSmall proteins encoded by small open-reading frames (sORFs) (≤70 aa) were overlooked for decades due to methodological reasons and are thus often missing in genome annotations. Novel detection methods such as ribosome profiling (Ribo-Seq) and mass spectrometry optimized for small proteins (peptidomics) have opened up a new field of interest and several catalogs of small proteins in bacteria and archaea have been recently reported. Many translated sORFs have been discovered in genomic locations previously thought to b...
Source: Current Opinion in Microbiology - September 30, 2023 Category: Microbiology Authors: Britta Jordan Katrin Weidenbach Ruth A Schmitz Source Type: research
Structure-guided metagenome mining to tap microbial functional diversity
Curr Opin Microbiol. 2023 Sep 21;76:102382. doi: 10.1016/j.mib.2023.102382. Online ahead of print.ABSTRACTScientists now have access to millions of accurate three-dimensional (3D) models of protein structures. How do we leverage 3D structural models to learn about microbial functions encoded in metagenomes? Here, we review recent developments using protein structural features to mine metagenomes from diverse environments ranging from the human gut to soil and ocean viromes. We compare 3D protein structural methods to characterize antibiotic resistance phenotypes, nutrient cycling, and host-drug-microbe interactions. Broadl...
Source: Current Opinion in Microbiology - September 23, 2023 Category: Microbiology Authors: Serina L Robinson Source Type: research
Structure-guided metagenome mining to tap microbial functional diversity
Curr Opin Microbiol. 2023 Sep 21;76:102382. doi: 10.1016/j.mib.2023.102382. Online ahead of print.ABSTRACTScientists now have access to millions of accurate three-dimensional (3D) models of protein structures. How do we leverage 3D structural models to learn about microbial functions encoded in metagenomes? Here, we review recent developments using protein structural features to mine metagenomes from diverse environments ranging from the human gut to soil and ocean viromes. We compare 3D protein structural methods to characterize antibiotic resistance phenotypes, nutrient cycling, and host-drug-microbe interactions. Broadl...
Source: Current Opinion in Microbiology - September 23, 2023 Category: Microbiology Authors: Serina L Robinson Source Type: research
Structure-guided metagenome mining to tap microbial functional diversity
Curr Opin Microbiol. 2023 Sep 21;76:102382. doi: 10.1016/j.mib.2023.102382. Online ahead of print.ABSTRACTScientists now have access to millions of accurate three-dimensional (3D) models of protein structures. How do we leverage 3D structural models to learn about microbial functions encoded in metagenomes? Here, we review recent developments using protein structural features to mine metagenomes from diverse environments ranging from the human gut to soil and ocean viromes. We compare 3D protein structural methods to characterize antibiotic resistance phenotypes, nutrient cycling, and host-drug-microbe interactions. Broadl...
Source: Current Opinion in Microbiology - September 23, 2023 Category: Microbiology Authors: Serina L Robinson Source Type: research
Structure-guided metagenome mining to tap microbial functional diversity
Curr Opin Microbiol. 2023 Sep 21;76:102382. doi: 10.1016/j.mib.2023.102382. Online ahead of print.ABSTRACTScientists now have access to millions of accurate three-dimensional (3D) models of protein structures. How do we leverage 3D structural models to learn about microbial functions encoded in metagenomes? Here, we review recent developments using protein structural features to mine metagenomes from diverse environments ranging from the human gut to soil and ocean viromes. We compare 3D protein structural methods to characterize antibiotic resistance phenotypes, nutrient cycling, and host-drug-microbe interactions. Broadl...
Source: Current Opinion in Microbiology - September 23, 2023 Category: Microbiology Authors: Serina L Robinson Source Type: research
Structure-guided metagenome mining to tap microbial functional diversity
Curr Opin Microbiol. 2023 Sep 21;76:102382. doi: 10.1016/j.mib.2023.102382. Online ahead of print.ABSTRACTScientists now have access to millions of accurate three-dimensional (3D) models of protein structures. How do we leverage 3D structural models to learn about microbial functions encoded in metagenomes? Here, we review recent developments using protein structural features to mine metagenomes from diverse environments ranging from the human gut to soil and ocean viromes. We compare 3D protein structural methods to characterize antibiotic resistance phenotypes, nutrient cycling, and host-drug-microbe interactions. Broadl...
Source: Current Opinion in Microbiology - September 23, 2023 Category: Microbiology Authors: Serina L Robinson Source Type: research
Structure-guided metagenome mining to tap microbial functional diversity
Curr Opin Microbiol. 2023 Sep 21;76:102382. doi: 10.1016/j.mib.2023.102382. Online ahead of print.ABSTRACTScientists now have access to millions of accurate three-dimensional (3D) models of protein structures. How do we leverage 3D structural models to learn about microbial functions encoded in metagenomes? Here, we review recent developments using protein structural features to mine metagenomes from diverse environments ranging from the human gut to soil and ocean viromes. We compare 3D protein structural methods to characterize antibiotic resistance phenotypes, nutrient cycling, and host-drug-microbe interactions. Broadl...
