We begin by summarizing work on the phylogenetic distribution of proteins, as this directly impacts which. Dokholyan department of biochemistry and biophysics, the university of north carolina at chapel hill, school of medicine, chapel hill, nc 27599 abstract understanding the design of the universe of protein structures may provide insights into protein evolution. All of the aarss are multidomain proteins, but the exact number and fold of each domain is speci. Asprs has a catalytic domain shown in blue, an anticodon binding domain orange, sometimes also referred to as the nterminal domain, and an insertion domain. The evolutionary mechanics of domain organization in. Protein domain architectures link evolutionarily related proteins and underscore their shared functions. The general flow of this thesis begins with a single eukaryotic genome s. Domain treebased analysis of protein architecture evolution. Comparative hic reveals that ctcf underlies evolution of. Analysis of the protein domain and domain architecture content in. Intrachain 3d segment swapping spawns the evolution of new multidomain protein architectures. Protein domains are generally thought to correspond to units of evolution.
Almost all growth comes from new multidomain architectures that are combinations of domains. There has been a dynamic, lineagewise expansion of domain architectures during plant evolution. Experimental support for the evolution of symmetric protein architecture from a simple peptide motif jihun lee and michael blaber1 department of biomedical sciences, florida state university, tallahassee fl 323064300 edited by brian w. Mar 14, 2007 the field of protein folding has traditionally focused almost exclusively on the study of individual domains in isolation. Despite the evidences of domain gain and loss in various organisms, the mechanism through which these dynamics are achieved is largely unknown. The architecture of the protein domain universe nikolay v. Evolution of protein domain promiscuity in eukaryotes. To perform this analysis, we built a database of 116 proteomes of different eukaryotic taxa electronic supplementary material, table s7, representing the entire eukaryotic diversity. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable. Such domains often carry their function with them when they get inserted into different proteins during evolution. Jul 15, 2010 domains are evolutionarily conserved regions of proteins with generally independent structural and functional properties. An approach for purifying nuclear proteins that bind directly to the hyperphosphorylated. Once a domain or protein has duplicated, it can evolve a new or modified function either by sequence divergence or by combining with other domains to form a multidomain protein with a new series of domains. Protein domains are the structural, functional and evolutionary units of the protein.
Architectures are useful for classifying evolutionarily related proteins, in particular to detect evolutionarily distant homologs based on shared domains. Changes to architectures indicate divergence of protein sequence and structure that may affect the function of the protein. Feb 09, 2007 read modeling the evolution of protein domain architectures using maximum parsimony, journal of molecular biology on deepdyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips. Feb 09, 2007 to study protein evolution, we will consider domain architectures, which unlike domain combinations fully specify the sequential organization of conserved units in entire proteins. Gene fusionfission is a major contributor to evolution of.
These protein domains are essentially the main components of globular proteins and are the most principal level at which protein function and protein interactions can be understood. Figure 2 representations of the domain architectures of human p60 tim. To study the evolution of protein domain architecture we developed a new algorithm based on the maximum parsimony criterion to infer ancestral architectures. In plants, because only the arabidopsis and rice genomes have been included in such. The conserved domain database cdd is a freely available resource for the annotation of sequences with the locations of conserved protein domain footprints, as well as functional sites and motifs inferred from these footprints. Evolutionary analysis of the global landscape of protein. The evolution of protein domain families biochemical. Protein domain architectures are the linear arrangements of domain s in individual proteins. Evolution and classification of the crisprcas systems. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined.
Adjacent domains in a protein are less similar than nonadjacent domains. The evolutionary tree of bacterial mutt proteins suggested that the double mutt domain proteins in d. The nbslrr architectures of plant rproteins and metazoan. Evolution of double muttnudix domaincontaining proteins. Evolution of sdomain receptorlike kinases in land plants. Pdf evolution of protein architectures inferred from. Finally, we examine whether all known cases of a given domain architecture can be assumed to have a single common origin monophyly or have evolved convergently polyphyly. Ncbis conserved domain database and tools for protein. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. Is such domain versatility or promiscuity a persistent feature of a. Protein domain architectures are the linear arrangements of. It includes protein domain and protein family models curated in house by. The architectural design of networks of protein domain.
Structural symmetry is observed in many different protein architectures, and gene duplication and fusion is the gen. We then predicted the protein domain architectures and produced a matrix of presenceabsence of each protein domain across all the eukaryotic taxa see 2. Structure, function and evolution of multidomain proteins. The supradomain occurs in 35 different domain architectures, and 6 of these are given here. Experimental support for the evolution of symmetric. Changes in this information may bring about new folds, functions and protein architectures. Evolution of domain promiscuity in eukaryotic genomesa. Intrachain 3d segment swapping spawns the evolution of new multidomain protein architectures andras szilagyi1,2, yang zhang2,3. Evolutionary dynamics of protein domain architecture in plants.
