Protein domain analysis in the era of complete genomes

Domains present one of the most useful levels at which to understand protein function, and domain family-based analysis has had a profound impact on the study of individual proteins. Protein domain discovery has been progressing steadily over the past 30 years. What are the realistically achievable goals of sequence-based domain analysis, and how far off are they for the sequences encoded in eukaryotic genomes? Here we address some of the issues involved in better coverage of sequence-based domain annotation, and the integration of these results within the wider context of genomes, structures and function.     

MHYT, a new integral membrane sensor domain

MHYT, a new conserved protein domain with a likely signaling function, is described. This domain consists of six transmembrane segments, three of which contain conserved methionine, histidine, and tyrosine residues that are projected to lie near the outer face of the cytoplasmic membrane. In Synechocystis sp. PCC6803, this domain forms the N-terminus of the sensor histidine kinase Slr2098. In Pseudomonas aeruginosa and several other organisms, the MHYT domain forms the N-terminal part of a three-domain protein together with previously described GGDEF and EAL domains, both of which have been associated with signal transduction due to their presence in likely signaling proteins. In Bacillus subtilis YkoW protein, an additional PAS domain is found between the MHYT and GGDEF domains. A ykoW null mutant of B. subtilis did not exhibit any growth alterations, consistent with a non-essential, signaling role of this protein. A model of the membrane topology of the MHYT domain indicates that its conserved residues could coordinate one or two copper ions, suggesting a role in sensing oxygen, CO, or NO.     

Directly observed hydrogen bonds at calcium-binding-sites of calmodulin in solution relate to affinity of the calcium-binding

Molecular tuning to calcium-binding in the EF-hand motif of holo-calmodulin was studied in solution by NMR ^h3J_NC′ H-bond couplings. In the N-terminus lobe of holo-calmodulin, the glutamate crucial for Ca²⁺ coordination has network of H-bonds weaker than inferred from the X-ray crystal structure. This glutamate at position 12 appears shifted away from the Ca²⁺ preferred coordination, which can explain the lower affinity of the calcium-binding to the N-terminus with respect to C-terminus EF hands.     

The crystal structure of plant-specific calcium-binding protein AtCBL2 in complex with the regulatory domain of AtCIPK14

Calcium signals mediate a multitude of plant responses to external stimuli. Calcineurin B-like (CBL) proteins and their target kinases, CBL-interacting protein kinases (CIPKs), represent important relays in plant calcium signaling. CBL interacts with CIPK through a conserved motif (NAF/FISL motif) within the C-terminal regulatory domain. To better understand the functional role of the CBL-CIPK system, we determined the crystal structure of AtCBL2 in complex with the regulatory domain of AtCIPK14 at 1.2 Å resolution. The NAF/FISL motif is inserted into a hydrophobic crevice within AtCBL2, accompanied by a large displacement of the helices and loop on the opposite side of the NAF/FISL motif from the C-terminal region, which shields the hydrophobic crevice in free form. Ca²⁺ are coordinated within four EF hands in AtCBL2 in bound form. This calcium coordination pattern differs from that in the structure of the SOS3-SOS2 complex previously reported. Structural comparison of the two structures shows that the recognition of CBL by CIPK is performed in a similar manner, but inherent interactions confer binding affinity and specificity.     

The excised heat-shock domain of alphaB crystallin is a folded, proteolytically susceptible trimer with significant surface hydrophobicity and a tendency to self-aggregate upon heating

The lens protein, alpha-crystallin, is a molecular chaperone that prevents the thermal aggregation of other proteins. The C-terminal domain of this protein (homologous to domains present in small heat-shock proteins) is implicated in chaperone function, although the domain itself has been reported to show no chaperone activity. Here, we show that the domain can be excised out of the intact alphaB polypeptide and recovered directly in pure form through the transfer of CNBr digests of whole lens homogenates into urea-containing buffer, followed by dialysis-based refolding of digests under acidic conditions and a single gel-filtration purification step. The folded (beta sheet) domain thus obtained is found to be (a) predominantly trimeric, and to display (b) significant surface hydrophobicity, (c) a marked tendency to undergo degradation, and (d) a tendency to aggregate upon heating, and on exposure to UV light. Thus, the twin 'chaperone' features of multimericity and surface hydrophobicity are clearly seen to be insufficient for this domain to function as a chaperone. Since alpha-crystallin interacts with its substrates through hydrophobic interactions, the hydrophobicity of the excised domain indicates that separation of domains may regulate function; at the same time, the fact is also highlighted that surface hydrophobicity is a liability in a chaperone since heating strengthens hydrophobic interactions and can potentially promote self-aggregation. Thus, it would appear that the role of the N-terminal domain in alpha-crystallin is to facilitate the creation of a porous, hollow structural framework of >/=24 subunits in which solubility is effected through increase in the ratio of exposed surface area to buried volume. Trimers of interacting C-terminal domains anchored to this superstructure, and positioned within its interior, might allow hydrophobic surfaces to remain accessible to substrates without compromising solubility.     

