The impact of extremophiles on structural genomics (and vice versa)

  title={The impact of extremophiles on structural genomics (and vice versa)},
  author={Francis E. Jenney Jr and Michael W. W. Adams},
The advent of the complete genome sequences of various organisms in the mid-1990s raised the issue of how one could determine the function of hypothetical proteins. While insight might be obtained from a 3D structure, the chances of being able to predict such a structure is limited for the deduced amino acid sequence of any uncharacterized gene. A template for modeling is required, but there was only a low probability of finding a protein closely-related in sequence with an available structure… 
Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome
The model archaeon Pyrococcus furiosus grows optimally near 100°C on carbohydrates and peptides and is of high plasticity, and the availability of the COM1 sequence will be critical for the future studies of this model hyperthermophile.
Novel Multiprotein Complexes Identified in the Hyperthermophilic Archaeon Pyrococcus furiosus by Non-denaturing Fractionation of the Native Proteome*S
Virtually all cellular processes are carried out by dynamic molecular assemblies or multiprotein complexes, the compositions of which are largely undefined. They cannot be predicted solely from
Presence of structural homologs of ubiquitin in haloalkaliphilic Archaea.
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Thermus thermophilus as biological model
Thermus spp is one of the most wide spread genuses of thermophilic bacteria, with isolates found in natural as well as in man-made thermal environments. The high growth rates, cell yields of the
Bioprospecting in the genomic age.
Mycobacterium thermoresistibile as a source of thermostable orthologs of Mycobacterium tuberculosis proteins
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An Efficient Strategy for Small-Scale Screening and Production of Archaeal Membrane Transport Proteins in Escherichia coli
Here, an efficient strategy for heterologous production of membrane transport proteins in E. coli is described and can be easily applied to many more membrane proteins.
Análisis de la respiración de nitrito en Thermus thermophilus
Draft genomic sequences of PD and CD strains of Thermus thermophilus are obtained and it is shown that Thermus forms along with Deinococcus a distinct bacterial phylum, for which an ancient origin has been proposed and discussed.
Major players on the microbial stage: why archaea are important.
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Partial and complete denitrification in Thermus thermophilus: lessons from genome drafts.
No homologues of NosZ were found despite nitrogen balance supports the idea that such activity actually exists, and the whole nar-nir-nor denitrification supercluster was identified as part of a variable region of a megaplasmid.


Crystallographic analyses of hyperthermophilic proteins.
  • D. Rees
  • Biology
    Methods in enzymology
  • 2001
Developments in Structural Genomics: Protein Purification and Function Interpretation
Three newly determined structures by the pilot structural genomics projects were shown to demonstrate how to decipher biological function from the 3-D structure of a novel protein and how to interpret the structure-function relationship and its application on drug design.
Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics.
The crystal structure of one such protein, MJ0577, from a hyperthermophile, Methanococcus jannaschii, at 1.7-A resolution is reported, indicating that structure-based assignment of molecular function is a viable approach for the large-scale biochemical assignment of proteins and for discovering new motifs, a basic premise of structural genomics.
High-throughput production of Pyrococcus furiosus proteins: considerations for metalloproteins.
Development of the production pipeline with attention to prediction and incorporation of cofactors is described, suggesting lack of the appropriate cofactor or of the partner protein necessary to form a complex are major reasons why many recombinant proteins are insoluble.
Integrating Structure, Bioinformatics, and Enzymology to Discover Function
The function for a protein is determined using a strategy that integrates structural and bioinformatics data with parallel experimental screening for enzymatic activity using a catalytic triad similar to that of the catalytic Triad of hydrolases.
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline
  • S. Lesley, P. Kuhn, R. Stevens
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2002
The design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima is described and successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes.
A scaleable and integrated crystallization pipeline applied to mining the Thermotoga maritima proteome
The Joint Center for Structural Genomics (JCSG), established in 2000 under the NIH/NIGMS Protein Structure Initiative, has developed and implemented an integrated high-throughput structure pipeline and applied it in a 2-tiered approach to mining the proteome of the thermophilic bacterium Thermotoga maritima.
Structural proteomics of an archaeon
Of the first 10 structures determined, several provided clues to biochemical functions that were not detectable from sequence analysis, and in many cases these putative functions could be readily confirmed by biochemical methods, demonstrating that structural proteomics is feasible and can play a central role in functional genomics.
Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics
The complete 1,751,377-bp sequence of the genome of the thermophilic archaeon Methanobacterium thermoautotrophicum deltaH has been determined by a whole-genome shotgun sequencing approach. A total of