Evolution of intrinsic disorder in eukaryotic proteins

Conformational flexibility conferred though regions of intrinsic structural disorder allows proteins to behave as dynamic molecules. While it is well-known that intrinsically disordered regions can undergo disorder-to-order transitions in real-time as part of their function, we also are beginning to learn more about the dynamics of disorder-to-order transitions along evolutionary time-scales. Intrinsically disordered regions endow proteins with functional promiscuity, which is further enhanced by the ability of some of these regions to undergo real-time disorder-to-order transitions. Disorder content affects gene retention after whole genome duplication, but it is not necessarily conserved. Altered patterns of disorder resulting from evolutionary disorder-to-order transitions indicate that disorder evolves to modify function through refining stability, regulation, and interactions. Here, we review the evolution of intrinsically disordered regions in eukaryotic proteins. We discuss the interplay between secondary structure and disorder on evolutionary time-scales, the importance of disorder for eukaryotic proteome expansion and functional divergence, and the evolutionary dynamics of disorder.     

The role of key residues in structure, function, and stability of cytochrome-c

Cytochrome-c (cyt-c), a multi-functional protein, plays a significant role in the electron transport chain, and thus is indispensable in the energy-production process. Besides being an important component in apoptosis, it detoxifies reactive oxygen species. Two hundred and eighty-five complete amino acid sequences of cyt-c from different species are known. Sequence analysis suggests that the number of amino acid residues in most mitochondrial cyts-c is in the range 104?±?10, and amino acid residues at only few positions are highly conserved throughout evolution. These highly conserved residues are Cys14, Cys17, His18, Gly29, Pro30, Gly41, Asn52, Trp59, Tyr67, Leu68, Pro71, Pro76, Thr78, Met80, and Phe82. These are also known as “key residues”, which contribute significantly to the structure, function, folding, and stability of cyt-c. The three-dimensional structure of cyt-c from ten eukaryotic species have been determined using X-ray diffraction studies. Structure analysis suggests that the tertiary structure of cyt-c is almost preserved along the evolutionary scale. Furthermore, residues of N/C-terminal helices Gly6, Phe10, Leu94, and Tyr97 interact with each other in a specific manner, forming an evolutionary conserved interface. To understand the role of evolutionary conserved residues on structure, stability, and function, numerous studies have been performed in which these residues were substituted with different amino acids. In these studies, structure deals with the effect of mutation on secondary and tertiary structure measured by spectroscopic techniques; stability deals with the effect of mutation on T _m (midpoint of heat denaturation), ?G _D (Gibbs free energy change on denaturation) and folding; and function deals with the effect of mutation on electron transport, apoptosis, cell growth, and protein expression. In this review, we have compiled all these studies at one place. This compilation will be useful to biochemists and biophysicists interested in understanding the importance of conservation of certain residues throughout the evolution in preserving the structure, function, and stability in proteins.     

PHAB toxins: a unique family of predatory sea anemone toxins evolving via intra-gene concerted evolution defines a new peptide fold

Sea anemone venoms have long been recognized as a rich source of peptides with interesting pharmacological and structural properties, but they still contain many uncharacterized bioactive compounds. Here we report the discovery, three-dimensional structure, activity, tissue localization, and putative function of a novel sea anemone peptide toxin that constitutes a new, sixth type of voltage-gated potassium channel (K_V) toxin from sea anemones. Comprised of just 17 residues, κ-actitoxin-Ate1a (Ate1a) is the shortest sea anemone toxin reported to date, and it adopts a novel three-dimensional structure that we have named the Proline-Hinged Asymmetric β-hairpin (PHAB) fold. Mass spectrometry imaging and bioassays suggest that Ate1a serves a primarily predatory function by immobilising prey, and we show this is achieved through inhibition of Shaker-type K_V channels. Ate1a is encoded as a multi-domain precursor protein that yields multiple identical mature peptides, which likely evolved by multiple domain duplication events in an actinioidean ancestor. Despite this ancient evolutionary history, the PHAB-encoding gene family exhibits remarkable sequence conservation in the mature peptide domains. We demonstrate that this conservation is likely due to intra-gene concerted evolution, which has to our knowledge not previously been reported for toxin genes. We propose that the concerted evolution of toxin domains provides a hitherto unrecognised way to circumvent the effects of the costly evolutionary arms race considered to drive toxin gene evolution by ensuring efficient secretion of ecologically important predatory toxins.     

