Legionella pneumophila LidA affects nucleotide binding and activity of the host GTPase Rab1

Legionella pneumophila, the causative agent of a severe pneumonia known as Legionnaires' disease, intercepts material from host cell membrane transport pathways to create a specialized vacuolar compartment that supports bacterial replication. Delivery of bacterial effector proteins into the host cell requires the Dot/Icm type IV secretion system. Several effectors, including SidM, SidD, and LepB, were shown to target the early secretory pathway by manipulating the activity of the host GTPase Rab1. While the function of these effectors has been well characterized, the role of another Rab1-interacting protein from L. pneumophila, the effector protein LidA, is poorly understood. Here, we show that LidA binding to Rab1 stabilized the Rab1-guanosine nucleotide complex, protecting it from inactivation by GTPase-activating proteins (GAPs) and from nucleotide extraction. The protective effect of LidA on the Rab1-guanine nucleotide complex was concentration dependent, consistent with a 1:1 stoichiometry of the LidA-Rab1 complex. The central coiled-coil region of LidA was sufficient for Rab1 binding and to prevent GAP-mediated inactivation or nucleotide extraction from Rab1. In addition, the central region mediated binding to phosphatidylinositol 3-phosphate and other phosphoinositides. When bound to Rab1, LidA interfered with the covalent modification of Rab1 by phosphocholination or AMPylation, and it also blocked de-AMPylation of Rab1 by SidD and dephosphocholination by Lem3. Based on these findings, we propose a role for LidA in bridging the membrane of the Legionella-containing vacuole (LCV) with that of secretory transport vesicles surrounding the LCV.     

Legionella pneumophila Strain 130b Possesses a Unique Combination of Type IV Secretion Systems and Novel Dot/Icm Secretion System Effector Proteins

Legionella pneumophila is a ubiquitous inhabitant of environmental water reservoirs. The bacteria infect a wide variety of protozoa and, after accidental inhalation, human alveolar macrophages, which can lead to severe pneumonia. The capability to thrive in phagocytic hosts is dependent on the Dot/Icm type IV secretion system (T4SS), which translocates multiple effector proteins into the host cell. In this study, we determined the draft genome sequence of L. pneumophila strain 130b (Wadsworth). We found that the 130b genome encodes a unique set of T4SSs, namely, the Dot/Icm T4SS, a Trb-1-like T4SS, and two Lvh T4SS gene clusters. Sequence analysis substantiated that a core set of 107 Dot/Icm T4SS effectors was conserved among the sequenced L. pneumophila strains Philadelphia-1, Lens, Paris, Corby, Alcoy, and 130b. We also identified new effector candidates and validated the translocation of 10 novel Dot/Icm T4SS effectors that are not present in L. pneumophila strain Philadelphia-1. We examined the prevalence of the new effector genes among 87 environmental and clinical L. pneumophila isolates. Five of the new effectors were identified in 34 to 62% of the isolates, while less than 15% of the strains tested positive for the other five genes. Collectively, our data show that the core set of conserved Dot/Icm T4SS effector proteins is supplemented by a variable repertoire of accessory effectors that may partly account for differences in the virulences and prevalences of particular L. pneumophila strains.Many bacterial pathogens use specialized protein secretion systems to deliver into host cells virulence effector proteins that interfere with the antimicrobial responses of the host and facilitate the survival of the pathogen (5, 10, 22, 76). The components of these secretion systems are highly conserved. Comparative bioinformatic analysis of pathogen genomes revealed an ever-increasing number of proteins that are likely to be translocated virulence effectors. Only a few effectors have been characterized, and their biochemical functions are unknown, yet the identification of translocated effector proteins and their mechanism of action is fundamental to understanding the pathogenesis of many bacterial infections.Legionella pneumophila is the etiological agent of Legionnaires’ disease, which is an acute form of pneumonia (34, 66). L. pneumophila serogroup 1 accounts for more than 90% of all cases worldwide. Although L. pneumophila is an environmental organism, its ability to survive and replicate in amoebae, such as Acanthamoeba castellanii, has equipped the organism with the capacity to replicate in human cells (45, 58, 68, 80). Following the inhalation of aerosols containing L. pneumophila into the human lung, the bacteria promote their uptake by alveolar macrophages and epithelial cells (21, 44, 71), where they replicate within an intracellular vacuole that avoids fusion with the endocytic pathway (46, 47). L. pneumophila evades endosome fusion by establishing a replicative vacuole that shares many characteristics with the endoplasmic reticulum (ER) (48, 53, 89). The formation of the unique Legionella-containing vacuole (LCV) requires the Dot (defective in organelle trafficking)/Icm (intracellular multiplication) type IV secretion system (T4SS) (85, 91).Type IV secretion systems are versatile multiprotein complexes that can transport DNA and proteins to recipient bacteria or host cells (19, 36). Based on structural and organizational similarity, three main T4SS classes have been distinguished: T4SSA, T4SSB, and genomic island-associated T4SS (GI-T4SS) (3, 51). The genetic organization and components of T4SSA have high similarity to the classical VirB4/VirD4 transfer DNA (T-DNA) transfer system of Agrobacterium tumefaciens (3). In the sequenced L. pneumophila strains, three distinct T4SSAs with different prevalences among strains have been described: Lvh, Trb-1, and Trb-2 (37, 83, 86). The Lvh (Legionella vir homologues) T4SSA is not required for intracellular bacterial replication in macrophages and amoebae but seems to contribute to infection at lower temperatures and inclusion in Acanthamoeba castellanii cysts (6, 78, 86).The Dot/Icm T4SSB secretes and translocates multiple bacterial effector proteins into the vacuolar membrane and cytosol of the host cell (31, 70). The functions of the great majority of these proteins are unknown. Several effectors have similarity to eukaryotic proteins or carry eukaryotic motifs (7, 16, 25). They are predicted to allow L. pneumophila to manipulate host cell processes by functional mimicry (31, 70). Many of the effectors have paralogues or belong to related protein families that are likely to have overlapping functions.Comparative analysis of the recent L. pneumophila genome sequences has revealed their diversity and plasticity (16, 18, 88). This plasticity enables the bacterium to acquire new genetic factors, including new effector proteins that enhance bacterial replication and survival in eukaryotic cells. This has resulted in a diverse species in which 7 to 11% of the genes in each L. pneumophila isolate are strain specific (38). Some of the diversity occurs among genes encoding Dot/Icm effectors, including those within the same family. For example some ankyrin repeat and F-box effector genes are highly conserved, while others vary considerably between L. pneumophila isolates (16, 41, 62, 73, 75). Even though it is not experimentally proven, the subsequent selection of Dot/Icm effectors among different L. pneumophila isolates might reflect their usefulness in host-pathogen interactions, whereby different effector repertoires are maintained during adaptation to different environmental niches or hosts. This may then translate into differences in virulence during opportunistic infection.In this study, we sequenced the genome of L. pneumophila serogroup 1 strain 130b (ATCC BAA-74, also known as Wadsworth or AA100) (29, 30) and analyzed the sequence for T4SSs and novel Dot/Icm effectors. This analysis established that the strain encodes a unique combination of T4SSs and a set of Dot/Icm effectors that had not been described previously but that are present in a range of clinical and environmental L. pneumophila isolates. The new effectors represent the latest members of an ever-growing list of T4SS substrates and presumably reflect the great capacity of L. pneumophila for adaptation to a variety of hosts.     

