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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Combinations of ancestral modules in proteins
Yehoshua Sobolevsky1, Zakharia M Frenkel, Edward N Trifonov
1Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel.
Twenty-seven omnipresent protein sequence elements, conserved since the last universal common ancestor (LUCA), were identified in prokaryotic proteomes. These elements, forming closed-loop modules, suggest a common evolutionary origin and may illuminate early protein evolution.
Area of Science:
- Biochemistry
- Molecular Biology
- Evolutionary Biology
Background:
- Identified 27 omnipresent protein sequence elements (6-9 amino acids) from 15 diverse prokaryotic proteomes.
- These elements are conserved across all studied proteomes, suggesting Last Universal Common Ancestor (LUCA) origin.
- Elements identified as parts of conserved closed loops (25-30 residues) in crystallized protein structures.
Purpose of the Study:
- To investigate the origin and evolutionary significance of omnipresent protein sequence elements.
- To analyze the grouping and functional involvement of these conserved elements.
- To explore the potential common sequence origin of these elements through sequence space network analysis.
Main Methods:
- Extraction of 27 omnipresent protein sequence elements from 15 prokaryotic proteomes.
- Analysis of elements within crystallized protein structures to identify conserved closed loops.
- Grouping of elements into seven distinct clusters (e.g., Aleph, Beth) and analysis of their combinations in proteins.
- Sequence space network analysis to investigate common sequence origins.
Main Results:
- All 27 elements are present in all 15 proteomes, conserved since LUCA and forming closed-loop modules.
- Elements grouped into seven distinct clusters, with Aleph (18 elements) and Beth (4 elements) being the largest.
- LUCA modules appear in various combinations within protein molecules, correlating with protein function.
- Sequence space network analysis indicates a potential common sequence origin for many of the 27 elements.
Conclusions:
- The identified omnipresent elements represent conserved LUCA modules forming closed-loop structures.
- These modules exhibit diverse combinations and functional roles across prokaryotic proteins.
- Evidence suggests a common ancestral origin for these elements, offering insights into early protein evolution.
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