Phylogenetic distribution, functional epitopes and evolution of the CSαβ superfamily

A superfamily of proteins often conserves a common structural scaffold but develops diverse biochemical and biological functions during evolution. The understanding of evolutionary mechanisms responsible for this diversity is of fundamental importance not only in structural genomics but also in nature-guided drug design. A superfamily of peptides with a conserved CSalphabeta structural motif provides a considerably intriguing example to approach such an issue. The peptides from this superfamily have wide origins, ranging from plants to animals, and exhibit diverse biological activities, varying from a sweet-tasting protein to antibacterial defensins and animal toxins targeting ion channels. This review describes the phylogenetic distribution and structural classifi cation of this unique scaffold and provides new insights into its functional diversity from the perspective of sequence, structure and evolution.     

Adaptation and its analogues: Biological categories for biosemantics

“Teleosemantic” or “biosemantic” theories form a strong naturalistic programme in the philosophy of mind and language. They seek to explain the nature of mind and language by recourse to a natural history of “proper functions” as selected-for effects of language- and thought-producing mechanisms. However, they remain vague with respect to the nature of the proposed analogy between selected-for effects on the biological level and phenomena that are not strictly biological, such as reproducible linguistic and cultural forms. This essay critically explores various interpretations of this analogy. It suggests that these interpretations can be explicated by contrasting adaptationist with pluralist readings of the evolutionary concept of adaptation. Among the possible interpretations of the relations between biological adaptations and their analogues in language and culture, the two most relevant are a linear, hierarchical, signalling-based model that takes its cues from the evolution of co-operation and joint intentionality and a mutualistic, pluralist model that takes its cues from mimesis and symbolism in the evolution of human communication. Arguing for the merits of the mutualistic model, the present analysis indicates a path towards an evolutionary pluralist version of biosemantics that will align with theories of cognition as being environmentally “scaffolded”. Language and other cultural forms are partly independent reproducible structures that acquire proper functions of their own while being integrated with organism-based cognitive traits in co-evolutionary fashion.     

Common evolution of waprin and kunitz-like toxin families in Australian venomous snakes

The venoms of Australian snakes contain a myriad of pharmacologically active toxin components. This study describes the identification and comparative analysis of two distinct toxin families, the kunitztype serine protease inhibitors and waprins, and demonstrates a previously unknown evolutionary link between the two. Multiple cDNA and full-length gene isoforms were cloned and shown to be composed of three exons separated by two introns. A high degree of identity was observed solely within the first exon which coded for the propeptide sequence and its cleavage site, and indicates that each toxin family has arisen from a gene duplication event followed by diversification only within the portion of the gene coding for the functional toxin. It is proposed that while the mechanism of toxin secretion is highly conserved, diversification of mature toxin sequences allows for the existence of multiple protein isoforms in the venom to adapt to variations within the prey environment.     

The making of an intrinsic property: “Symmetry heuristics” in early particle physics

Mathematical invariances, usually referred to as “symmetries”, are today often regarded as providing a privileged heuristic guideline for understanding natural phenomena, especially those of micro-physics. The rise of symmetries in particle physics has often been portrayed by physicists and philosophers as the “application” of mathematical invariances to the ordering of particle phenomena, but no historical studies exist on whether and how mathematical invariances actually played a heuristic role in shaping microphysics. Moreover, speaking of an “application” of invariances conflates the formation of concepts of new intrinsic degrees of freedom of elementary particles with the formulation of models containing invariances with respect to those degrees of freedom. I shall present here a case study from early particle physics (ca. 1930–1954) focussed on the formation of one of the earliest concepts of a new degree of freedom, baryon number, and on the emergence of the invariance today associated to it. The results of the analysis show how concept formation and “application” of mathematical invariances were distinct components of a complex historical constellation in which, beside symmetries, two further elements were essential: the idea of physically conserved quantities and that of selection rules. I shall refer to the collection of different heuristic strategies involving selection rules, invariances and conserved quantities as the “SIC-triangle” and show how different authors made use of them to interpret the wealth of new experimental data. It was only a posteriori that the successes of this hybrid “symmetry heuristics” came to be attributed exclusively to mathematical invariances and group theory, forgetting the role of selection rules and of the notion of physically conserved quantity in the emergence of new degrees of freedom and new invariances. The results of the present investigation clearly indicate that opinions on the role of symmetries in fundamental physics need to be critically reviewed in the spirit of integrated history and philosophy of science.     