Structural Insights into the Pseudomonas aeruginosa Type VI Virulence Effector Tse1 Bacteriolysis and Self-protection Mechanisms

Recently, it was identified that Pseudomonas aeruginosa competes with rival cells to gain a growth advantage using a novel mechanism that includes two interrelated processes as follows: employing type VI secretion system (T6SS) virulence effectors to lyse other bacteria, and at the same time producing specialized immunity proteins to inactivate their cognate effectors for self-protection against mutual toxicity. To explore the structural basis of these processes in the context of functional performance, the crystal structures of the T6SS virulence effector Tse1 and its complex with the corresponding immunity protein Tsi1 were determined, which, in association with mutagenesis and Biacore analyses, provided a molecular platform to resolve the relevant structural questions. The results indicated that Tse1 features a papain-like structure and conserved catalytic site with distinct substrate-binding sites to hydrolyze its murein peptide substrate. The immunity protein Tsi1 interacts with Tse1 via a unique interactive recognition mode to shield Tse1 from its physiological substrate. These findings reveal both the structural mechanisms for bacteriolysis and the self-protection against the T6SS effector Tse1. These mechanisms are significant not only by contributing to a novel understanding of niche competition among bacteria but also in providing a structural basis for antibacterial agent design and the development of new strategies to fight P. aeruginosa.     

Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants

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Structural Insights into the Unique Modes of Relaxin-Binding and Tethered-Agonist Mediated Activation of RXFP1 and RXFP2

Our poor understanding of the mechanism by which the peptide-hormone H2 relaxin activates its G protein coupled receptor, RXFP1 and the related receptor RXFP2, has hindered progress in its therapeutic development. Both receptors possess large ectodomains, which bind H2 relaxin, and contain an N-terminal LDLa module that is essential for receptor signaling and postulated to be a tethered agonist. Here, we show that a conserved motif (GDxxGWxxxF), C-terminal to the LDLa module, is critical for receptor activity. Importantly, this motif adopts different structures in RXFP1 and RXFP2, suggesting distinct activation mechanisms. For RXFP1, the motif is flexible, weakly associates with the LDLa module, and requires H2 relaxin binding to stabilize an active conformation. Conversely, the GDxxGWxxxF motif in RXFP2 is more closely associated with the LDLa module, forming an essential binding interface for H2 relaxin. These differences in the activation mechanism will aid drug development targeting these receptors.     

