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Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain

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Structural features and the persistence of acquired proteins.

Hema Prasad Narra¹, Matthew H J Cordes, Howard Ochman

¹Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.

|October 17, 2008

Summary

ORFan genes, lacking homologs, were studied for their persistence in bacterial genomes. Persistent ORFan and HOP genes in E. coli are more likely to encode soluble, functional proteins.

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Area of Science:

Microbiology
Genomics
Structural Biology

Background:

ORFan genes are abundant in bacterial genomes but their functions are largely unknown due to a lack of homologous genes.
Understanding the characteristics of ORFan genes is crucial for deciphering their roles in bacterial evolution and adaptation.

Purpose of the Study:

To investigate the properties of ORFan genes that contribute to their long-term presence in the Escherichia coli lineage.
To compare ORFan genes with heterogeneous occurrence in prokaryotes (HOPs) genes, which possess homologs in other bacteria.

Main Methods:

Selection of 54 ORFan and HOP genes from different evolutionary depths within the E. coli lineage.
Cloning, expression, and purification of selected genes.
Circular dichroism (CD) spectroscopy to analyze the secondary structures of the encoded proteins.

Main Results:

A majority of the selected genes were expressed, with 18 yielding sufficient soluble protein for structural analysis.
Among the analyzed proteins, 50% were significantly alpha-helical, 16.7% were predominantly beta-sheet, and 33.3% had intermediate or indeterminate structures.
While HOPs showed a higher yield of soluble proteins, ORFans shared most other tested features with HOPs, suggesting similar evolutionary pressures.

Conclusions:

Genes, including ORFans, that persist in the E. coli lineage are more likely to encode soluble and folded proteins.
Persistent ORFan and HOP genes exhibit environmental modulation of gene expression, indicating functional relevance.
The study suggests that persistence in a genome correlates with protein solubility, structural integrity, and potential functionality.