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Article
Open AccessBioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation
Cyanophycin is a bacterial biopolymer used for storage of fixed nitrogen. It is composed of a backbone of L-aspartate residues with L-arginines attached to each of their side chains. Cyanophycin is produced by...
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Article
Open AccessA cryptic third active site in cyanophycin synthetase creates primers for polymerization
Cyanophycin is a nitrogen reserve biopolymer in many bacteria that has promising industrial applications. Made by cyanophycin synthetase 1 (CphA1), it has a poly-L-Asp backbone with L-Arg residues attached to ...
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Article
Open AccessStructures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module
Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional protein...
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Article
Structures and function of the amino acid polymerase cyanophycin synthetase
Cyanophycin is a natural biopolymer produced by a wide range of bacteria, consisting of a chain of poly-l-Asp residues with l-Arg residues attached to the β-carboxylate sidechains by isopeptide bonds. Cyanophycin...
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Article
Open AccessThe chaperone HSPB1 prepares protein aggregates for resolubilization by HSP70
In human cells under stress conditions, misfolded polypeptides can form potentially cytotoxic insoluble aggregates. To eliminate aggregates, the HSP70 chaperone machinery extracts and resolubilizes polypeptide...
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Article
Open AccessNeonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization
Exposure to antibiotics in the first days of life is thought to affect various physiological aspects of neonatal development. Here, we investigate the long-term impact of antibiotic treatment in the neonatal p...
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Article
Open AccessAuthor Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
The original version of this Article contained errors in Fig. 4. In panel a, the labels ‘F420-reducing NiFe hydrogenase (group 3a)’ and ‘Group 2 NiFe hydrogenase’ were misplaced. These errors have been correct...
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Article
Open AccessHydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
The evolution of aerobic respiration was likely linked to the origins of oxygenic Cyanobacteria. Close phylogenetic neighbors to Cyanobacteria, such as Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), ...
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Article
A distinct abundant group of microbial rhodopsins discovered using functional metagenomics
Many organisms capture or sense sunlight using rhodopsin pigments1,2, which are integral membrane proteins that bind retinal chromophores. Rhodopsins comprise two distinct protein families 1 ...
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Protocol
E. coli-Based Selection and Expression Systems for Discovery, Characterization, and Purification of Ubiquitylated Proteins
Ubiquitylation is an eukaryotic signal that regulates most cellular pathways. However, four major hurdles pose challenges to study ubiquitylation: (1) high redundancy between ubiquitin (Ub) cascades, (2) ubiqu...
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Article
A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells
Cyanobacteria are important contributors to primary production in the open oceans. Over the past decade, various photosynthesis-related genes have been found in viruses that infect cyanobacteria (cyanophages)....
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Article
Open AccessThousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth’s biogeochemical cycles. However, little is known about how complex micr...
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Article
Open AccessMajor bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems
Current understanding of microorganism–virus interactions, which shape the evolution and functioning of Earth’s ecosystems, is based primarily on cultivated organisms. Here we investigate thousands of viral an...
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Article
Unusual biology across a group comprising more than 15% of domain Bacteria
More than 15% of the bacterial domain consists of a radiation of phyla about which very little is known; here, metagenomics is used to reconstruct 8 complete and 789 draft genomes from more than 35 of these ph...
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Article
Open AccessMicrobes in the neonatal intensive care unit resemble those found in the gut of premature infants
The source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW, <1,500 g) neonate...
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Article
Open AccessGenome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life
The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be simil...
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Article
Open AccessCommunity genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling
Sediments are massive reservoirs of carbon compounds and host a large fraction of microbial life. Microorganisms within terrestrial aquifer sediments control buried organic carbon turnover, degrade organic con...
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Article
Genomic island variability facilitates Prochlorococcus–virus coexistence
Prochlorococcus cyanobacteria are extremely abundant in the oceans, as are the viruses that infect them. How hosts and viruses coexist in nature remains unclear, although the presence of both susceptible and resi...
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Chapter and Conference Paper
Pathway-Based Functional Analysis of Metagenomes
Metagenomic data enables the study of microbes and viruses through their DNA as retrieved directly from the environment in which they live. Functional analysis of metagenomes explores the abundance of gene fam...
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Article
Photosystem I gene cassettes are present in marine virus genomes
Like plant chloroplasts, the photosynthetic membranes of marine cyanobacteria contain two photosystems: photosystem II (PSII) mediates electron transfer from water to plastoquinones and PSI mediates electron t...