Structural and Functional Investigations of Matrilin-1 A-domains Reveal Insights into Their Role in Cartilage ECM Assembly

Matrilin-1 is expressed predominantly in cartilage and co-localizes with matrilin-3 with which it can form hetero-oligomers. We recently described novel structural and functional features of the matrilin-3 A-domain (M3A) and demonstrated that it bound with high affinity to type II and IX collagens. Interactions preferentially occurred in the presence of Zn²⁺ suggesting that matrilin-3 has acquired a requirement for specific metal ions for activation and/or molecular associations. To understand the interdependence of matrilin-1/-3 hetero-oligomers in extracellular matrix (ECM) interactions, we have extended these studies to include the two matrilin-1 A-domains (i.e. M1A1 and M1A2 respectively). In this study we have identified new characteristics of the matrilin-1 A-domains by describing their glycosylation state and the effect of N-glycan chains on their structure, thermal stability, and protein-protein interactions. Initial characterization revealed that N-glycosylation did not affect secretion of these two proteins, nor did it alter their folding characteristics. However, removal of the glycosylation decreased their thermal stability. We then compared the effect of different cations on binding between both M1A domains and type II and IX collagens and showed that Zn²⁺ also supports their interactions. Finally, we have demonstrated that both M1A1 domains and biglycan are essential for the association of the type II·VI collagen complex. We predict that a potential role of the matrilin-1/-3 hetero-oligomer might be to increase multivalency, and therefore the ability to connect various ECM components. Differing affinities could act to regulate the integrated network, thus coordinating the organization of the macromolecular structures in the cartilage ECM.     

Transient Exposure of Pulmonary Surfactant to Hyaluronan Promotes Structural and Compositional Transformations into a Highly Active State

Pulmonary surfactant is a lipid-protein complex that lowers surface tension at the respiratory air-liquid interface, stabilizing the lungs against physical forces tending to collapse alveoli. Dysfunction of surfactant is associated with respiratory pathologies such as acute respiratory distress syndrome or meconium aspiration syndrome where naturally occurring surfactant-inhibitory agents such as serum, meconium, or cholesterol reach the lung. We analyzed the effect of hyaluronan (HA) on the structure and surface behavior of pulmonary surfactant to understand the mechanism for HA-promoted surfactant protection in the presence of inhibitory agents. In particular, we found that HA affects structural properties such as the aggregation state of surfactant membranes and the size, distribution, and order/packing of phase-segregated lipid domains. These effects do not require a direct interaction between surfactant complexes and HA and are accompanied by a compositional reorganization of large surfactant complexes that become enriched with saturated phospholipid species. HA-exposed surfactant reaches very high efficiency in terms of rapid and spontaneous adsorption of surfactant phospholipids at the air-liquid interface and shows significantly improved resistance to inactivation by serum or cholesterol. We propose that physical effects pertaining to the formation of a meshwork of interpenetrating HA polymer chains are responsible for the changes in surfactant structure and composition that enhance surfactant function and, thus, resistance to inactivation. The higher resistance of HA-exposed surfactant to inactivation persists even after removal of the polymer, suggesting that transient exposure of surfactant to polymers like HA could be a promising strategy for the production of more efficient therapeutic surfactant preparations.     

Thermodynamics and Kinetics of Single-Chain Monellin Folding with Structural Insights into Specific Collapse in the Denatured State Ensemble

Proteins, which behave as random coils in high denaturant concentrations undergo collapse transition similar to polymers on denaturant dilution. We study collapse in the denatured ensemble of single-chain monellin (MNEI) using a coarse-grained protein model and molecular dynamics simulations. The model is validated by quantitatively comparing the computed guanidinium chloride and pH-dependent thermodynamic properties of MNEI folding with the experiments. The computed properties such as the fraction of the protein in the folded state and radius of gyration (R_g) as function of [GuHCl] are in good agreement with the experiments. The folded state of MNEI is destabilized with an increase in pH due to the deprotonation of the residues Glu24 and Cys42. On decreasing [GuHCl], the protein in the unfolded ensemble showed specific compaction. The R_g of the protein decreased steadily with [GuHCl] dilution due to increase in the number of native contacts in all the secondary structural elements present in the protein. MNEI folding kinetics is complex with multiple folding pathways and transiently stable intermediates are populated in these pathways. In strong stabilizing conditions, the protein in the unfolded ensemble showed transition to a more compact unfolded state where R_g decreased by ≈ 17% due to the formation of specific native contacts in the protein. The intermediate populated in the dominant MNEI folding pathway satisfies the structural features of the dry molten globule inferred from experiments.     