The PWAPA cassette: Intimate association of a PHD-like finger and a winged-helix domain in proteins included in histone-modifying complexes

Polycomb complexes function as enforcers of epigenetically repressed state, balanced by an antagonist state mediated by Trithorax. Using sensitive methods of sequence analysis, we show here that Polycomb-like proteins (PCLs) contain a tandem of intimately associated domains, which we named PWAPA and which is also present in ASH2L, a member of the Trithorax group. Polycomb-like proteins and ASH2L belong to the PCR2 and MLL histone methyltransferase complexes, respectively. A PWAPA cassette is also present in ATAC2, a component of the ATAC histone acetyltransferase complex. The recently solved structure of the PWAPA tandem of ASH2L has revealed that it consist in a PHD-like finger followed by a helix-winged-helix (WH) domain, able to bind DNA. The modeling of the 3D structure of the different members of the PWAPA family suggests that the PHD-like finger might be able, at least for some proteins of the family, to bind methylated marks on histones. The PWAPA PHD/WH cassette might thus be involved in the combined recognition of DNA and specific (perhaps methylation) mark(s) on histones, thereby allowing the recruitment of specific chromatin-modifying activities at these sites. The observations reported here should help to unravel the exact role played by the PWAPA cassette in the different proteins of the PWAPA family, and especially in the antagonistic activities of PcG and TrxG proteins.     

Number and brightness analysis of sFRP4 domains in live cells demonstrates vesicle association signal of the NLD domain and dynamic intracellular responses to Wnt3a

The Wnts are secreted, lipidated glycoproteins that play a role in cellular processes of differentiation, proliferation, migration, survival, polarity and stem cell self-renewal. The majority of Wnts biological effects are through binding to specific frizzled (Fzd) receptor complexes leading to activation of downstream pathways. Secreted frizzled-related proteins (sFRPs) were first identified as antagonists of Wnt signalling by binding directly to Wnts. They comprise two domains, a Fzd-like cysteine rich domain (CRD) and a netrin-like domain (NLD). Subsequently sFRPs have been shown to also interact with Fzd receptors and more diverse functions have been identified, including potentiation of Wnt signalling. Many aspects of the biology of this family remain to be elucidated. We used the number and brightness (N&B) method, a technique based on fluorescence fluctuation analysis, to characterise the intracellular aggregation and trafficking of sFRP4 domains. We expressed sFRP4 and its’ domains as EGFP fusions and then characterised the effect of endogenous Wnt3a by fluorescence confocal imaging. We observed vesicular trafficking of sFRP4 and that the NLD domain has a vesicular association signal. We found that sFRP4 and the CRD formed oligomeric aggregates in the perinuclear region while the NLD was distributed evenly throughout the cell with a larger proportion of aggregates. Most significantly we observed intracellular redistribution of sFRP4 in response to Wnt3a suggesting that Wnt3a can modulate intracellular localisation and secretion of sFRP4. Our results reveal a number of novel findings regarding sFRP4 which are likely to have relevance to this wider family.     

Petenaeaceae,a new angiosperm family in Huerteales with a distant relationship to Gerrardina (Gerrardinaceae)

Petenaea cordata (from northern Central America) was first described in Elaeocarpaceae and later placed in Tiliaceae, but most authors have been uncertain about its familial affinities. It was considered a taxon incertae sedis in the Angiosperm Phylogeny Group classification (APG III). A recent collection was made in Guatemala, and analysis of both rbcL and atpB in the large Soltis et al. angiosperm matrix, the most completely sampled study published to date, indicated a moderately supported relationship to Tapiscia (Tapisciaceae, the only member of the newly recognized order Huerteales in this matrix; 81% bootstrap support). We then conducted a more restricted analysis using the Bayer et al. rbcL/atpB matrix for Malvales supplemented with the other genera of Huerteales from published studies. Our results indicate a distant, weakly supported sister‐group relationship to the African genus Gerrardina (Gerrardinaceae; Huerteales). After comparison of the characters cited in the literature and an examination of herbarium material of both genera, we could find no obvious synapomorphies for Gerrardina and Petenaea or any other relationship of the latter, and we therefore propose the new monogeneric family, Petenaeaceae. The polymorphic order Huerteales now comprises four small families: Dipentodontaceae, Gerrardinaceae, Petenaeaceae and Tapisciaceae. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 16–25.     

