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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
TLDR
T tandem affinity purification was used to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae to identify protein–protein interactions, which will help future studies on individual proteins as well as functional genomics and systems biology.
Interaction network containing conserved and essential protein complexes in Escherichia coli
TLDR
Insight is provided into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.
Draft Genome of the Filarial Nematode Parasite Brugia malayi
TLDR
Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during ∼350 million years of evolution, they largely remain in linkage on chromosomal units.
The phylogenetic extent of metabolic enzymes and pathways.
TLDR
This work examines the phylogenetic distribution of the full-known metabolic complement of Escherichia coli, using sequence comparison against taxa-specific databases to show for the first time and in a comprehensive way that metabolism is conserved at the enzyme level.
Bacteriome.org—an integrated protein interaction database for E. coli
TLDR
Bacteriome.org is presented, a resource that combines locally generated interaction and evolutionary datasets with a previously generated knowledgebase, to provide an integrated view of the Escherichia coli interactome.
An exponential core in the heart of the yeast protein interaction network.
TLDR
The connections established by yeast proteins are studied and a preferential attachment between essential proteins is discovered and it is proposed that this core exponential network may represent a generic scaffold around which organism-specific and taxon-specific proteins and interactions coalesce.
The origins of apicomplexan sequence innovation.
TLDR
A systematic analysis of protein family and domain incidence across the Apicomplexa reveals domains that may be important to parasite survival and constructed taxonomic profiles that reveal the extent of apicom Plexan sequence diversity.
The conservation and evolutionary modularity of metabolism
TLDR
These findings point to an emerging picture in which a core of enzyme activities involving amino acid, energy, carbohydrate and lipid metabolism have evolved to provide the basic functions required for life, however, the precise complement of enzymes associated within this core for each species is flexible.
The Modular Organization of Protein Interactions in Escherichia coli
TLDR
A global view of the modular organization of the E. coli proteome is provided and several case examples are presented, including both well characterized and novel biochemical systems that yield unique insights into structural and evolutionary relationships in bacterial networks.
The global landscape of sequence diversity
TLDR
This study provides a unique perspective of sequence conservation across the three domains of life through the use of partial genome datasets, which should prove valuable for future computational and biochemical analyses aimed at understanding evolutionary and functional relationships.
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