Source: Current Opinion in Microbiology - September 23, 2023 Category: Microbiology Authors: Serina L Robinson Source Type: research
The skin mycobiome and intermicrobial interactions in the cutaneous niche
Curr Opin Microbiol. 2023 Sep 11;76:102381. doi: 10.1016/j.mib.2023.102381. Online ahead of print.ABSTRACTMammalian microbiomes have coevolved with their host to establish a stable homeostatic relationship. Multifaceted commensal-host and commensal-commensal interactions contribute to the maintenance of the equilibrium with an impact on diverse host physiological processes. Despite constant exposure to physical and chemical insults from the environment, the skin harbors a surprisingly stable microbiome. The fungal compartment of the skin microbiome, the skin mycobiome, is unique in that it is dominated by a single fungus, ...
Source: Current Opinion in Microbiology - September 13, 2023 Category: Microbiology Authors: Meret Tuor Salom é LeibundGut-Landmann Source Type: research
Design of synthetic bacterial biosensors
Curr Opin Microbiol. 2023 Sep 11;76:102380. doi: 10.1016/j.mib.2023.102380. Online ahead of print.ABSTRACTNovel whole-cell bacterial biosensor designs require an emphasis on moving toward field deployment. Many current sensors are characterized under specified laboratory conditions, which frequently do not represent actual deployment conditions. To this end, recent developments such as toolkits for probing new host chassis that are more robust to environments of interest, have paved the way for improved designs. Strategies for rational tuning of genetic components or tools such as genetic amplifiers or designs that allow p...
Source: Current Opinion in Microbiology - September 13, 2023 Category: Microbiology Authors: Alyssa J Chiang Jeff Hasty Source Type: research
The skin mycobiome and intermicrobial interactions in the cutaneous niche
Curr Opin Microbiol. 2023 Sep 11;76:102381. doi: 10.1016/j.mib.2023.102381. Online ahead of print.ABSTRACTMammalian microbiomes have coevolved with their host to establish a stable homeostatic relationship. Multifaceted commensal-host and commensal-commensal interactions contribute to the maintenance of the equilibrium with an impact on diverse host physiological processes. Despite constant exposure to physical and chemical insults from the environment, the skin harbors a surprisingly stable microbiome. The fungal compartment of the skin microbiome, the skin mycobiome, is unique in that it is dominated by a single fungus, ...
Source: Current Opinion in Microbiology - September 13, 2023 Category: Microbiology Authors: Meret Tuor Salom é LeibundGut-Landmann Source Type: research
Design of synthetic bacterial biosensors
Curr Opin Microbiol. 2023 Sep 11;76:102380. doi: 10.1016/j.mib.2023.102380. Online ahead of print.ABSTRACTNovel whole-cell bacterial biosensor designs require an emphasis on moving toward field deployment. Many current sensors are characterized under specified laboratory conditions, which frequently do not represent actual deployment conditions. To this end, recent developments such as toolkits for probing new host chassis that are more robust to environments of interest, have paved the way for improved designs. Strategies for rational tuning of genetic components or tools such as genetic amplifiers or designs that allow p...
Source: Current Opinion in Microbiology - September 13, 2023 Category: Microbiology Authors: Alyssa J Chiang Jeff Hasty Source Type: research
The skin mycobiome and intermicrobial interactions in the cutaneous niche
Curr Opin Microbiol. 2023 Sep 11;76:102381. doi: 10.1016/j.mib.2023.102381. Online ahead of print.ABSTRACTMammalian microbiomes have coevolved with their host to establish a stable homeostatic relationship. Multifaceted commensal-host and commensal-commensal interactions contribute to the maintenance of the equilibrium with an impact on diverse host physiological processes. Despite constant exposure to physical and chemical insults from the environment, the skin harbors a surprisingly stable microbiome. The fungal compartment of the skin microbiome, the skin mycobiome, is unique in that it is dominated by a single fungus, ...
Source: Current Opinion in Microbiology - September 13, 2023 Category: Microbiology Authors: Meret Tuor Salom é LeibundGut-Landmann Source Type: research
Design of synthetic bacterial biosensors
Curr Opin Microbiol. 2023 Sep 11;76:102380. doi: 10.1016/j.mib.2023.102380. Online ahead of print.ABSTRACTNovel whole-cell bacterial biosensor designs require an emphasis on moving toward field deployment. Many current sensors are characterized under specified laboratory conditions, which frequently do not represent actual deployment conditions. To this end, recent developments such as toolkits for probing new host chassis that are more robust to environments of interest, have paved the way for improved designs. Strategies for rational tuning of genetic components or tools such as genetic amplifiers or designs that allow p...
Source: Current Opinion in Microbiology - September 13, 2023 Category: Microbiology Authors: Alyssa J Chiang Jeff Hasty Source Type: research