Protein folds: molecular systematics in three dimensions

Advances in methods of structure determination have led to the accumulation of large amounts of protein structural data. Some 500 distinct protein folds have now been characterized, representing one-third of all globular folds that exist. The range of known structural types and the relatively large fraction of the protein universe that has already been sampled have greatly facilitated the discovery of some unifying principles governing protein structure and evolutionary relationships. These include a highly skewed distribution of topological arrangements of secondary-structure elements that favors a few very common connectivities and a highly skewed distribution in the capacity of folds to accommodate unrelated sequences. These and other observations suggest that the number of folds is far fewer than the number of genes, and that the fold universe is dominated by a small number of giant attractors that accommodate large numbers of unrelated sequences. Thus all basic protein folds will likely be determined in the near future, laying the foundation for a comprehensive understanding of the biochemical and cellular functions of whole organisms.     

Evolution of the Cdk-activator Speedy/RINGO in vertebrates

Successful completion of the cell cycle relies on the precise activation and inactivation of cyclin-dependent kinases (Cdks) whose activity is mainly regulated by binding to cyclins. Recently, a new family of Cdk regulators termed Speedy/RINGO has been discovered, which can bind and activate Cdks but shares no apparent amino acid sequence homology with cyclins. All Speedy proteins share a conserved domain of approximately 140 amino acids called “Speedy Box”, which is essential for Cdk binding. Speedy/RINGO proteins display an important role in oocyte maturation in Xenopus. Interestingly, a common feature of all Speedy genes is their predominant expression in testis suggesting that meiotic functions may be the most important physiological feature of Speedy genes. Speedy homologs have been reported in mammals and can be traced back to the most primitive clade of chordates (Ciona intestinalis). Here, we investigated the evolution of the Speedy genes and have identified a number of new Speedy/RINGO proteins. Through extensive analysis of numerous species, we discovered diverse evolutionary histories: the number of Speedy genes varies considerably among species, with evidence of substantial gains and losses. Despite the interspecies variation, Speedy is conserved among most species examined. Our results provide a complete picture of the Speedy gene family and its evolution.     

Structure and evolution of the genetic code viewed from the perspective of the experimentally expanded amino acid repertoire in vivo

Much effort has been devoted recently to expanding the amino acid repertoire in protein biosynthesis in vivo. From such experimental work it has emerged that some of the non-canonical amino acids are accepted by the cellular translational machinery while others are not, i.e. we have learned that some determinants must exist and that they can even be anticipated. Here, we propose a conceptual framework by which it should be possible to assess deeper levels of the structure of the genetic code, and based on this experiment to understand its evolution and establishment. First, we propose a standardised repertoire of 20 amino acids as a basic set of conserved building blocks in protein biosynthesis in living cells to be the main criteria for genetic code structure and evolutionary considerations. Second, based on such argumentation, we postulate the structure and evolution of the genetic code in the form of three general statements: (i) the nature of the genetic code is deterministic; (ii) the genetic code is conserved and universal; (iii) the genetic code is the oldest known level of complexity in the evolution of living organisms that is accessible to our direct observation and experimental manipulations. Such statements are discussed as our working hypotheses that are experimentally tested by recent findings in the field of expanded amino acid repertoire in vivo. Received 30 June 1999; accepted 9 July 1999     

Ca2+/Calmodulin-dependent Protein Kinases

In this article the calcium/calmodulin-dependent protein kinases are reviewed. The primary focus is on the structure and function of this diverse family of enzymes, and the elegant regulation of their activity. Structures are compared in order to highlight the conserved architecture of their catalytic domains with respect to each other as well as protein kinase A, a prototype for kinase structure. In addition to reviewing structure and function in these enzymes, the variety of biological processes for which they play a mediating role are also examined. Finally, how the enzymes become activated in the intracellular setting is considered by exploring the reciprocal interactions that exist between calcium binding to calmodulin when interacting with the CaM-kinases.     

Phylogenetic origin of LI-cadherin revealed by protein and gene structure analysis

The intestine specific LI-cadherin differs in its overall structure from classical and desmosomal cadherins by the presence of seven instead of five cadherin repeats and a short cytoplasmic domain. Despite the low sequence similarity, a comparative protein structure analysis revealed that LI-cadherin may have originated from a five-repeat predecessor cadherin by a duplication of the first two aminoterminal repeats. To test this hypothesis, we cloned the murine LI-cadherin gene and compared its structure to that of other cadherins. The intron-exon organization, including the intron positions and phases, is perfectly conserved between repeats 3–7 of LI-cadherin and 1–5 of classical cadherins. Moreover, the genomic structure of the repeats 1–2 and 3–4 is identical for LI-cadherin and highly similar to that of the repeats 1–2 of classical cadherins. These findings strengthen our assumption that LI-cadherin originated from an ancestral cadherin with five domains by a partial gene duplication event.Received 22 December 2003; received after revision 9 February 2004; accepted 27 February 2004     