CK2 beta, which inhibits Mos function, binds to a discrete domain in the N-terminus of Mos

Progesterone stimulates G2-arrested Xenopus oocytes to synthesize Mos, a MAPK kinase kinase required for the coordinated activation of cdc2 and the G2/Meiosis I (MI) transition. Mos leads to activation of MAPK, Rsk, and the inhibition of the cdc2 inhibitor Myt1. Previous work identified CK2 beta as a Mos-interacting protein, and suggested that CK2 beta acts as a negative regulator by setting a threshold above which newly made Mos must accumulate to activate MAPK. However, it had not been demonstrated that CK2 beta directly inhibits Mos. We report here that Mos (52-115) is required for CK2 beta binding and can serve as a portable binding domain. To test whether CK2 beta acts at the level of Mos or on a downstream component, we took advantage of previous work that showed injection of Mos arrests rapidly dividing embryonic cells. We find that coinjection of CK2 beta and Mos into embryonic cells inhibits the ability of Mos to arrest cell division. In contrast, CK2 beta does not inhibit the mitotic arrest induced by injection of active Rsk. These results argue that CK2 beta directly binds and inhibits Mos rather than a downstream component, and support that CK2 beta functions as a molecular buffer that prevents premature MAPK activation and oocyte maturation.     

An electromyographic study of the pectoralis major in Atelines and Hylobates,with special reference to the Evolution of a pars clavicularis

Among primates there is striking variation in the extent of the origin of pectoralis major from the clavicle. A significant clavicular attachment (pars clavicularis) occurs only in Alouatta, Lagothrix, Hylobates, Pan (troglodytes, paniscus and gorilla), and Homo. Interpreting this trait in nonhuman primates as an adaptation to frequent use of a mobile forelimb in climbing and suspension is contraindicated by the absence of a clavicular origin in Ateles and Pongo. We have undertaken a telemetered electromyographic study to determine any special role of the most cranial part of the pectoralis major in comparison to its caudal part, and to the deltoid, during vertical climbing, pronograde quadrupedalism, and armswinging in Ateles, Lagothrix, Alouatta, and Hylobates. The results show that the cranial pectoralis major possesses a role not shared by the caudal fibers: initiation of the recovery phase of the locomotor cycle. When ability to execute rapid or powerful recovery of the adducted forelimb is required in an animal with a shoulder joint lying on a plane cranial to that of the manubrium, the movement will be facilitated if the origin of the pectoralis major is extended onto the clavicle. Such is the case in nonhuman primates possessing this trait. The absence of a clavicular origin in Ateles and Pongo may be related to diminished selective pressures to perfect locomotor modes such as pronograde quadrupedalism, armswinging, or climbing thick vertical trunks, that demand rapid or powerful recovery of the adducted forelimb. If the arboreal ancestor of humans had evolved a clavicular origin of pectoralis major, this animal would be preadapted for certain uses of the forelimb in its bipedal descendant.     

Structural insights into a StART-like domain in Lam4 and its interaction with sterol ligands

Sterols are essential components of cellular membranes and shape their biophysical properties. The recently discovered family of Lipid transfer proteins Anchored at Membrane contact sites (LAMs) has been suggested to carry out intracellular sterol traffic using StART-like domains. Here, we studied the second StART-like domain of Lam4p from S. cerevisiae by NMR. We show that NMR data are consistent with the StART-like domain structure, and that several functionally important regions within the domain exhibit significant conformational dynamics. NMR titration experiments confirm sterol binding to the canonical sterol-binding site and suggest a role of membrane interactions on the thermodynamics and kinetics of sterol binding.     

