Galpha Gbetagamma dissociation may be due to retraction of a buried lysine and disruption of an aromatic cluster by a GTP-sensing Arg Trp pair

A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family

The evolution of eukaryotic cellular complexity is interwoven with the extensive diversification of many protein families. One key family is the ARF GTPases that act in eukaryote-specific processes, including membrane traffic, tubulin assembly, actin dynamics, and cilia-related functions. Unfortunately, our understanding of the evolution of this family is limited. Sampling an extensive set of available genome and transcriptome sequences, we have assembled a data set of over 2,000 manually curated ARF family genes from 114 eukaryotic species, including many deeply diverged protist lineages, and carried out comprehensive molecular phylogenetic analyses. These reconstructed as many as 16 ARF family members present in the last eukaryotic common ancestor, nearly doubling the previously inferred ancient system complexity. Evidence for the wide occurrence and ancestral origin of Arf6, Arl13, and Arl16 is presented for the first time. Moreover, Arl17, Arl18, and SarB, newly described here, are absent from well-studied model organisms and as a result their function(s) remain unknown. Analyses of our data set revealed a previously unsuspected diversity of membrane association modes and domain architectures within the ARF family. We detail the step-wise expansion of the ARF family in the metazoan lineage, including discovery of several new animal-specific family members. Delving back to its earliest evolution in eukaryotes, the resolved relationship observed between the ARF family paralogs sets boundaries for scenarios of vesicle coat origins during eukaryogenesis. Altogether, our work fundamentally broadens the understanding of the diversity and evolution of a protein family underpinning the structural and functional complexity of the eukaryote cells.

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations

Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs), which describe these sequence correlations implicitly. By characterizing such correlations one may hope to obtain information regarding functionally-relevant properties that have thus far evaded detection. To do so, we infer a hiHMM distribution from sequence data using Bayes’ theorem and Markov chain Monte Carlo (MCMC) sampling, which is widely recognized as the most effective approach for characterizing a complex, high dimensional distribution. Other routines then map correlated residue patterns to available structures with a view to hypothesis generation. When applied to N-acetyltransferases, this reveals sequence and structural features indicative of functionally important, yet generally unknown biochemical properties. Even for sets of proteins for which nothing is known beyond unannotated sequences and structures, this can lead to helpful insights. We describe, for example, a putative coenzyme-A-induced-fit substrate binding mechanism mediated by arginine residue switching between salt bridge and π-π stacking interactions. A suite of programs implementing this approach is available (psed.igs.umaryland.edu).

Protein sequence data, when gathered in great quantity, contain important but implicit biological information manifest as statistical correlations. Here we describe an approach to access this information by comprehensively modeling and characterizing the distribution of sequences belonging to a major protein superfamily. This approach takes as input a large set of unaligned sequences belonging to the superfamily. By applying the minimum description length principle, it seeks the statistical model that best explains the sequences while avoiding over-fitting the data. It concurrently aligns the sequences and, to model evolutionary divergence, partitions them into subgroups that are hierarchically-arranged based upon correlated residue patterns. Auxiliary routines create PyMOL scripts to visualize the locations of correlated residues within available structures. Because these correlations likely arise from structural and biochemical constraints, they can help elucidate protein properties important for functional specificity. Comparing and contrasting sequence and structural features in this way may therefore suggest, in the light of published studies, plausible biological hypotheses for experimental investigation. We illustrate this approach with N-acetyltransferases.

Discovery of Novel DENN Proteins: Implications for the Evolution of Eukaryotic Intracellular Membrane Structures and Human Disease

The tripartite DENN module, comprised of a N-terminal longin domain, followed by DENN, and d-DENN domains, is a GDP-GTP exchange factor (GEFs) for Rab GTPases, which are regulators of practically all membrane trafficking events in eukaryotes. Using sequence and structure analysis we identify multiple novel homologs of the DENN module, many of which can be traced back to the ancestral eukaryote. These findings provide unexpected leads regarding key cellular processes such as autophagy, vesicle-vacuole interactions, chromosome segregation, and human disease. Of these, SMCR8, the folliculin interacting protein-1 and 2 (FNIP1 and FNIP2), nitrogen permease regulator 2 (NPR2), and NPR3 are proposed to function in recruiting Rab GTPases during different steps of autophagy, fusion of autophagosomes with the vacuole and regulation of cellular metabolism. Another novel DENN protein identified in this study is C9ORF72; expansions of the hexanucleotide GGGGCC in its first intron have been recently implicated in amyotrophic lateral sclerosis (ALS) and fronto-temporal dementia (FTD). While this mutation is proposed to cause a RNA-level defect, the identification of C9ORF72 as a potential DENN-type GEF raises the possibility that at least part of the pathology might relate to a specific Rab-dependent vesicular trafficking process, as has been observed in the case of some other neurological conditions with similar phenotypes. We present evidence that the longin domain, such as those found in the DENN module, are likely to have been ultimately derived from the related domains found in prokaryotic GTPase-activating proteins of MglA-like GTPases. Thus, the origin of the longin domains from this ancient GTPase-interacting domain, concomitant with the radiation of GTPases, especially of the Rab clade, played an important role in the dynamics of eukaryotic intracellular membrane systems.

Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms

Certain residues have no known function yet are co-conserved across distantly related protein families and diverse organisms, suggesting that they perform critical roles associated with as-yet-unidentified molecular properties and mechanisms. This raises the question of how to obtain additional clues regarding these mysterious biochemical phenomena with a view to formulating experimentally testable hypotheses. One approach is to access the implicit biochemical information encoded within the vast amount of genomic sequence data now becoming available. Here, a new Gibbs sampling strategy is formulated and implemented that can partition hundreds of thousands of sequences within a major protein class into multiple, functionally-divergent categories based on those pattern residues that best discriminate between categories. The sampler precisely defines the partition and pattern for each category by explicitly modeling unrelated, non-functional and related-yet-divergent proteins that would otherwise obscure the analysis. To aid biological interpretation, auxiliary routines can characterize pattern residues within available crystal structures and identify those structures most likely to shed light on the roles of pattern residues. This approach can be used to define and annotate automatically subgroup-specific conserved domain profiles based on statistically-rigorous empirical criteria rather than on the subjective and labor-intensive process of manual curation. Incorporating such profiles into domain database search sites (such as the NCBI BLAST site) will provide biologists with previously inaccessible molecular information useful for hypothesis generation and experimental design. Analyses of P-loop GTPases and of AAA+ ATPases illustrate the sampler's ability to obtain such information.

Comparative genomics uncovers novel structural and functional features of the heterotrimeric GTPase signaling system

Though the heterotrimeric G-proteins signaling system is one of the best studied in eukaryotes, its provenance and its prevalence outside of model eukaryotes remains poorly understood. We utilized the wealth of sequence data from recently sequenced eukaryotic genomes to uncover robust G-protein signaling systems in several poorly studied eukaryotic lineages such as the parabasalids, heteroloboseans and stramenopiles. This indicated that the Gα subunit is likely to have separated from the ARF-like GTPases prior to the last eukaryotic common ancestor. We systematically identified the structure and sequence features associated with this divergence and found that most of the neomorphic positions in Gα form a ring of residues centered on the nucleotide binding site, several of which are likely to be critical for interactions with the RGS domain for its GAP function. We also present evidence that in some of the potentially early branching eukaryotic lineages, like Trichomonas, Gα is likely to function independently of the Gβγ subunits. We were able to identify previously unknown Gγ subunits in Naegleria, suggesting that the trimeric version was already present by the time of the divergence of the heteroloboseans from the remaining eukaryotes. Evolution of Gα subunits is dominated by several independent lineage-specific expansions (LSEs). In most of these cases there are concomitant, independent LSEs of RGS proteins along with an extraordinary diversification of their domain architectures. The diversity of RGS domains from Naegleria in particular, which has the largest complement of Gα and RGS proteins for any eukaryote, provides new insights into RGS function and evolution. We uncovered a new class of soluble ligand receptors of bacterial origin with RGS domains and an extraordinary diversity of membrane-linked, redox-associated, adhesion-dependent and small molecule-induced G-protein signaling networks that evolved in early-branching eukaryotes, independently of parallel systems in animals. Furthermore, this newly characterized diversity of RGS domains helps in defining their ancestral conserved interfaces with Gα and also those interfaces that are prone to extensive lineage-specific diversification and are thereby responsible for selectivity in Gα-RGS interactions. Several mushrooms show LSEs of Gαs but not of RGS proteins pointing to the probable differentiation of Gαs in conjunction with mating-type diversity. When combined with the characterization of the 7TM receptors (GPCRs), it becomes apparent that, through much of eukaryotic evolution, cells contained both 7TM receptors that acted as GEFs and those as GAPs (with C-terminal RGS domains) for Gαs. Only in some lineages like animals and stramenopiles the 7TM receptors were restricted to GEF only roles, probably due to selection imposed by the rate-constants of the Gαs that underwent lineage-specific expansion in them. In the alveolate lineage the 7TM receptors occur independently of heterotrimeric G-proteins, suggesting the prevalence of G-protein-independent signaling in these organisms.

Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases

Background

Certain residues within proteins are highly conserved across very distantly related organisms, yet their (presumably critical) structural or mechanistic roles are completely unknown. To obtain clues regarding such residues within Arf and Arf-like (Arf/Arl) GTPases--which function as on/off switches regulating vesicle trafficking, phospholipid metabolism and cytoskeletal remodeling--I apply a new sampling procedure for comparative sequence analysis, termed multiple category Bayesian Partitioning with Pattern Selection (mcBPPS).

Results

The mcBPPS sampler classified sequences within the entire P-loop GTPase class into multiple categories by identifying those evolutionarily-divergent residues most likely to be responsible for functional specialization. Here I focus on categories of residues that most distinguish various Arf/Arl GTPases from other GTPases. This identified residues whose specific roles have been previously proposed (and in some cases corroborated experimentally and that thus serve as positive controls), as well as several categories of co-conserved residues whose possible roles are first hinted at here. For example, Arf/Arl/Sar GTPases are most distinguished from other GTPases by a conserved aspartate residue within the phosphate binding loop (P-loop) and by co-conserved residues nearby that, together, can form a network of salt-bridge and hydrogen bond interactions centered on the GTPase active site. Residues corresponding to an N-[VI] motif that is conserved within Arf/Arl GTPases may play a role in the interswitch toggle characteristic of the Arf family, whereas other, co-conserved residues may modulate the flexibility of the guanine binding loop. Arl8 GTPases conserve residues that strikingly diverge from those typically found in other Arf/Arl GTPases and that form structural interactions suggestive of a novel interswitch toggle mechanism.

Conclusions

This analysis suggests specific mutagenesis experiments to explore mechanisms underlying GTP hydrolysis, nucleotide exchange and interswitch toggling within Arf/Arl GTPases. More generally, it illustrates how the mcBPPS sampler can complement traditional evolutionary analyses by providing an objective, quantitative and statistically rigorous way to explore protein functional-divergence in molecular detail. Because the sampler classifies the input sequences at the same time, it can be used to generate subgroup profiles, in which functionally-divergent categories of residues are annotated automatically.

Reviewers

This article was reviewed by Frank Eisenhaber, L Aravind and Daniel Gaston (nominated by Eric Bapteste). For the full reviews, go to the Reviewers' comments section.

Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily

The evolutionary and physical deformability patterns of members of the Ras GTPase superfamily were investigated by Principal Component and Elastic Network-Normal Mode analyses. The study helped to decipher the dynamics information encrypted into the conserved core and to separate the trans-family intrinsic flexibility associated with a common function from the protein motions related to functional specialization of selected families or family members. The conserved core is dynamically divided into two lobes. The deformation modes, which allow the Ras GTPases to accomplish their switching function, are conserved along evolution and are localized in lobe 1 portions close to the nucleotide. These modes lead to functional specialization when associated with evolution-driven deformations of protein portions essentially located in lobe 2, distal from the nucleotide, and involved in peculiar interactions with membrane, guanine nucleotide exchange factors, or effectors. Overall, a complete picture of the functional and evolutionary dynamics of the Ras superfamily emerges.

Trp fluorescence reveals an activation-dependent cation-pi interaction in the Switch II region of Galphai proteins

Crystal structures of Galpha(i) (and closely related family member Galpha(t)) reveal much of what we currently know about G protein structure, including changes which occur in Switch regions. Galpha(t) exhibits a low rate of basal (uncatalyzed) nucleotide exchange and an ordered Switch II region in the GDP-bound state, unlike Galpha(i), which exhibits higher basal exchange and a disordered Switch II region in Galpha(i)GDP structures. Using purified Galpha(i) and Galpha(t), we examined the intrinsic tryptophan fluorescence of these proteins, which reports conformational changes associated with activation and deactivation of Galpha proteins. In addition to the expected enhancement in tryptophan fluorescence intensity, activation of GalphaGDP proteins was accompanied by a modest but notable red shift in tryptophan emission maxima. We identified a cation-pi interaction between tryptophan and arginine residues in the Switch II of Galpha(i) family proteins that mediates the observed red shift in emission maxima. Furthermore, amino-terminal myristoylation of Galpha(i) resulted in a less polar environment for tryptophan residues in the GTPase domain, consistent with an interaction between the myristoylated amino terminus and the GTPase domain of Galpha proteins. These results reveal unique insights into conformational changes which occur upon activation and deactivation of G proteins in solution.