MicroRNA degeneracy and pluripotentiality within a Lavallière-tie architecture confers robustness to gene expression networks

Modularity, feedback control, functional redundancy and bowtie architecture have been proposed as key factors that confer robustness to complex biological systems. MicroRNAs (miRNAs) are highly conserved but functionally dispensable. These antinomic properties suggest that miRNAs fine-tune gene expression rather than act as genetic switches. We synthesize published and unpublished data and hypothesize that miRNA pluripotentiality acts to buffer gene expression, while miRNA degeneracy tunes the expression of targets, thus providing robustness to gene expression networks. Furthermore, we propose a Lavallière-tie architecture by integrating signal transduction, miRNAs and protein expression data to model complex gene expression networks.     

2’-5’ Oligoadenylate synthetase shares active site architecture with the archaeal CCA-adding enzyme

The 2'-5' oligoadenylate synthetases (OAS) are interferon-induced antiviral enzymes that recognise virally produced dsRNA and initiate an RNA destabilisation within the infected cell. We compared the structure of OAS to that of poly adenosine polymerase (PAP) and the class I CCA-adding enzyme from Archeoglobus fulgidus (AfCCA). This comparison revealed a strong structural homology between the three enzyme families. In particular, the active sites of OAS and CCA class I enzymes are highly conserved. We conducted an extensive mutagenesis of amino acid residues within the putative active site in OAS, thereby identifying enzymatically important residues and confirming the common active site architecture for OAS and the AfCCA. Our findings also have profound implications for our understanding of the evolutionary origin of the OAS enzymes and suggest that the OAS proteins diverged from a common 3'-specific ancestor at the beginning of metazoan evolution.     

Richard Lewontin and the “complications of linkage”

During the 1960s and 1970s population geneticists pushed beyond models of single genes to grapple with the effect on evolution of multiple genes associated by linkage. The resulting models of multiple interacting loci suggested that blocks of genes, maybe even entire chromosomes or the genome itself, should be treated as a unit. In this context, Richard Lewontin wrote his famous 1974 book The Genetic Basis of Evolutionary Change, which concludes with an argument for considering the entire genome as the unit of selection as a result of linkage. Why did Lewontin and others devote so much intellectual energy to the “complications of linkage” in the 1960s and 1970s? We argue that this attention to linkage should be understood in the context of research on chromosomal inversions and co-adapted gene complexes that occupied mid-century evolutionary genetics. For Lewontin, the complications of linkage were an extension of this chromosomal focus expressed in the new language of models for linkage disequilibrium.     

The role of symmetry in the interpretation of physical theories

The symmetries of a physical theory are often associated with two things: conservation laws (via e.g. Noether׳s and Schur׳s theorems) and representational redundancies (“gauge symmetry”). But how can a physical theory׳s symmetries give rise to interesting (in the sense of non-trivial) conservation laws, if symmetries are transformations that correspond to no genuine physical difference? In this paper, I argue for a disambiguation in the notion of symmetry. The central distinction is between what I call “analytic” and “synthetic“ symmetries, so called because of an analogy with analytic and synthetic propositions. “Analytic“ symmetries are the turning of idle wheels in a theory׳s formalism, and correspond to no physical change; “synthetic“ symmetries cover all the rest. I argue that analytic symmetries are distinguished because they act as fixed points or constraints in any interpretation of a theory, and as such are akin to Poincaré׳s conventions or Reichenbach׳s ‘axioms of co-ordination’, or ‘relativized constitutive a priori principles’.     

Narratives of Charles Darwin Down Under

Despite the fact that Charles Darwin spent several months in Australia in the final year of his Beagle voyage that circumnavigated the globe, most studies that deal with Darwin's life or his discovery of evolution spend little time discussing his Australian period, if it is mentioned at all. His time there is largely deemed to have produced little of significance in comparison to his visits to other places such as the Galápagos Islands, which has long been mythologized as providing the key sources of observable data that ultimately led Darwin to develop his evolutionary speculations. In recent years, however, Darwin's period in Australia has received more attention, most notably a series of studies detailing the observations and connections Darwin made while in New South Wales, Tasmania, and King George Sound. While much of this literature has provided an important corrective to previous Darwin scholarship that had largely ignored Darwin's period in Australia, it has also worked to perpetuate a romantic and heroic view of scientific discovery by suggesting that Darwin's key “evolutionary revelation” was made not in the Galápagos Islands but in the Blue Mountains, a claim that has been recently made in print and online. This paper therefore examines the historical literature on Darwin Down Under, focussing in particular on this recent romantic turn that seeks to situate Australia as the key site of inspiration for Darwin's theory of evolution.     

