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

@article{Jenney2007TheIO,
  title={The impact of extremophiles on structural genomics (and vice versa)},
  author={F. E. Jenney and M. Adams},
  journal={Extremophiles},
  year={2007},
  volume={12},
  pages={39-50}
}
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… Expand
View on Springer
ncbi.nlm.nih.gov
48 Citations
Background Citations
16

48 Citations

Citation Type

Citation Type

Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome
TLDR
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. Expand
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… Expand
Presence of structural homologs of ubiquitin in haloalkaliphilic Archaea.
TLDR
The amplification and proteomic analysis of a 400-bp DNA fragment from the haloalkaliphilic archaeon Natrialba magadii shows the presence in Archaea of structural homologs of ubiquitin- related proteins. Expand
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… Expand
Bioprospecting in the genomic age.
TLDR
A number of recent advances in bioprospecting are discussed within the context of the genomic age, which promises great advances in the search for useful biocatalysts. Expand
Mycobacterium thermoresistibile as a source of thermostable orthologs of Mycobacterium tuberculosis proteins
TLDR
This study establishes a thermophilic mycobacterial model organism, Mycobacterium thermoresistibile (Mth), and introduces a thermophile as a source of protein for the study of a closely related human pathogen and marks a new approach to solving challenging myc Cobacterial protein structures. Expand
An Efficient Strategy for Small-Scale Screening and Production of Archaeal Membrane Transport Proteins in Escherichia coli
TLDR
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. Expand
Análisis de la respiración de nitrito en Thermus thermophilus
We have obtained draft genomic sequences of PD (partial denitrificant) and CD (complete denitrificant) strains of Thermus thermophilus. Their genomes are similar in size to that of the aerobic… Expand
Major players on the microbial stage: why archaea are important.
TLDR
Evidence is outlined by an increasingly large and productive group of scientists that demonstrates not only that the Archaea contribute significantly to global nutrient cycling, but also that they compete successfully in 'mainstream' environments. Expand
Partial and complete denitrification in Thermus thermophilus: lessons from genome drafts.
TLDR
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. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 112 REFERENCES
Crystallographic analyses of hyperthermophilic proteins.
  • D. Rees
  • Biology, Medicine
  • Methods in enzymology
  • 2001
TLDR
The focus of this chapter is to review the status and some general implications of crystallographic studies on hyperthermophilic proteins, with emphasis on relevant technical aspects of the structure determination, quality of the crystals, and conclusions about thermal stability and other properties of these fascinating proteins. Expand
Developments in Structural Genomics: Protein Purification and Function Interpretation
TLDR
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. Expand
Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics.
  • T. Zarembinski, L. Hung, +4 authors S. Kim
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
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. Expand
Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability.
Despite numerous studies, understanding the structural basis of protein stability in thermophilic organisms has remained elusive. One of the main reasons is the limited number of thermostable protein… Expand
High-throughput production of Pyrococcus furiosus proteins: considerations for metalloproteins.
TLDR
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. Expand
Integrating Structure, Bioinformatics, and Enzymology to Discover Function
TLDR
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. Expand
Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing.
TLDR
Three-dimensional protein folds were assigned to all ORFs of the recently sequenced genome of the hyperthermophilic archaeon Pyrobaculum aerophilum for the selection of attractive targets for crystallographic or NMR structure determination. Expand
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline
  • S. Lesley, P. Kuhn, +25 authors R. Stevens
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 2002
TLDR
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. Expand
A scaleable and integrated crystallization pipeline applied to mining the Thermotoga maritima proteome
TLDR
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. Expand
Structural proteomics of an archaeon
TLDR
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. Expand
...
1
2
3
4
5
...