Changes in this information may bring about new folds, functions and protein architectures. The n to cterminal series of domains in a protein is its domain architecture. 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. Evolution of protein domain promiscuity in eukaryotes core. Here, we assign proteins to groups with related domain compositions and functional properties, termed domain clubs, which we use to compare. Intrachain 3d segment swapping spawns the evolution of new. Figure 2 representations of the domain architectures of human p60 tim. 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. Domain architectures and catalytic functions of enzymes constitute the centerpieces of a metabolic network. Intrachain 3d segment swapping spawns the evolution of new multidomain protein architectures. Ausubela,b,1 adepartment of molecular biology, massachusetts general hospital, boston, ma 02114. Key words protein evolution, protein structure, sequence analysis, domain. Pdf intrachain 3d segment swapping spawns the evolution. 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.
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. Protein domain architectures provide a fast, efficient and scalable. The supradomain occurs in 35 different domain architectures, and 6 of these are given here. 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. Protein sequences change faster than protein structure and proteins with. Iyer lakshminarayan, 1 and carl wu 2 1 national center for biotechnology information, national library of medicine. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineagespecific. 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.
One domain may appear in a variety of different proteins. Modeling the evolution of protein domain architectures using. May 19, 2015 protein domains are generally thought to correspond to units of evolution. The structure of the protein universe and genome evolution. 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. Domain architectures of the scm3p protein provide insights into centromere function and evolution l. An evolutionary analysis of the domain content of proteins. Intrachain 3d segment swapping spawns the evolution of new multidomain protein architectures andras szilagyi1,2, yang zhang2,3. Reassessing domain architecture evolution of metazoan proteins. Jul 15, 2010 domains are evolutionarily conserved regions of proteins with generally independent structural and functional properties. We have only very recently begun to understand the evolution of protein domain architecture. Experimental support for the evolution of symmetric protein. Evolution of protein domain architectures chapter pdf available in methods in molecular biology clifton, n.
The architecture of the protein domain universe nikolay v. The general flow of this thesis begins with a single eukaryotic genome s. In view of the fact that appearance of novel protein domain. The domain architecture of a protein is defined as the ordered pattern of its pfama domains bateman et al. Next, we study the principles of protein domain architecture evolution and how these have been inferred from. Evolutionary analysis of the global landscape of protein. The architectural design of networks of protein domain. Ncbis conserved domain database and tools for protein.
Evolutionary dynamics of protein domain architecture in. Evolution of protein domain promiscuity in eukaryotes. 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. 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. 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. It includes protein domain and protein family models curated in house by. Domains are basic evolutionary units of proteins and most proteins have more than one domain. One of the significant conclusions was that changes in domain architecture preferentially occur at protein termini 17,18. 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. Research article open access evolutionary dynamics of. During protein evolution, novel domain arrangements are continuously formed. Jul 07, 2009 the protein universe is the set of all proteins of all organisms.
The nbslrr architectures of plant rproteins and metazoan. The evolution of protein domain families biochemical. Evolution of double muttnudix domaincontaining proteins. Symmetry is a central theme in protein structure, function, and evolution. Pdf protein domains are the structural, functional and evolutionary units of the protein.
Many proteins consist of several structural domains. Evolution of domain promiscuity in eukaryotic genomesa. In plants, because only the arabidopsis and rice genomes have been included in such. Gene duplicationfusion is a basic and important gene innovation mechanism for the evolution of double muttnudix domain proteins. 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. Protein domain architectures link evolutionarily related proteins and underscore their shared functions. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. Next, we study the principles of protein domain architecture evolution and how these have been inferred from distributions of extant domain. 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. Evolution of sdomain receptorlike kinases in land plants. 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.
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. These promiscuous domains are, typically, involved in proteinprotein interactions and play crucial roles in interaction networks, particularly those that contribute to signal transduction. 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. 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. 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. Protein domains are generally thought to correspond to units of evolution. Evolution and classification of the crisprcas systems. 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. Materials and methods domain architecture definition. Chapter 8 evolution of protein domain architectures. Pdf evolution of protein domain architectures researchgate. 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.
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. Jan 04, 2011 symmetry is a central theme in protein structure, function, and evolution. Mar 14, 2007 the field of protein folding has traditionally focused almost exclusively on the study of individual domains in isolation. A systematic comparativegenomic analysis of promiscuous domains in eukaryotes is described. Modeling the evolution of protein domain architectures. Finally, we use inferred domain architectures of ancestral genomes to trace the evolution of domain promiscuity in eukaryotic genomes. Evolutionary dynamics of protein domain architecture in plants.