Rapid, transient methylation of four proteins in aggregative amoebae of Dictyostelium discoideum as a response to stimulation with cyclic AMP

In Dictyostelium discoideum, extracellular cAMP induces chemotaxis and cell aggregation. Suspensions of cAMP-sensitive cells are shown to respond to a 10(-6) M cAMP-pulse with increased methylation of 4 proteins with app. Mr 110000, 46000, 28000 and 16000. The Mr 110000 and 28000 proteins show a triphasic response with maxima 15, 60 and 150-180 s after stimulation. The responses of the Mr 46000 and 16000 proteins are monophasic, maxima being reached 3 and 15 s after stimulation, respectively. Optimal responses of methylation are observed over 10(-7) - 10(-6) M cAMP. The methylation reaction may be involved in the processing of the chemotactic signal.     

The Large Hsp70 Grp170 Binds to Unfolded Protein Substrates in Vivo with a Regulation Distinct from Conventional Hsp70s

The Hsp70 superfamily is a ubiquitous chaperone class that includes conventional and large Hsp70s. BiP is the only conventional Hsp70 in the endoplasmic reticulum (ER) whose functions include: assisting protein folding, targeting misfolded proteins for degradation, and regulating the transducers of the unfolded protein response. The ER also possesses a single large Hsp70, the glucose-regulated protein of 170 kDa (Grp170). Like BiP it is an essential protein, but its cellular functions are not well understood. Here we show that Grp170 can bind directly to a variety of incompletely folded protein substrates in the ER, and as expected for a bona fide chaperone, it does not interact with folded secretory proteins. Our data demonstrate that Grp170 and BiP associate with similar molecular forms of two substrate proteins, but while BiP is released from unfolded substrates in the presence of ATP, Grp170 remains bound. In comparison to conventional Hsp70s, the large Hsp70s possess two unique structural features: an extended C-terminal α-helical domain and an unstructured loop in the putative substrate binding domain with an unknown function. We find that in the absence of the α-helical domain the interaction of Grp170 with substrates is reduced. In striking contrast, deletion of the unstructured loop results in increased binding to substrates, suggesting the presence of unique intramolecular mechanisms of control for the chaperone functions of large Hsp70s.     

An oat coleoptile wall protein that induces wall extension in vitro and that is antigenically related to a similar protein from cucumber hypocotyls

Plant cell walls expand considerably during cell enlargement, but the biochemical reactions leading to wall expansion are unknown. McQueen-Mason et al. (1992, Plant Cell 4, 1425) recently identified two proteins from cucumber (Cucumis sativus L.) that induced extension in walls isolated from dicotyledons, but were relatively ineffective on grass coleoptile walls. Here we report the identification and partial characterization of an oat (Avena sativa L.) coleoptile wall protein with similar properties. The oat protein has an apparent molecular mass of 29 kDa as revealed by sodium dodecyl sulfate-polyacrylamide gel eletrophoresis. Activity was optimal between pH 4.5 and 5.0, which makes it a suitable candidate for acid growth responses of plant cell walls. The oat protein induced extension in walls from oat coleoptiles, cucumber hypocotyls and pea (Pisum sativum L.) epicotyls and was specifically recognized by an antibody raised against the 29-kDa wall-extension-inducing protein from cucumber hypocotyls. Contrary to the situation in cucumber walls, the acid-extension response in heat-inactivated oat walls was only partially restored by oat or cucumber wall-extension proteins. Our results show that an antigenically conserved protein in the walls of cucumber and oat seedlings is able to mediate a form of acid-induced wall extension. This implies that dicotyledons and grasses share a common biochemical mechanism for at least part of acid-induced wall extensions, despite the significant differences in wall composition between these two classes of plants.Abbreviations ConA concanavalin A - CM carboxymethyl - DEAE diethylaminoethyl - DTT dithiothreitol - Ex29 29-kDa expansin     

An algorithm for a decomposition of weighted digraphs: with applications to life cycle analysis in ecology

In the analysis of organism life cycles in ecology, comparisons of life cycles between species or between different types of life cycles within species are frequently conducted. In matrix population models, partitioning of the elasticity matrix is used to quantify the separate contributions of different life cycles to the population growth rate. Such partition is equivalent to a decomposition of the life cycle graph of the population. A graph theoretic spanning tree method to carry out the decomposition was formalized by Wardle [Ecology 79(7), 2539–2549 (1998)]. However there are difficulties in realizing a suitable decomposition for complex life histories using the spanning-tree method. One of the problems is the occurrence of life cycles that contain contradictory directions that defy biological interpretation. We propose an algorithmic approach for decomposing a directed, weighted graph. The graph is to be decomposed into two parts. The first part is a set of simple cycles that contain no contradictory directions and that consist of edges of equal weight. The second part of the decomposition is a subgraph in which no such simple cycles are obtainable. When applied to life cycle analysis in ecology, the proposed method will guarantee a complete decomposition of the life cycle graph into individual life cycles containing no contradictory directions. Although the research described in this article has been funded in part by the United States Environmental Protection Agency through STAR cooperative agreement R-82940201-0 to the University of Chicago, it has not been subjected to the Agency’s required peer and policy review and therefore does not necessarily reflect the views of the Agency and no official endorsement should be inferred.     

csmA,a gene encoding a class V chitin synthase with a myosin motor-like domain of Aspergillus nidulans,is translated as a single polypeptide and regulated in response to osmotic conditions

The csmA gene of Aspergillus nidulans encodes a polypeptide that consists of an N-terminal myosin motor-like domain and a C-terminal chitin synthase domain. csmA null mutants showed marked abnormalities in polarized growth, hyphal wall integrity, and conidiophore development. Furthermore, the growth of the csmA null mutants was sensitive to low osmotic conditions. In an effort to investigate the intracellular behavior of the csmA product (CsmA) and the regulation of its production, we constructed strains that produced CsmA tagged with nine repeats of the hemagglutinin A (HA) epitope at its COOH terminus (CsmA-HA) instead of CsmA. Western blot analysis with anti-HA antibody showed that the entire coding region of csmA was translated as a single polypeptide with an approximate molecular mass of 210kDa. CsmA-HA was produced during vegetative growth; however, its yield was significantly reduced under high osmotic conditions, suggesting that the role of CsmA in growth and morphogenesis is particularly important under low osmotic conditions.     

Crystal structure of the polyextremophilic alpha-amylase AmyB from Halothermothrix orenii: details of a productive enzyme-substrate complex and an N domain with a role in binding raw starch

The gene for a membrane-bound, halophilic, and thermostable α-amylase, AmyB, from Halothermothrix orenii was cloned and sequenced. The crystal structure shows that, in addition to the typical domain organization of family 13 glycoside hydrolases, AmyB carries an additional N-terminal domain (N domain) that forms a large groove—the N-C groove—some 30 Å away from the active site. The structure of AmyB with the inhibitor acarbose at 1.35 Å resolution shows that a nonasaccharide has been synthesized through successive transglycosylation reactions of acarbose. Unexpectedly, in a complex of wild-type AmyB with α-cyclodextrin and maltoheptaose at 2.2 Å resolution, a maltotetraose molecule is bound in subsites − 1 to + 3, spanning the cleavage point at − 1/+ 1, with the − 1 glucosyl residue present as a ²S_o skew boat. This wild-type AmyB complex was obtained in the presence of a large excess of substrate, a condition under which it is possible to capture Michaelis complexes, which may explain the observed binding across − 1/+ 1 and ring distortion. We observe three methionine side chains that serve as “binding platforms” for glucosyl rings in AmyB, a seemingly rare occurrence in carbohydrate-binding proteins. The structures and results from the biochemical characterization of AmyB and AmyB lacking the N domain show that the N domain increases binding of the enzyme to raw starch. Furthermore, theoretical modeling suggests that the N-C groove can accommodate, spatially and chemically, large substrates such as A-starch.     

An intermediate-voltage electron microscopic study of freeze-substituted generative cell in pear (Pyrus communis L.): features with relevance to cell-cell communication between the two cells of a germinating pollen

The ultrastructure of the generative cell (GC) wall complex in germinating pear (Pyrus communis L.) pollen was studied with the aim of identifying features that may shed light on the mechanism of uptake of substances by the GC from its host, the vegetative cell (VC). The techniques of rapid freeze-fixation and freeze-substitution, serial sectioning, and conventional and intermediate-voltage transmission electron microscopy were employed. The wall complex consisted of two plasma membranes (PMs), one derived from the GC and the other from the VC. A nonfibrillar wall material occurred in the space between the two PMs. Plasmodesmata could not be identified in this wall complex. However, in localized areas the wall complex formed processes that protruded into the VC cytoplasm. In other areas, the wall complex showed certain cup-shaped invaginations. Certain double membrane bound multivesicular bodies occurred in the GC cytoplasm; their morphological characteristics indicated that they may have been derived from the GC wall complex. The data indicate that in pear the GC surface is amplified by wall processes, presumably to perform a role analogous to transfer cells.