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The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
The subsystem approach is described, the first release of the growing library of populated subsystems is offered, and the SEED is the first annotation environment that supports this model of annotation. Expand
Inhibition of Mutation and Combating the Evolution of Antibiotic Resistance
It is shown in vitro that LexA cleavage is induced during RecBC-mediated repair of ciprofloxacin-mediated DNA damage and that this results in the derepression of the SOS-regulated polymerases Pol II, Pol IV and Pol V, which collaborate to induce resistance-conferring mutations. Expand
Deciphering synonymous codons in the three domains of life: Co‐evolution with specific tRNA modification enzymes
The strategies organisms use to decode synonymous codons in cytosolic protein synthesis are not uniform. The complete isoacceptor tRNA repertoire and the type of modified nucleoside found at theExpand
ClpX, an alternative subunit for the ATP-dependent Clp protease of Escherichia coli. Sequence and in vivo activities.
It appears that selectivity of degradation by ClpP in vivo is determined by interaction ofclpP with different regulatory ATPase subunits, and Mutations in either clpX or clpP abolish degradation of the highly unstable lambda O protein in vivo. Expand
Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes
This work presents the first comprehensive assessment of the B-vitamin synthesis capabilities of the human gut microbiota, and proposes that in addition to diet, the gut microbiota is an important source of B- vitamins, and that changes in the Gut microbiota composition can severely affect the authors' dietary B-Vitamin requirements. Expand
Complete Reconstitution of the Human Coenzyme A Biosynthetic Pathway via Comparative Genomics*
Using comparative genomics, human genes encoding the last four enzymatic steps in CoA biosynthesis are identified and human recombinant bifunctional phosphopantetheine adenylyltransferase/dephospho-CoA kinase was kinetically characterized. Expand
Mutations in PROSC Disrupt Cellular Pyridoxal Phosphate Homeostasis and Cause Vitamin-B6-Dependent Epilepsy.
These studies suggest that PROSC is involved in intracellular homeostatic regulation of PLP, supplying this cofactor to apoenzymes while minimizing any toxic side reactions. Expand
Incorporation of nonnatural amino acids into proteins.
The genetic code is established by the aminoacylation of transfer RNA, reactions in which each amino acid is linked to its cognate tRNA that, in turn, harbors the nucleotide triplet (anticodon)Expand
The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA
This work lays the foundation for elucidating the function of a protein family found in every sequenced genome to date and understanding the role of t6A in vivo. Expand
A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life
A link between COG0523 and regulation by zinc in Archaea is predicted and two COG523 genes are induced upon zinc depletion in a eukaryotic reference organism, Chlamydomonas reinhardtii. Expand