We then predicted the protein domain architectures and produced a matrix of presenceabsence of each protein domain across all the eukaryotic taxa see 2. 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. Evolution eukaryotic protein domains as functional units of. 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. 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. All of the aarss are multidomain proteins, but the exact number and fold of each domain is speci. Domain architectures of the scm3p protein provide insights. Domain treebased analysis of protein architecture evolution.
Changes to architectures indicate divergence of protein sequence and structure that may affect the function of the protein. Pdf evolutionary dynamics of protein domain architecture in plants. 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. We end by a discussion of some available tools for computational analysis or exploitation of protein domain architectures and their evolution. R molecular architecture and evolution of a modular spider. The evolutionary tree of bacterial mutt proteins suggested that the double mutt domain proteins in d. Second, sequence and function might differ across evolutionary scales. 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. Gtp hydrolysis in the ploop domain drives the conformational change in the translation proteins domain, which is then transmitted onto the ribosome. 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. 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.
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. Evolution of domain architectures and catalytic functions of. 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. Protein domains, domain assignment, identification and. The nbslrr architectures of plant rproteins and metazoan nlrs evolved in independent events jonathan m. There has been a dynamic, lineagewise expansion of domain architectures during plant evolution. Is such domain versatility or promiscuity a persistent feature of a. Structural symmetry is observed in many different protein architectures, and gene duplication and fusion is the gen. Evolution of protein domain architectures springerlink. Protein domain architectures are the linear arrangements of.
Evolution of protein function by domain swapping 35 enzymatic activities necessary for a sequential set of reactions srere, 1987. Each domain has an intrinsic combinatorial propensity, and the effects of this have been studied using measures of domain versatility or promiscuity. Molecular architecture and evolution of a modular spider silk protein gene cheryl y. One subset of such domain architectures is domain repeats, i. Proteins having the same domain architecture are likely to have similar. 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. The inset at left shows a protein of known structure, which contains the supradomain. Adjacent domains in a protein are less similar than nonadjacent domains. Domain combinations in protein sequences are important biological and evolutionary features. The evolutionary mechanics of domain organization in. Given the ancestral architectures on the tree, we were able to track the origin of each architecture.
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. 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 begin by summarizing work on the phylogenetic distribution of proteins, as this directly impacts which domain architectures can be formed in different species. Structure, function and evolution of multidomain proteins. 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. We have presented a novel algorithm for analyzing protein architecture evolution based on domain trees. Eukaryotic protein domains as functional units of cellular.
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. The algorithm uses maximum parsimony to infer ancestral architectures. We analyzed 96 species across all kingdoms to find cases where a domain architecture had been created multiple times independently. An approach for purifying nuclear proteins that bind directly to the hyperphosphorylated. Pdf evolution of protein architectures inferred from. Analysis of the protein domain and domain architecture content in. Design of protein function leaps by directed domain. Almost all growth comes from new multidomain architectures that are combinations of domains. Protein domain architectures are the linear arrangements of domain s in individual proteins. With the present and still increasing wealth of sequences and. Domains are evolutionarily conserved regions of proteins with generally independent structural and functional properties. Major impact of gene prediction errors vol 2, pg 449, 2011. Reconstruction of protein domain evolution using singlecell. We conclude that gene fusionfission is a major contributor to modular evolution of multi domain bacterial proteins.
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. Domain tree based analysis of protein architecture evolution. Experimental support for the evolution of symmetric. Each domain forms a compact threedimensional structure and often can be independently stable and folded.
Evolution of protein architectures inferred from phylogenomic analysis of cath. Nov 14, 2002 the structure of the protein universe and genome evolution. Protein domains are structural, functional, and evolutionary units of proteins 9, 10 and are. Comparative hic reveals that ctcf underlies evolution of.
This attention to single domain protein fragments or small proteins has. The folding and evolution of multidomain proteins nature. Gene fusionfission is a major contributor to evolution of. Such domains often carry their function with them when they get inserted into different proteins during evolution. To study the evolution of protein domain architecture we developed a new algorithm based on the maximum parsimony criterion to infer ancestral architectures. 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. Intrachain 3d segment swapping spawns the evolution of. Architectures are useful for classifying evolutionarily related proteins, in particular to detect evolutionarily distant homologs based on shared domains. We begin by summarizing work on the phylogenetic distribution of proteins, as this directly impacts which. Despite the evidences of domain gain and loss in various organisms, the mechanism through which these dynamics are achieved is largely unknown. Chapter 8 evolution of protein domain architectures core. 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.
917 1168 1223 1369 1334 1396 1367 493 32 331 866 1275 57 602 377 586 839 414 354 904 1337 969 607 472 952 533 1464 42 1387 108 1257 482 1458 238 809 1276 1477 11 1261 1481 1122 380 1042