Signatures of domain shuffling in the human genome

To elucidate the role of exon shuffling in shaping the complexity of the human genome/proteome, we have systematically analyzed intron phase distributions in the coding sequence of human protein domains. We found that introns at the boundaries of domains show high excess of symmetrical phase combinations (i.e., 0-0, 1-1, and 2-2), whereas nonboundary introns show no excess symmetry. This suggests that exon shuffling has primarily involved rearrangement of structural and functional domains as a whole. Furthermore, we found that domains flanked by phase 1 introns have dramatically expanded in the human genome due to domain shuffling and that 1-1 symmetrical domains and domain families are nonrandomly distributed with respect to their age. The predominance and extracellular location of 1-1 symmetrical domains among domains specific to metazoans suggests that they are associated with the rise of multicellularity. On the other hand, 0-0 symmetrical domains tend to be over-represented among ancient protein domains that are shared between the eukaryotic and prokaryotic kingdoms, which is compatible with the suggestion of primordial domain shuffling in the progenote. To see whether the human data reflect general genomic patterns of metazoans, similar analyses were done for the nematode Caenorhabditis elegans. Although the C. elegans data generally concur with the human patterns, we identified fewer intron-bounded domains in this organism, consistent with the lower complexity of C. elegans genes. [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: Z. Gu and R. Stevens.]

Loopy proteins appear conserved in evolution

Over the last decade, structural biologists have unravelled many proteins that appear natively disordered. Common assumptions are that many of these proteins adopt structure through binding and that the structural flexibility enables them to adopt different functions. Here, we investigated regions of more than 70 sequence-consecutive residues that have no regular secondary structure (NORS). Analysing 31 entirely sequenced organisms, we predicted five times as many proteins with NORS regions (loopy proteins) in eukaryotes (20%) than in prokaryotes and archaeas (4%). Thousands of these NORS regions were over 150 residues long. The amino acid composition of NORS regions differed from that of loops in PDB. Although NORS proteins had significantly more residues in low-complexity regions than other proteins, simple cut-off thresholds for sequence bias missed most NORS regions. On average, NORS regions were evolutionarily at least as conserved as their flanking regions. Furthermore, yeast proteins with NORS regions had more protein-protein interaction partners than other proteins. Regulatory and transcription-related functions were over-represented in loopy proteins, biosynthesis and energy metabolism were under-represented. Overall, our analysis confirmed that proteins with non-regular structures appear to play important functional roles, and they may adopt as yet unknown types of protein structures.

Strategies for the identification, the assembly and the classification of integrated biological systems in completely sequenced genomes

The proteins involved in a single biological process may form a stable supra-molecular assembly or be transiently in interaction. Although, the first annotation steps of a complete genome may allow the identification of the different partners, their assembly in a functional system, referred to as an integrated system, is a domain where methodological effort has to be done. Indeed, the knowledge required to assemble partners of such systems should be explicitly included in annotation software. The availability of a complete genome, and therefore of all the proteins encoded by that genome, motivated the development of automated approaches through the coordinated combination of different bio-informatic methods allowing the identification of the different partners, their assembly and the classification of the reconstructed systems in functional categories. In this data flux, the identification of the sequence partners represents the principal bottleneck. Here, we describe and compare the results obtained with different classes of methods (BLASTP2, PSI-BLAST, MAST and META-MEME) applied to the identification in complete genomes of a given family of integrated systems: the ABC transporters. PSI-BLAST appears to significantly outperform motif-based methods, and the results are discussed according to the nature of the proteins and the structure of the sub-families.

[A evolutionary approach to identification of orthologous relationship across proteomes]

How to identify the true orthologous and paralogous relationships among protein families is still a key problem in genome annotation and comparative protemics. Here, a evolutionary approach to ascertainment of the orthologous relationships across the genomes is developed. Forty-four cases of protein families are used in the test for the evolutionary approach. Compared with the method of COG (cluster of orthologous groups of proteins), this approach can generally identify the orthologous relationships and accurately predict the genome function.

A comparative study on feature selection and classification methods using gene expression profiles and proteomic patterns

Feature selection plays an important role in classification. We present a comparative study on six feature selection heuristics by applying them to two sets of data. The first set of data are gene expression profiles from Acute Lymphoblastic Leukemia (ALL) patients. The second set of data are proteomic patterns from ovarian cancer patients. Based on features chosen by these methods, error rates of several classification algorithms were obtained for analysis. Our results demonstrate the importance of feature selection in accurately classifying new samples.

Heterozygosity: an expanding role in proteomics

The human genome sequence provides the framework for understanding the biology of human cell function. The next step is to intensify the investigation of protein function in the context of complex biological systems. Cellular functions are carried out by molecular complexes acting in concert rather than by single molecules or single reactions. Parallels have been drawn between scale-free nonbiologic networks and functionally interconnected metabolic pathways in the cell. Modeling of metabolic networks, in which functional modules or subnetworks represent individual related pathways, will lead to the prediction of protein function in the larger context of a complex system. Depending on the robustness of these metabolic networks, single-gene defects alone or in combination with other gene defects and the environment have the potential for invoking a spectrum of alterations in the integrity of a given network. The overall purpose of this review is to highlight the importance of simple heterozygosity for one pathogenic mutation or combinatorial heterozygosity for two or more mutations within or between individual genes in altering the stability of metabolic networks. Several forms of heterozygosity are considered, e.g., intra- and interallelic heterozygosity and double heterozygosity. The concepts of synergistic heterozygosity, loss of heterozygosity, and mitochondrial DNA heteroplasmy also are discussed in relation to the quantitative effects of coexisting mutations on the phenotypic expression of disease.

Domain combinations in archaeal, eubacterial and eukaryotic proteomes

There is a limited repertoire of domain families that are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products, and at the level of genes, duplication, recombination, fusion and fission are the processes that produce new genes. We attempt to gain an overview of these processes by studying the evolutionary units in proteins, domains, in the protein sequences of 40 genomes. The domain and superfamily definitions in the Structural Classification of Proteins Database are used, so that we can view all pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 783 out of the 859 superfamilies in SCOP in these genomes, and the 783 families occur in 1307 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour; 209 families do not make combinations with other families. This type of pattern can be described as a scale-free network. We also study the N to C-terminal orientation of domain pairs and domain repeats. The phylogenetic distribution of domain combinations is surveyed, to establish the extent of common and kingdom-specific combinations. Of the kingdom-specific combinations, significantly more combinations consist of families present in all three kingdoms than of families present in one or two kingdoms. Hence, we are led to conclude that recombination between common families, as compared to the invention of new families and recombination among these, has also been a major contribution to the evolution of kingdom-specific and species-specific functions in organisms in all three kingdoms. Finally, we compare the set of the domain combinations in the genomes to those in the RCSB Protein Data Bank, and discuss the implications for structural genomics.