Modular protein domains are functional units that can be modified through the acquisition of new intrinsic activities or by the formation of novel domain combinations, thereby contributing to the evolution of proteins with new biological properties. Finally, we use inferred domain architectures of ancestral genomes to trace the evolution of domain promiscuity in eukaryotic genomes. Reconstruction of protein domain evolution using singlecell. Protein domains are structural, functional and evolutionary building blocks that, within one protein, can form various architectures that may be composed of one or several domains. We begin by summarizing work on the phylogenetic distribution of proteins, as this directly impacts which domain architectures can be formed in different species. Protein domains, domain assignment, identification and. These promiscuous domains are, typically, involved in proteinprotein interactions and play crucial roles in interaction networks, particularly those that contribute to signal transduction. Structural symmetry is observed in many different protein architectures, and gene duplication and fusion is the generally hypothesized mechanism for the emergence of symmetric architecture from simpler i. Domain architectures of the scm3p protein provide insights.
Cell reports article comparative hic reveals that ctcf underlies evolution of chromosomal domain architecture matteo vietri rudan,1 christopher barrington,1 stephen henderson,1 christina ernst,2 duncan t. Many proteins consist of several structural domains. The proteins of such a set can also be placed in an evolutionary tree, and the evolution of all multi domain architectures containing the reference domain can be expressed in terms of insertions and deletions of other domains along this tree to form the extant domain architectures. Design of protein function leaps by directed domain interface evolution jin huang, akiko koide, koki makabe, and shohei koide department of biochemistry and molecular biology, university of chicago, 929 east 57th street, chicago, il 60637. Research article open access evolutionary dynamics of. A protein domain is a conserved part of a given protein sequence and tertiary structure that can evolve, function, and exist independently of the rest of the protein chain. Modeling the evolution of protein domain architectures using. The folding and evolution of multidomain proteins nature. We have presented a novel algorithm for analyzing protein architecture evolution based on domain trees. The inset at left shows a protein of known structure, which contains the supradomain.
Modeling the evolution of protein domain architectures. Evolution of protein domain architectures chapter pdf available in methods in molecular biology clifton, n. Jul 07, 2009 the protein universe is the set of all proteins of all organisms. Odom,2 amos tanay,3 and suzana hadjur1, 1research department of cancer biology, cancer institute, university college london, 72 huntley street, london wc1e 6bt, uk. Proteins having the same domain architecture are likely to have similar. A systematic comparativegenomic analysis of promiscuous domains in eukaryotes is described. Domain combinations in protein sequences are important biological and evolutionary features. Next, we study the principles of protein domain architecture evolution and how these have been inferred from distributions of extant domain. An evolutionary analysis of the domain content of proteins. One domain may appear in a variety of different proteins. The domain architectures present in cbm14containing proteins are also mapped on the species phylogenetic tree, with tree branches colored based on the species taxonomic classification at the phylum.
Protein domain architectures pdas, in which single domains are linked to form multipledomain proteins, are a major molecular form used by evolution for the diversification of protein functions. Here, we assign proteins to groups with related domain compositions and functional properties, termed domain clubs, which we use to compare. Next, we study the principles of protein domain architecture evolution and how these have been inferred from distributions of extant domain arrangements. We conclude that gene fusionfission is a major contributor to modular evolution of multi domain bacterial proteins. The domain architecture of a protein is defined as the ordered pattern of its pfama domains bateman et al. Here, all currently known sequences are analyzed in terms of families that have single domain or multidomain architectures and whether they have a known threedimensional structure. Materials and methods domain architecture definition. One of the significant conclusions was that changes in domain architecture preferentially occur at protein termini 17,18. Each domain forms a compact threedimensional structure and often can be independently stable and folded. Iyer lakshminarayan, 1 and carl wu 2 1 national center for biotechnology information, national library of medicine.
R molecular architecture and evolution of a modular spider. With the present and still increasing wealth of sequences and. The n to cterminal series of domains in a protein is its domain architecture. Evolutionary dynamics of protein domain architecture in.
Evolution of protein domain promiscuity in eukaryotes core. Chapter 8 evolution of protein domain architectures. Protein domain architectures pdas, in which single domains are linked to form multiple domain proteins, are a major molecular form used by evolution for the diversification of protein functions. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineagespecific. The structure of the protein universe and genome evolution. The nbslrr architectures of plant rproteins and metazoan nlrs evolved in independent events jonathan m. Although only a fairly limited set of domains has been created during evolution, combining these domains in different ways has led to the huge number of observed protein domain architectures. Nov 14, 2002 the structure of the protein universe and genome evolution. Domains are basic evolutionary units of proteins and most proteins have more than one domain. One subset of such domain architectures is domain repeats, i. Evolution of protein domain architectures springerlink. Gtp hydrolysis in the ploop domain drives the conformational change in the translation proteins domain, which is then transmitted onto the ribosome. Evolution of protein function by domain swapping 35 enzymatic activities necessary for a sequential set of reactions srere, 1987.
