Gerstein, M. & Hegyi, H. Comparing microbial genomes in terms of protein structure: surveys of a finite parts list. FEMS Microbiol. Rev. 22, 277

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
FEMS Microbiology Reviews (Impact Factor: 13.24). 11/1998; 22(4):277-304. DOI: 10.1016/S0168-6445(98)00019-9
Source: PubMed


We give an overview of the emerging field of structural genomics, describing how genomes can be compared in terms of protein structure. As the number of genes in a genome and the total number of protein folds are both quite limited, these comparisons take the form of surveys of a finite parts list, similar in respects to demographic censuses. Fold surveys have many similarities with other whole-genome characterizations, e.g., analyses of motifs or pathways. However, structure has a number of aspects that make it particularly suitable for comparing genomes, namely the way it allows for the precise definition of a basic protein module and the fact that it has a better defined relationship to sequence similarity than does protein function. An essential requirement for a structure survey is a library of folds, which groups the known structures into 'fold families.' This library can be built up automatically using a structure comparison program, and we described how important objective statistical measures are for assessing similarities within the library and between the library and genome sequences. After building the library, one can use it to count the number of folds in genomes, expressing the results in the form of Venn diagrams and 'top-10' statistics for shared and common folds. Depending on the counting methodology employed, these statistics can reflect different aspects of the genome, such as the amount of internal duplication or gene expression. Previous analyses have shown that the common folds shared between very different microorganisms, i.e., in different kingdoms, have a remarkably similar structure, being comprised of repeated strand-helix-strand super-secondary structure units. A major difficulty with this sort of 'fold-counting' is that only a small subset of the structures in a complete genome are currently known and this subset is prone to sampling bias. One way of overcoming biases is through structure prediction, which can be applied uniformly and comprehensively to a whole genome. Various investigators have, in fact, already applied many of the existing techniques for predicting secondary structure and transmembrane (TM) helices to the recently sequenced genomes. The results have been consistent: microbial genomes have similar fractions of strands and helices even though they have significantly different amino acid composition. The fraction of membrane proteins with a given number of TM helices falls off rapidly with more TM elements, approximately according to a Zipf law. This latter finding indicates that there is no preference for the highly studied 7-TM proteins in microbial genomes. Continuously updated tables and further information pertinent to this review are available over the web at

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Available from: Hedi Hegyi, Feb 01, 2014
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    • "Molecular evolutionists were cognizant of the limitation of looking at the history of only few component parts, which by definition could be divergent. When genomic sequences became widely available, pioneers jumped onto the bandwagon of evolutionary genomics and the possibility of gaining systemic knowledge from entire repertoires of genes and molecules (e.g., [35] [36] [37] [38] [39]). The genomic revolution, for example, quickly materialized in gene content trees that reconstructed the evolution of genomes directly from their evolutionary units, the genes (e.g., [37] [39] [40]), or the domain constituents of the translated proteins [35] [41]. "
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    ABSTRACT: The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.
    Archaea 06/2014; 2014(12). DOI:10.1155/2014/590214 · 2.71 Impact Factor
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    • "It is important to keep in mind that these methodologies have limitations, especially if they are used to gain insights into the relation between the 3D structure and activity of poorly characterized proteins. Knowledge-based model generators and evaluators assume surjective relations between structure and activity, since the common idea of modellers of protein 3D structures is to assist in the grouping of protein structures based on similar attributes (Gerstein & Hegyi, 1998; Domingues et al., 2000; Skolnick et al., 2000). Therefore, in these cases knowledge of the protein 3D structure may provide inaccurate information about the activity (Martin et al., 1998). "
    Protein Interactions, 03/2012; , ISBN: 978-953-51-0244-1
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    • "The function of such proteins can be predicted based on the arrangement of distinct domains [7] in them since this arrangement in proteomes reflects the fundamental evolutionary differences in their genomes [8]. But with proteins containing more than one domain, the general function can only be suggested. "
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    ABSTRACT: High-throughput genome sequencing has led to data explosion in sequence databanks, with an imbalance of sequence-structure-function relationships, resulting in a substantial fraction of proteins known as hypothetical proteins. Functions of such proteins can be assigned based on the analysis and characterization of the domains that they are made up of. Domains are basic evolutionary units of proteins and most proteins contain multiple domains. A subset of multidomain proteins is fused domains (overlapping domains), wherein sequence overlaps between two or more domains occur. These fused domains are a result of gene fusion events and their implication in diseases is well established. Hence, an attempt has been made in this paper to identify the fused domain containing hypothetical proteins from human genome homologous to parkinsonian targets present in KEGG database. The results of this research identified 18 hypothetical proteins, with domains fused with ubiquitin domains and having homology with targets present in parkinsonian pathway.
    09/2011; 2011:265253. DOI:10.5402/2011/265253
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