Structural Studies of Soybean Calmodulin Isoform 4 Bound to the Calmodulin-binding Domain of Tobacco Mitogen-activated Protein Kinase Phosphatase-1 Provide Insights into a Sequential Target Binding Mode

The calcium regulatory protein calmodulin (CaM) binds in a calcium-dependent manner to numerous target proteins. The calmodulin-binding domain (CaMBD) region of Nicotiana tabacum MAPK phosphatase has an amino acid sequence that does not resemble the CaMBD of any other known Ca²⁺-CaM-binding proteins. Using a unique fusion protein strategy, we have been able to obtain a high resolution solution structure of the complex of soybean Ca²⁺-CaM4 (SCaM4) and this CaMBD. Complete isotope labeling of both parts of the complex in the fusion protein greatly facilitated the structure determination by NMR. The 12-residue CaMBD region was found to bind exclusively to the C-lobe of SCaM4. A specific Trp and Leu side chain are utilized to facilitate strong binding through a novel “double anchor” motif. Moreover, the orientation of the helical peptide on the surface of Ca²⁺-SCaM4 is distinct from other known complexes. The N-lobe of Ca²⁺-SCaM4 in the complex remains free for additional interactions and could possibly act as a calcium-dependent adapter protein. Signaling through the MAPK pathway and increases in intracellular Ca²⁺ are both hallmarks of the plant stress response, and our data support the notion that coordination of these responses may occur through the formation of a unique CaM-MAPK phosphatase multiprotein complex.Calmodulin (CaM)² is a ubiquitous intracellular Ca²⁺ sensor protein that plays an essential role in various Ca²⁺ signaling pathways. Contiguous and unique CaM-binding domain (CaMBD) regions are found widely distributed in many different types of CaM target proteins including protein phosphatases and kinases, cytoskeletal proteins, ion channels, and pumps (1, 2). Even though the CaMBD from various proteins share relatively poor amino acid sequence similarity, the majority of CaMBD become α-helical upon binding to CaM, and they can be grouped into either the 1-5-10 or the 1-8-14 motif, where the first and the last number indicate the position of two hydrophobic anchor residues that attach the CaMBD to the two binding pockets of the bilobal Ca²⁺-CaM. However, several noncanonical classes of CaMBD have also been identified. For example, in the CaMBD of the MARCKS protein, the two anchor residues are separated by a single amino acid residue (3). On the other hand, in the recently determined crystal structure of Ca²⁺-CaM complexed with the CaMBD of the skeletal muscle ryanodine receptor RYR1, they are separated by 15 residues (1–17 motif) (4). Bulky hydrophobic side chains of residues such as Trp, Leu, Phe, and Ile are most commonly utilized as anchor residues (see Fig. 1a), and these are usually deeply inserted into the hydrophobic target-binding pocket of either the N- or C-lobe of Ca²⁺-CaM. However, in several cases, including the N-methyl-d-aspartate receptors (NMDAR) (5) and the voltage-gated Ca²⁺ channels (Cav1–2) (6, 7), a polar side chain from Thr or Tyr has also been found to act as an anchor residue. In almost all Ca²⁺-CaM complexes studied to date, the two lobes of Ca²⁺-CaM become collapsed on the helical CaMBD, and they form a globular complex structure. An exception was found in the case of the Ca²⁺-CaM complex with an incomplete CaMBD from the plasma membrane Ca²⁺ pump (C20W), where only the C-lobe of Ca²⁺-CaM binds to the CaMBD, and the N-lobe was free in solution (8). The versatility of CaM target protein binding has been discussed in many recent reviews (for example, Refs. 2, 9–11).Open in a separate windowFIGURE 1.a, amino acid sequences of CaMBD from tobacco NtMKP1 (residues 438–449), Arabidopsis AtMKP1 (residues 451–462), and rice OsMKP1 (residues 456–467) are compared with various CaMBDs. The sequences are aligned at the position of the first hydrophobic anchor residue. The hydrophobic anchor residues are colored in red, while the other hydrophobic residues are shown in green. The basic residues and acidic residues are colored in cyan and pink, respectively. The residue numbers of the NtMKP1 sequence in SCaM4-NtMKP1/NtMKP1 protein are also indicated. b, schematic drawing of the two fusion proteins, SCaM4-NtMKP1 and SCaM4CT-NtMKP1.In plant cells, Ca²⁺ signals, arising from various extracellular stimuli such as abiotic stresses, hormones, or phytopathogens are mediated by multiple CaM isoforms to create specific cellular responses. In contrast, only a single CaM protein exists in animal cells. For example, the model plant Arabidopsis thaliana has nine CaM genes (CaM1–9) encoding seven different CaM isoforms (12, 13). Five distinct CaM genes (SCaM1–5) encoding four different CaM proteins have been identified