Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins

Ainali, Chrysanthi; Simon, Michelle; Freilich, Shiri; Espinosa, Octavio; Hazelwood, Lee; Tsoka, Sophia; Ouzounis, Christos A.; Hancock, John M.
January 2011
BMC Evolutionary Biology;2011, Vol. 11 Issue 1, p142
Academic Journal
Background: Cellular ATP levels are generated by glucose-stimulated mitochondrial metabolism and determine metabolic responses, such as glucose-stimulated insulin secretion (GSIS) from the β-cells of pancreatic islets. We describe an analysis of the evolutionary processes affecting the core enzymes involved in glucose-stimulated insulin secretion in mammals. The proteins involved in this system belong to ancient enzymatic pathways: glycolysis, the TCA cycle and oxidative phosphorylation. Results: We identify two sets of proteins, or protein coalitions, in this group of 77 enzymes with distinct evolutionary patterns. Members of the glycolysis, TCA cycle, metabolite transport, pyruvate and NADH shuttles have low rates of protein sequence evolution, as inferred from a human-mouse comparison, and relatively high rates of evolutionary gene duplication. Respiratory chain and glutathione pathway proteins evolve faster, exhibiting lower rates of gene duplication. A small number of proteins in the system evolve significantly faster than co-pathway members and may serve as rapidly evolving adapters, linking groups of co-evolving genes. Conclusions: Our results provide insights into the evolution of the involved proteins. We find evidence for two coalitions of proteins and the role of co-adaptation in protein evolution is identified and could be used in future research within a functional context.


Related Articles

  • A comprehensive analysis of non-sequential alignments between all protein structures. Abyzov, Alexej; Ilyin, Valentin A. // BMC Structural Biology;2007, Vol. 7, p78 

    Background: The majority of relations between proteins can be represented as a conventional sequential alignment. Nevertheless, unusual non-sequential alignments with different connectivity of the aligned fragments in compared proteins have been reported by many researchers. It is interesting to...

  • Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display. Pal, Arumay; Bahadur, Ranjit Prasad; Ray, Partha Sarathi; Chakrabarti, Pinak // BMC Bioinformatics;2009, Vol. 10, Special section p1 

    Background: Depending on chemical features residues have preferred locations -- interior or exterior -- in protein structures, which also determine how many other residues are found around them. The close packing of residues is the hallmark of protein interior and protein-protein interaction...

  • WildSpan: mining structured motifs from protein sequences. Chen-Ming Hsu; Chien-Yu Chen; Baw-Jhiune Liu // Algorithms for Molecular Biology;2011, Vol. 6 Issue 1, p6 

    Background: Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually...

  • Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins. Marsico, Annalisa; Henschel, Andreas; Winter, Christof; Tuukkanen, Anne; Vassilev, Boris; Scheubert, Kerstin; Schroeder, Michael // BMC Bioinformatics;2010, Vol. 11, p204 

    Background: A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably...

  • APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. O. O'Sullivan; M. Zehnder; D. Higgins; P. Bucher; A. Grosdidier; C. Notredame // Bioinformatics;Jan2009 Supplement, Vol. 19, p215 

    Motivation: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple...

  • Prediction of the translocon-mediated membrane insertion free energies of protein sequences. Yungki Park; Volkhard Helms // Bioinformatics;May2008, Vol. 24 Issue 10, p1271 

    Motivation: Helical membrane proteins (HMPs) play crucial roles in a variety of cellular processes. Unlike water-soluble proteins, HMPs need not only to fold but also get inserted into the membrane to be fully functional. This process of membrane insertion is mediated by the translocon complex....

  • SH3-like Fold Proteins are Structurally Conserved and Functionally Divergent. Kishan, K. V. Radha; Agrawal, Vishal // Current Protein & Peptide Science;Apr2005, Vol. 6 Issue 2, p143 

    The folding space for all the protein sequences is limited. Therefore it was observed that many proteins, whose sequences are not related, have similar fold characteristics. The fold databases like SCOP and CATH have classified various protein folds. However, in-depth analysis of the functional...

  • Expression and Molecular Characterization of Spherical Particles Derived from the Genome of the Hyperthermophilic Euryarchaeote Pyrococcus furiosus. Namba, Kazunori; Hagiwara, Kyoji; Tanaka, Hideaki; Nakaishi, Yuichiro; Khoon Tee Chong; Yamashita, Eiki; Armah, George Enyimah; Ono, Yasuko; Ishino, Yoshizumi; Omura, Toshihiro; Tsukihara, Tomitake; Nakagawa, Atsushi // Journal of Biochemistry;Aug2005, Vol. 138 Issue 2, p193 

    Spherical particles (SPs) of approximately 30 nm in diameter were found in the hyperthermophilic archaeon Pyrococcus furiosus. The SPs contained no nucleic acid and were composed of a single 39-kDa protein. The amino acid sequences of the amino-terminal and internal fragments were identical to...

  • Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. Yaniv Loewenstein; Elon Portugaly; Menachem Fromer; Michal Linial // Bioinformatics;Jul2008, Vol. 24 Issue 13, pi41 

    Motivation: UPGMA (average linking) is probably the most popular algorithm for hierarchical data clustering, especially in computational biology. However, UPGMA requires the entire dissimilarity matrix in memory. Due to this prohibitive requirement, UPGMA is not scalable to very large datasets....


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics