In:
Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 7 ( 2012-02-14)
Abstract:
In conclusion, we used biochemistry and bioinformatics to demonstrate the displacement of an essential, “universal” protein by a completely unrelated one in one branch of the tree of life. The structure of ThermoDBP reveals a unique solution to the problem of ssDNA binding. This result suggests that even the most fundamental, ubiquitous proteins can be replaced during evolution. We proceeded to characterize the properties of the Ttx1576 protein, (which we renamed “ThermoDBP” for Thermoproteales DNA-binding protein), showing that it has all the biochemical properties consistent with a role as a functional SSB, including a clear preference for ssDNA binding and low sequence specificity. Using crystallographic analysis, we solved the structure of the DNA-binding domain of ThermoDBP, revealing a protein fold with a prominent cleft punctuated with aromatic amino acid residues and lined by positively charged residues. The structure of ThermoDBP immediately suggested a mechanism for the binding of ssDNA along the cleft that is reminiscent of the binding clefts of canonical SSB proteins but is unrelated to them in sequence and detailed structure. The two ssDNA-binding domains are linked by a C-terminal helical coiled-coil domain that allows ThermoDBP to dimerize ( Fig. P1 ). Because a functional SSB is likely to be essential for any organism, we reasoned that the Thermoproteales might have lost the canonical SSB gene and replaced it with another, unrelated gene. To test this hypothesis, we undertook a two-pronged approach comprising a combination of bioinformatics and biochemistry. The bioinformatic analysis involved a search for any genes that were common to the 10 Thermoproteales species lacking the canonical SSB and that were not found in any other genome. Remarkably, only a single gene fits these criteria, ttx1576 . This observation is clearly compatible with the possibility that the Ttx1576 protein compensates functionally for the missing SSB protein in Thermoproteales. The biochemical route involved direct purification and identification of proteins that could bind to ssDNA in one of the Thermoproteales, Thermoproteus tenax . This approach resulted in the identification of the product of the gene ttx1576 as a candidate for the missing SSB. Rapid advances in genome-sequencing technology over the past 15 y yielded a wealth of new information on many divergent parts of the tree of life that can be mined for information to illuminate all aspects of biology. The tree of life consists of three fundamental divisions known as “domains”: Eukarya (organisms with a nucleus where DNA is stored, including plants, fungi, animals) and the prokaryotic Bacteria and Archaea, which lack a nucleus ( 1 ). One of the most highly conserved proteins found in all three domains is the SSB protein, which binds and protects ssDNA during replication and repair of damage to the genome. It is an essential protein that is thought to have been present in the last common ancestor of all extant life ( 2 ). The defining feature of all known SSBs is the oligonucleotide-binding (OB) fold shown in Fig. P1 . Recently we noted that one group of archaeal species, the Thermoproteales, lack a detectable gene for the SSB protein in their genomes ( 3 ). Proteins are the major structural and operational components of cells. Even the simplest organisms possess hundreds of different proteins, and more complex organisms typically have many thousands. Because all living beings, from microbes to humans, are related by evolution, they share a core set of proteins in common. Proteins perform fundamental roles in key metabolic processes and in the processing of information from DNA via RNA to proteins. A notable example is the ssDNA-binding protein, SSB, which is essential for DNA replication and repair and is widely considered to be one of the few core universal proteins shared by all life forms. Here we demonstrate that one branch of the tree of life has lost this “ubiquitous” protein and replaced it with another, unrelated one. This finding has important implications for our understanding of the plasticity of evolution.
Type of Medium:
Online Resource
ISSN:
0027-8424
,
1091-6490
DOI:
10.1073/pnas.1113277108
Language:
English
Publisher:
Proceedings of the National Academy of Sciences
Publication Date:
2012
detail.hit.zdb_id:
209104-5
detail.hit.zdb_id:
1461794-8
SSG:
11
SSG:
12
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