so far in the soybean genome (14). Despite the relatively high amino acid sequence identity among these CaM isoforms (50–90%), each isoform is utilized to regulate different target enzymes related to specific cellular responses (15, 16). For example, the expression of two soybean CaM isoforms, SCaM4 and 5 is markedly up-regulated after pathogen infection, and these two proteins can activate the enzyme nitric-oxide synthase (NOS) (17). Production of nitric oxide is thought to be one of the early events in the plant defense reactions (18, 19). On the other hand, SCaM1 is incapable of activation of the NOS enzyme, and it does in fact act as a competitive inhibitor. Likewise, in Nicotiana tabacum (tobacco), the CaM isoforms NtCaM1 and NtCaM13 are overexpressed in tobacco leaf tissue in response to wounding and the TMV-triggered hypersensitive reaction, respectively (20). Recently, we have addressed the question as to how distinct CaM isoforms can give rise to selectivity in their target regulation by determining the solution structures of the two soybean CaM isoforms, SCaM1 and SCaM4 (21). However, there are currently no structures available for plant CaM isoforms in a complex with a target CaMBD peptide, although many such complex structures have been determined for animal CaM. Therefore, determining the structure of plant CaM-target complexes and uncovering their unique features relative to those of animal CaM or other plant CaM isoforms will undoubtedly enhance our understanding of the CaM-target regulation mechanisms in plants and mammals.The mitogen-activated protein kinase cascade (MAPK cascade) is an important signal transduction pathway in animals, yeast as well as in plants (22). The activity of MAPK is regulated via phosphorylation by its immediate upstream regulator, MAPK kinase (MAPKK). Following activation, MAPKs are dephosphorylated and inactivated by MAPK phosphatases. Recently, the MAPK phosphatase from tobacco (NtMKP1) was shown to be a novel plant-specific CaM-binding protein (23). This finding indicated a possible link between the MAPK cascade and Ca²⁺ signaling pathways in plant cells. The MAPK cascade is thought to play an important role in plant defense signaling, and the accumulation of Ca²⁺ in plant cells is also a well-known response to pathogens and other stresses (for recent reviews, see Refs. 24, 25). The putative CaMBD reported for NtMKP1 (residues 396–447) is located directly upstream of the conserved Ser-rich domain in the middle of the protein. Mutagenesis studies have revealed that Trp⁴⁴⁰ and Leu⁴⁴³ are indispensable for Ca²⁺-CaM binding. More recently, we have tested various truncated versions of the CaMBD of NtMKP1 and narrowed it down to 12 residues (residues 438–449) (Fig. 1a) that are sufficient for Ca²⁺-CaM binding (26). Interestingly, the NtMKP1 CaMBD does not belong to any of the typical CaM-binding motif classes. Binding assays using isothermal titration calorimetry (ITC) as well as NMR titration studies for various SCaM isoforms, and their half-lobe fragments have revealed a novel sequential target binding mechanism for the Ca²⁺-CaM isoforms. The first strong binding event involves the C-lobe of Ca²⁺-CaM and the reported binding constant for NtMKP1 peptide was 10⁷–10⁸ m⁻¹. On the other hand, the binding of a second CaMBD of NtMKP1 occurs only through the N-lobe of Ca²⁺-CaM, and the binding constant was around 10⁵ m⁻¹ (26). To date, structural information about the manner in which Ca²⁺-CaM binds sequentially to the unusual amino acid sequence of the CaMBD of NtMKP1 is unavailable. Here, we have determined the solution NMR structure of the C-lobe fragment of SCaM4 (SCaM4CT) fused with the CaMBD of NtMKP1 (Fig. 1b). We have chosen SCaM4 over other SCaM isoforms, as the stress-induced SCaM4 would provide a more important connection between stress MAPK response and Ca²⁺ signaling. The interaction of the α-helical CaMBD of NtMKP1 with SCaM4CT domain is stabilized by hydrophobic interactions mainly through Trp⁴⁴⁰ and Leu⁴⁴³ in the NtMKP1 sequence. Moreover, the basic residue, Arg⁴⁴⁴ that is unusual at position 5 (Fig. 1a) stays outside of the hydrophobic patch, and it seems to form a unique hydrogen bond to Glu⁸⁴ of the SCaM4CT domain. The resulting orientation of the α-helical CaMBD relative to the SCaM4CT domain is therefore very different from those seen in the other previously reported Ca²⁺-CaM-target complexes. We have also studied binding of a synthetic CaMBD peptide to intact Ca²⁺-SCaM4 fused at the C-terminal end with the CaMBD of NtMKP1 (Fig. 1b) providing additional information about the role of the N-lobe of Ca²⁺-SCaM4 in NtMKP1 binding. Furthermore, we have studied the interactions between the N-lobe of Ca²⁺-SCaM4 and a second potential CaMBD in the C-terminal region of NtMKP1.     

Expression of magA in Legionella pneumophila Philadelphia-1 is developmentally regulated and a marker of formation of mature intracellular forms

Legionella pneumophila displays a biphasic developmental cycle in which replicating forms (RFs) differentiate postexponentially into highly infectious, cyst-like mature intracellular forms (MIFs). Using comparative protein profile analyses (MIFs versus RFs), we identified a 20-kDa protein, previously annotated as "Mip-like" protein, that was enriched in MIFs. However, this 20-kDa protein shared no similarity with Mip, a well-characterized peptidyl-prolyl isomerase of L. pneumophila, and for clarity we renamed it MagA (for "MIF-associated gene"). We monitored MagA levels across the growth cycle (in vitro and in vivo) by immunoblotting and established that MagA levels increased postexponentially in vitro (approximately 3-fold) and nearly 10-fold during MIF morphogenesis in HeLa cells. DNA sequence analysis of the magA locus revealed an upstream divergently transcribed gene, msrA, encoding a peptide methionine sulfoxide reductase and a shared promoter region containing direct and indirect repeat sequences as well as -10 hexamers often associated with stationary-phase regulation. While MagA has no known function, it contains a conserved CXXC motif commonly found in members of the thioredoxin reductase family and in AhpD reductases that are associated with alkylhydroperoxide reductase (AhpC), suggesting a possible role in protection from oxidative stress. MIFs from L. pneumophila strain Lp02 containing a magA deletion exhibited differences in Giménez staining, as well as an apparent increase in cytopathology to HeLa cells, but otherwise were unaltered in virulence traits. As demonstrated by this study, MagA appears to be a MIF-specific protein expressed late in intracellular growth that may serve as a useful marker of development.     

Structural and functional analysis of the ARF1-ARFGAP complex reveals a role for coatomer in GTP hydrolysis

The crystal structure of the complex of ARF1 GTPase bound to GDP and the catalytic domain of ARF GTPase-activating protein (ARFGAP) has been determined at 1.95 A resolution. The ARFGAP molecule binds to switch 2 and helix alpha3 to orient ARF1 residues for catalysis, but it supplies neither arginine nor other amino acid side chains to the GTPase active site. In the complex, the effector-binding region appears to be unobstructed, suggesting that ARFGAP could stimulate GTP hydrolysis while ARF1 maintains an interaction with its effector, the coatomer complex of COPI-coated vesicles. Biochemical experiments show that coatomer directly participates in the GTPase reaction, accelerating GTP hydrolysis a further 1000-fold in an ARFGAP-dependent manner. Thus, a tripartite complex controls the GTP hydrolysis reaction triggering disassembly of COPI vesicle coats.     

Structural and Functional Insights into (S)-Ureidoglycolate Dehydrogenase,a Metabolic Branch Point Enzyme in Nitrogen Utilization

Nitrogen metabolism is one of essential processes in living organisms. The catabolic pathways of nitrogenous compounds play a pivotal role in the storage and recovery of nitrogen. In Escherichia coli, two different, interconnecting metabolic routes drive nitrogen utilization through purine degradation metabolites. The enzyme (S)-ureidoglycolate dehydrogenase (AllD), which is a member of l-sulfolactate dehydrogenase-like family, converts (S)-ureidoglycolate, a key intermediate in the purine degradation pathway, to oxalurate in an NAD(P)-dependent manner. Therefore, AllD is a metabolic branch-point enzyme for nitrogen metabolism in E. coli. Here, we report crystal structures of AllD in its apo form, in a binary complex with NADH cofactor, and in a ternary complex with NADH and glyoxylate, a possible spontaneous degradation product of oxalurate. Structural analyses revealed that NADH in an extended conformation is bound to an NADH-binding fold with three distinct domains that differ from those of the canonical NADH-binding fold. We also characterized ligand-induced structural changes, as well as the binding mode of glyoxylate, in the active site near the NADH nicotinamide ring. Based on structural and kinetic analyses, we concluded that AllD selectively utilizes NAD⁺ as a cofactor, and further propose that His116 acts as a general catalytic base and that a hydride transfer is possible on the B-face of the nicotinamide ring of the cofactor. Other residues conserved in the active sites of this novel l-sulfolactate dehydrogenase-like family also play essential roles in catalysis.     

Structural Insights into FGFR Kinase Isoform Selectivity: Diverse Binding Modes of AZD4547 and Ponatinib in Complex with FGFR1 and FGFR4

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Structural Insights into the Interaction between a Potent Anti-inflammatory Protein,Viral CC Chemokine Inhibitor (vCCI), and the Human CC Chemokine,Eotaxin-1

Chemokines play important roles in the immune system, not only recruiting leukocytes to the site of infection and inflammation but also guiding cell homing and cell development. The soluble poxvirus-encoded protein viral CC chemokine inhibitor (vCCI), a CC chemokine inhibitor, can bind to human CC chemokines tightly to impair the host immune defense. This protein has no known homologs in eukaryotes and may represent a potent method to stop inflammation. Previously, our structure of the vCCI·MIP-1β (macrophage inflammatory protein-1β) complex indicated that vCCI uses negatively charged residues in β-sheet II to interact with positively charged residues in the MIP-1β N terminus, 20s region and 40s loop. However, the interactions between vCCI and other CC chemokines have not yet been fully explored. Here, we used NMR and fluorescence anisotropy to study the interaction between vCCI and eotaxin-1 (CCL11), a CC chemokine that is an important factor in the asthma response. NMR results reveal that the binding pattern is very similar to the vCCI·MIP-1β complex and suggest that electrostatic interactions provide a major contribution to binding. Fluorescence anisotropy results on variants of eotaxin-1 further confirm the critical roles of the charged residues in eotaxin-1. In addition, the binding affinity between vCCI and other wild type CC chemokines, MCP-1 (monocyte chemoattractant protein-1), MIP-1β, and RANTES (regulated on activation normal T cell expressed and secreted), were determined as 1.1, 1.2, and 0.22 nm, respectively. To our knowledge, this is the first work quantitatively measuring the binding affinity between vCCI and multiple CC chemokines.     

Structure,Function, and Insights into the Biosynthesis of a Head-to-Head Hydrocarbon in Shewanella oneidensis Strain MR-1

A polyolefinic hydrocarbon was found in nonpolar extracts of Shewanella oneidensis MR-1 and identified as 3,6,9,12,15,19,22,25,28-hentriacontanonaene (compound I) by mass spectrometry, chemical modification, and nuclear magnetic resonance spectroscopy. Compound I was shown to be the product of a head-to-head fatty acid condensation biosynthetic pathway dependent on genes denoted as ole (for olefin biosynthesis). Four ole genes were present in S. oneidensis MR-1. Deletion of the entire oleABCD gene cluster led to the complete absence of nonpolar extractable products. Deletion of the oleC gene alone generated a strain that lacked compound I but produced a structurally analogous ketone. Complementation of the oleC gene eliminated formation of the ketone and restored the biosynthesis of compound I. A recombinant S. oneidensis strain containing oleA from Stenotrophomonas maltophilia strain R551-3 produced at least 17 related long-chain compounds in addition to compound I, 13 of which were identified as ketones. A potential role for OleA in head-to-head condensation was proposed. It was further proposed that long-chain polyunsaturated compounds aid in adapting cells to a rapid drop in temperature, based on three observations. In S. oneidensis wild-type cells, the cellular concentration of polyunsaturated compounds increased significantly with decreasing growth temperature. Second, the oleABCD deletion strain showed a significantly longer lag phase than the wild-type strain when shifted to a lower temperature. Lastly, compound I has been identified in a significant number of bacteria isolated from cold environments.Currently, there is industrial interest in nongaseous microbial hydrocarbons for specialty chemical applications and, more recently, as high-energy biofuels (20, 27, 34). Microbes produce hydrocarbons of different types, for example, aliphatic isoprenoid compounds (20) and alkanes from fatty aldehyde decarbonylation (10). Fatty aldehyde decarbonylation is not well understood but offers a clean route to diesel fuels from fatty acids.Certain microbes also make a distinctly different class of long-chain hydrocarbons, generally C₂₅ to C₃₃ in chain length, that contain a double bond near the middle of the chain (1, 3, 5, 15, 30, 31, 33, 34). These long-chain olefinic hydrocarbons are thought to derive from processes different than isoprene condensation and decarbonylation mechanisms. This class of hydrocarbons has been shown by carbon-14-labeling studies (2) to derive from fatty acids. The process, described in 1929 by Channon and Chibnall (9), has become known as head-to-head hydrocarbon biosynthesis. Albro and Ditmar (3) defined the head-to-head condensation as coupling of the head (C₁) and the α-carbon (C₂) of two fatty acids with decarboxylation, a reaction that should not be confused with an acyloin-like carboxyl carbon-to-carboxyl carbon coupling. Products of the head-to-head mechanism have been identified in Gram-positive bacteria such as Micrococcus luteus (29, 30) and Arthrobacter aurescens (13) and in Gram-negative bacteria such as Stenotrophomonas maltophilia (28). Micrococcus and Arthrobacter strains produce fatty acids that are methyl branched terminally and subterminally (8, 29, 30). The long-chain olefinic hydrocarbons from those strains similarly contain a mixture of terminal and subterminal methyl group branching (2, 13, 31).Albro and Ditmar (3, 4) acquired direct evidence for the head-to-head mechanism occurring in microbial whole organisms and cell extracts. In cell extracts, it was shown that one of the fatty acid carboxyl groups is lost as carbon dioxide, with the remaining carbon atoms being retained in the resultant hydrocarbon (4). The hydrocarbons contain a double bond at the point of condensation. More recently, Beller et al. described the genes encoding head-to-head fatty acid condensation pathway enzymes from Micrococcus luteus, which are known as ole genes for the olefin products formed (5). Three genes from Micrococcus luteus were shown to confer on Escherichia coli the ability to make long-chain olefinic hydrocarbons. Two recent patent applications by L. Friedman et al. (18 September 2008, WO2008/113041; 4 December 2008, WO2008/147781) also described a three- or four-gene cluster as being involved in head-to-head hydrocarbon biosynthesis to make olefins. The patent applications identified homologs to ole genes in different bacteria, including strains of Shewanella.Bacteria of the genus Shewanella have been heavily studied over the last decade because they are widespread and have the ability to use a startling variety of electron acceptors for respiration (11). There are more than 20 completed genome sequences for Shewanella strains. The model system for studying Shewanella is S. oneidensis MR-1. The genome sequencing of S. oneidensis MR-1 was reported in 2002 (16), and the organism has been shown to be highly amenable to genetic manipulation (11).The present study used Shewanella oneidensis strain MR-1 as a model system to investigate hydrocarbon biosynthetic genes and the possible biological function of the proteins they encode. The hydrocarbon produced by the Ole proteins in S. oneidensis MR-1 was found to be very different from hydrocarbons previously identified as deriving from a head-to-head condensation mechanism (28, 29, 32). The product was identified here as 3,6,9,12,15,19,22,25,28-hentriacontanonaene by chemical modification studies, mass spectrometry, and nuclear magnetic resonance (NMR) spectroscopy. Previously, a similar polyolefin had been identified in many Antarctic bacteria (22). Cloning of a heterologous oleA gene into S. oneidensis MR-1 was found to produce a completely different set of products. A hydrocarbon deletion mutant showed a distinctly longer growth lag than wild-type cells when shifted to a lower temperature, suggesting that the ole genes in S. oneidensis MR-1 may aid the cells in adapting to a sudden drop in temperature.     