Whatever happened to SRY?

The mammalian sex-determining gene, SRY, was identified by positional cloning approximately 10 years ago. Since its discovery, intense research into this gene has been directed on two main fronts: elucidation of its function in development of the testis and examination of its singular evolutionary history. The role or SRY as the testis-determining factor (TDF) places it at a crucial point in the highly conserved morphogenetic process of vertebrate gonadogenesis. None of the genes that directly activate SRY nor any of its immediate downstream targets have yet been positively identified. Several genes, however, such as SF1, DAX1, and SOX9, whose spatial and temporal expression profiles overlap with that of SRY, are strongly implicated as co-regulators of gonadogenesis. Molecular genetic manipulation of these genes in mice has shown that they are indispensable to sexual development. Remarkably, its key position in this cascade of gene action has not protected SRY from strong yet poorly understood selective forces that have caused it to evolve rapidly in mammals. The evolution of SRY has been characterized not only by rapid sequence divergence within mammals, but also by structural changes such as intron insertion, gene amplification, and deletion.     

Fractal symmetry of protein interior: what have we learned?

The application of fractal dimension-based constructs to probe the protein interior dates back to the development of the concept of fractal dimension itself. Numerous approaches have been tried and tested over a course of (almost) 30 years with the aim of elucidating the various facets of symmetry of self-similarity prevalent in the protein interior. In the last 5 years especially, there has been a startling upsurge of research that innovatively stretches the limits of fractal-based studies to present an array of unexpected results on the biophysical properties of protein interior. In this article, we introduce readers to the fundamentals of fractals, reviewing the commonality (and the lack of it) between these approaches before exploring the patterns in the results that they produced. Clustering the approaches in major schools of protein self-similarity studies, we describe the evolution of fractal dimension-based methodologies. The genealogy of approaches (and results) presented here portrays a clear picture of the contemporary state of fractal-based studies in the context of the protein interior. To underline the utility of fractal dimension-based measures further, we have performed a correlation dimension analysis on all of the available non-redundant protein structures, both at the level of an individual protein and at the level of structural domains. In this investigation, we were able to separately quantify the self-similar symmetries in spatial correlation patterns amongst peptide–dipole units, charged amino acids, residues with the π-electron cloud and hydrophobic amino acids. The results revealed that electrostatic environments in the interiors of proteins belonging to ‘α/α toroid’ (all-α class) and ‘PLP-dependent transferase-like’ domains (α/β class) are highly conducive. In contrast, the interiors of ‘zinc finger design’ (‘designed proteins’) and ‘knottins’ (‘small proteins’) were identified as folds with the least conducive electrostatic environments. The fold ‘conotoxins’ (peptides) could be unambiguously identified as one type with the least stability. The same analyses revealed that peptide–dipoles in the α/β class of proteins, in general, are more correlated to each other than are the peptide–dipoles in proteins belonging to the all-α class. Highly favorable electrostatic milieu in the interiors of TIM-barrel, α/β-hydrolase structures could explain their remarkably conserved (evolutionary) stability from a new light. Finally, we point out certain inherent limitations of fractal constructs before attempting to identify the areas and problems where the implementation of fractal dimension-based constructs can be of paramount help to unearth latent information on protein structural properties.     

MICALs in control of the cytoskeleton,exocytosis, and cell death

MICALs form an evolutionary conserved family of multidomain signal transduction proteins characterized by a flavoprotein monooxygenase domain. MICALs are being implicated in the regulation of an increasing number of molecular and cellular processes including cytoskeletal dynamics and intracellular trafficking. Intriguingly, some of these effects are dependent on the MICAL monooxygenase enzyme and redox signaling, while other functions rely on other parts of the MICAL protein. Recent breakthroughs in our understanding of MICAL signaling identify the ability of MICALs to bind and directly modify the actin cytoskeleton, link MICALs to the docking and fusion of exocytotic vesicles, and uncover MICALs as anti-apoptotic proteins. These discoveries could lead to therapeutic advances in neural regeneration, cancer, and other diseases.