Next, we study the principles of protein domain architecture evolution and how these have been inferred from. May 19, 2015 protein domains are generally thought to correspond to units of evolution. Design of protein function leaps by directed domain. Intrachain 3d segment swapping spawns the evolution of new. To simplify the image, the order of the domains in each protein as well as intra protein domain duplications have not been taken into account. Architectures are useful for classifying evolutionarily related proteins, in particular to detect evolutionarily distant homologs based on shared domains rather than on pairwise sequence similarity. The algorithm uses maximum parsimony to infer ancestral architectures. The fraction of promiscuous domains in animals is shown to be significantly greater than that in fungi or plants. Second, sequence and function might differ across evolutionary scales. Furthermore, a maximum parsimony algorithm has been established to analyze the evolution of protein architectures, in particular domain fusion and fission, based on the inferred ancestral architecture at each node in the species trees or domain trees 25, 26. Jan 17, 2012 protein domains are the structural, functional and evolutionary units of the protein. Proteins are composed of evolutionarily conserved units called domains, often corresponding to subunits of the 3d structure of a protein, that have distinct molecular function and structure. Domain architectures of the scm3p protein provide insights into centromere function and evolution l. The domain architecture, or order of domains in a protein, is considered as a fundamental level of protein functional complexity holm and sander, 1994 and.
Pdf intrachain 3d segment swapping spawns the evolution. An important aspect of domain evolution is their atomic structure and biochemical function, which are both specified by the information in the amino acid sequence. Experimental support for the evolution of symmetric protein. In particular, domain shuffling was found to have an important role in the evolution of some signaling systems of metazoans, 23 in the development of typical characteristics of vertebrates and chordates, 24 and in the evolution of innate immune systems in both vertebrates and invertebrates. Advances in domain modeling and collection are making it possible to annotate a large fraction of known protein sequences by a linear ordering of their domains, yielding their architecture. Evolutionary dynamics of protein domain architecture in plants xuecheng zhang1,6, zheng wang2, xinyan zhang3,7,mihale1, jianguo sun3, dong xu2,4, jianlin cheng2,4 and gary stacey1,5 abstract background. Domain architectures and catalytic functions of enzymes constitute the centerpieces of a metabolic network. Domain tree based analysis of protein architecture evolution. Jan 14, 2009 protein domains are compact evolutionary units of structure and function that usually combine in proteins to produce complex domain arrangements. Symmetry is a central theme in protein structure, function, and evolution. Reassessing domain architecture evolution of metazoan proteins. Major impact of gene prediction errors vol 2, pg 449, 2011. Gene duplicationfusion is a basic and important gene innovation mechanism for the evolution of double muttnudix domain proteins. The olduvai domain, known until 2018 as duf1220 domain of unknown function 1220 and the nbpf repeat, is a protein domain that shows a striking human lineagespecific hls increase in copy number and appears to be involved in human brain evolution.
In view of the fact that appearance of novel protein domain. Domains are evolutionarily conserved regions of proteins with generally independent structural and functional properties. Key words protein evolution, protein structure, sequence analysis, domain. It has been suggested that in the early evolution of proteins, segments of polypeptide, unable to fold in isolation, may have collapsed together to form folded proto domains. Molecular architecture and evolution of a modular spider silk protein gene cheryl y.
Evolution eukaryotic protein domains as functional units of. Pdf evolution of protein domain architectures researchgate. Jan 04, 2011 symmetry is a central theme in protein structure, function, and evolution. Evolution of protein architectures inferred from phylogenomic analysis of cath. Protein sequences change faster than protein structure and proteins with. Pdf protein domains are the structural, functional and evolutionary units of the protein. Each domain has an intrinsic combinatorial propensity, and the effects of this have been studied using measures of domain versatility or promiscuity. Evolutionary reconstructions indicate that domain promiscuity is a volatile, relatively fastchanging feature of eukaryotic proteins, with few domains remaining promiscuous throughout the evolution of eukaryotes. We end by a discussion of some available tools for computational analysis or exploitation of protein domain architectures and their evolution.
Protein domains are structural, functional, and evolutionary units of proteins 9, 10 and are. Ausubela,b,1 adepartment of molecular biology, massachusetts general hospital, boston, ma 02114. Protein domain architectures provide a fast, efficient and scalable. Eukaryotic protein domains as functional units of cellular. We analyzed 96 species across all kingdoms to find cases where a domain architecture had been created multiple times independently. In order to study their evolution, we reconstructed genomebased phylogenetic trees of architectures from a census of domain structure and organization conducted at protein fold and foldsuperfamily levels in hundreds of fully sequenced genomes.
We have only very recently begun to understand the evolution of protein domain architecture. During protein evolution, novel domain arrangements are continuously formed. Jul 22, 2009 in previous work where protein evolution has been studied from the domain perspective, homology was assumed between the proteins with similar domain architectures, and differences in domain composition were looked for. This attention to single domain protein fragments or small proteins has. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Intrachain 3d segment swapping spawns the evolution of. Evolution of domain architectures and catalytic functions of. Pdf evolutionary dynamics of protein domain architecture in plants.
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