Crystal Structure of OXA-58 with the Substrate-Binding Cleft in a Closed State: Insights into the Mobility and Stability of the OXA-58 Structure

OXA-58 is a class D β-lactamase from the multi-drug resistant Acinetobacter baumannii. We determined the crystal structure of OXA-58 in a novel crystal, and revealed the structure of the substrate-binding cleft in a closed state, distinct from a previously reported OXA-58 crystal structure with the binding cleft in an open state. In the closed state, the movement of three loops (α3–α4, β6–β7, and β8–α10) forms an arch-like architecture over the binding cleft through interaction between the Phe113 residues of α3–α4 and Met225 of β6–β7. This structure suggests the involvement of these flexible loops in OXA-58 substrate binding. In contrast to the mobile loops, the Ω-loop appeared static, including the conserved loop residues and their hydrogen bonds; the pivotal residue Trp169 within the Ω-loop, ζ-carbamic acid of the modified base catalyst residue Lys86, and nucleophilic residue Ser83. The stability of OXA-58 was enhanced concomitant with an increase in the hydrolytic activity catalyzed by NaHCO₃-dependent ζ-carbamic acid formation, with an EC₅₀ of 0.34 mM. The W169A mutant enzyme was significantly thermally unstable even in the presence of 100 mM NaHCO₃, whereas the S83A mutant was stabilized with NaHCO₃-dependent activation. The ζ-carbamic acid was shown to increase not only OXA-58 hydrolytic activity but also OXA-58 stability through the formation of a hydrogen bond network connected to the Ω-loop with Ser83 and Trp169. Thus, the static Ω-loop is important for OXA-58 stability, whereas the mobile loops of the substrate-binding cleft form the basis for accommodation of the various substituents of β-lactam backbone.     

Biochemical and Structural Insights into RNA Binding by Ssh10b,a Member of the Highly Conserved Sac10b Protein Family in Archaea

Proteins of the Sac10b family are highly conserved in Archaea. Ssh10b, a member of the Sac10b family from the hyperthermophilic crenarchaeon Sulfolobus shibatae, binds to RNA in vivo. Here we show that binding by Ssh10b destabilizes RNA secondary structure. Structural analysis of Ssh10b in complex with a 25-bp RNA duplex containing local distortions reveals that Ssh10b binds the two RNA strands symmetrically as a tetramer with each dimer bound asymmetrically to a single RNA strand. Amino acid residues involved in double-stranded RNA binding are similar, but non-identical, to those in dsDNA binding. The dimer-dimer interaction mediated by the intermolecular β-sheet appears to facilitate the destabilization of base pairing in the secondary structure of RNA. Our results suggest that proteins of the Sac10b family may play important roles in RNA transactions requiring destabilization of RNA secondary structure in Sulfolobus.