G protein inactive and active forms investigated by simulation methods

Molecular dynamics and computational alanine scanning techniques have been used to investigate G proteins in their inactive state (the Galpha(i1)beta(1)gamma(2) heterotrimer) as well as in their empty and monomeric active states (Galpha(i1) subunit). We find that: (i) the residue Q204 of Galpha(i1) plays a key role for binding Gbeta(1)gamma(2) and is classified among the most relevant in the interaction with a key cellular partner, the so-called regulator of G protein signaling protein. The mutation of this residue to L, which is observed in a variety of diseases, provides still fair stability to the inactive state because of the formation of van der Waals interactions. (ii) The empty state turns out to adopt some structural features of the active one, including a previously unrecognized rearrangement of a key residue (K46). (iii) The so-called Switch IV region increases its mobility on passing from the empty to the active state, and, even more, to the inactive state. Such change in mobility could be important for its several structural and functional roles. (iv) A large scale motion of the helical domain in the inactive state might be important for GDP release upon activation by GPCR, consistently with experimental data.

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences

MOTIVATION

The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemical similarities and differences. A first step toward accessing such information is to statistically analyze these patterns, which, in turn, requires that one first identify and accurately align a very large set of protein sequences. Ideally, the set should include many distantly related, functionally divergent subgroups. Because it is extremely difficult, if not impossible for fully automated methods to align such sequences correctly, researchers often resort to manual curation based on detailed structural and biochemical information. However, multiply-aligning vast numbers of sequences in this way is clearly impractical.

RESULTS

This problem is addressed using Multiply-Aligned Profiles for Global Alignment of Protein Sequences (MAPGAPS). The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences. It relies on Karlin-Altschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed. Using as input a carefully curated multiple-profile alignment for P-loop GTPases, MAPGAPS correctly aligned weakly conserved sequence motifs within 33 distantly related GTPases of known structure. By comparison, the sequence- and structurally based alignment methods hmmalign and PROMALS3D misaligned at least 11 and 23 of these regions, respectively. When applied to a dataset of 65 million protein sequences, MAPGAPS identified, classified and aligned (with comparable accuracy) nearly half a million putative P-loop GTPase sequences.

AVAILABILITY

A C++ implementation of MAPGAPS is available at http://mapgaps.igs.umaryland.edu.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches

Ras-like GTPases function as on/off switches in intracellular signaling pathways. Their on or off state is communicated through conformational changes in the so-called switch I and II regions. It is commonly believed that the distinguishing molecular features of these GTPases are well known. Here, however, I identify-through a Bayesian iterative analysis of GTPase evolutionary divergence-a previously undescribed switch II structural component that (along with previously described, functionally critical residues) most distinguish these signaling pathway on/off switches from other GTPases. In certain Ras-like GTPases this newly-identified component forms an aromatic pocket around the negative-dipole moment at the end of a switch II helix with a positively charged residue inserted into the pocket. This helix is oriented in a specific direction away from the GTPase core, but is reoriented dramatically upon disruption of the charge-dipole pocket. The charge-dipole pocket occurs in both the on and off states and both the charge-dipole pocket and an alternative configuration occur within the unit cell of a single crystal structure of Rab5a GTPase in the off state. Thus, the charge-dipole pocket configuration is closely associated, not with the on or off state, but rather with formation of the outward-oriented helix and, as a result, with restructuring of the switch II N-terminal region, which has a critical role both in sensing the on/off state and in mediating GTP hydrolysis and nucleotide exchange.

Large nucleotide-dependent conformational change in Rab28

Rab GTPases are essential regulators of membrane trafficking. We report crystal structures of Rab28 in the active (GppNHp-bound) and inactive (GDP-3'P-bound) forms at 1.5 and 1.1A resolution. Rab28 is a distant member of the Rab family. While the overall fold of Rab28 resembles that of other Rab GTPases, it undergoes a larger nucleotide-dependent conformational change than other members of this family. Added flexibility resulting from a double-glycine motif at the beginning of switch 2 might partially account for this observation. The double-glycine motif, which is conserved in the Arf family, only occurs in Rab28 and Rab7B of the Rab family, and may have a profound effect on their catalytic activities.