Structural basis for c-di-GMP-mediated inside-out signaling controlling periplasmic proteolysis

The bacterial second messenger bis-(3'-5') cyclic dimeric guanosine monophosphate (c-di-GMP) has emerged as a central regulator for biofilm formation. Increased cellular c-di-GMP levels lead to stable cell attachment, which in Pseudomonas fluorescens requires the transmembrane receptor LapD. LapD exhibits a conserved and widely used modular architecture containing a HAMP domain and degenerate diguanylate cyclase and phosphodiesterase domains. c-di-GMP binding to the LapD degenerate phosphodiesterase domain is communicated via the HAMP relay to the periplasmic domain, triggering sequestration of the protease LapG, thus preventing cleavage of the surface adhesin LapA. Here, we elucidate the molecular mechanism of autoinhibition and activation of LapD based on structure-function analyses and crystal structures of the entire periplasmic domain and the intracellular signaling unit in two different states. In the absence of c-di-GMP, the intracellular module assumes an inactive conformation. Binding of c-di-GMP to the phosphodiesterase domain disrupts the inactive state, permitting the formation of a trans-subunit dimer interface between adjacent phosphodiesterase domains via interactions conserved in c-di-GMP-degrading enzymes. Efficient mechanical coupling of the conformational changes across the membrane is realized through an extensively domain-swapped, unique periplasmic fold. Our structural and functional analyses identified a conserved system for the regulation of periplasmic proteases in a wide variety of bacteria, including many free-living and pathogenic species.     

Characterization of cysteine thiol modifications based on protein microenvironments and local secondary structures

We have demonstrated earlier that protein microenvironments were conserved around disulfide‐bridged cystine motifs with similar functions, irrespective of diversity in protein sequences. Here, cysteine thiol modifications were characterized based on protein microenvironments, secondary structures and specific protein functions. Protein microenvironment around an amino acid was defined as the summation of hydrophobic contributions from the surrounding protein fragments and the solvent molecules present within its first contact shell. Cysteine functions (modifications) were grouped into enzymatic and non‐enzymatic classes. Modifications studied were—disulfide formation, thio‐ether formation, metal‐binding, nitrosylation, acylation, selenylation, glutathionylation, sulfenylation, and ribosylation. 1079 enzymatic proteins were reported from high‐resolution crystal structures. Protein microenvironments around cysteine thiol, derived from above crystal structures, were clustered into 3 groups—buried‐hydrophobic, intermediate and exposed‐hydrophilic clusters. Characterization of cysteine functions were statistically meaningful for 4 modifications (disulfide formation, thioether formation, sulfenylation, and iron/zinc binding) those have sufficient amount of data in the current dataset. Results showed that protein microenvironment, secondary structure and protein functions were conserved for enzymatic cysteine functions, in contrast to the same function from non‐enzymatic cysteines. Disulfide forming enzymatic cysteines were tightly packed within intermediate protein microenvironment cluster, have alpha‐helical conformation and mostly belonged to CxxC motif of electron transport proteins. Disulfide forming non‐enzymatic cysteines did not belong to conserved motif and have variable secondary structures. Similarly, enzymatic thioether forming cysteines have conserved microenvironment compared to non‐enzymatic cystienes. Based on the compatibility between protein microenvironment and cysteine modifications, more efficient drug molecules could be designed against cysteine‐related diseases.     

Chemistry of the binary mixture of 1,10-phenanthroline and zinc perchlorate hexahydrate in methanol and gas phase. Monohydroxo species and tricoordination of zinc and water clusters

ESIMS reveals that methanol solutions of 1:1, 1:2 and 1:3 mixtures of Zn(ClO₄)₂ · 6H₂O and 1,10-phenanthroline (phen) generate [Zn(phen)(OH)]⁺, [Zn(phen)(H₂O)₄(OH)]⁺, [Zn(phen)₂(H₂O)(OH)]⁺and [Zn(phen)₂(H₂O)₄(OH)]⁺ ions in the gas phase. DFT calculations at the B3LYP/LanL2DZ level show that zinc is planar tricoordinate in [Zn(phen)(OH)]⁺ and the cis configuration is more stable than the trans one for the hexacoordinate ion [Zn(phen)₂(H₂O)(OH)]⁺. DFT calculations also show that the [Zn(phen)(H₂O)₄(OH)]⁺ and [Zn(phen)₂(H₂O)₄(OH)]⁺ ions are actually [Zn(phen)(H₂O)(OH)]⁺ · 3H₂O and [Zn(phen)₂(H₂O)(OH)]⁺ · 3H₂O containing extended motifs of H-bonded water clusters. The aqua species corresponding to the monohydroxo ions are acidic. Their acid dissociations are modeled collectively by equilibrium (see below) where other ligands around Zn are not specified. An attempt is then made to estimate K_a

     

I32E and V36K double mutation in beta2-sheet abrogates amyloid beta peptide toxicity

Alzheimer's disease (AD) is the most common cause of dementia in the elderly, wherein, the accumulation of amyloid beta (Abeta) peptide as cytotoxic oligomers leads to neuropathologic changes. Transgenic mice with brain Abeta plaques immunized with aggregated Abeta have reduced amyloid burden and improved cognitive functions. However, such active immunization in humans led to a small but significant occurrence of meningoencephalitis in 6% AD volunteers due to Abeta induced toxicity. In an attempt to develop safer alternative vaccines, the design of a highly soluble peptide homologous to Abeta (Abeta-EK), that has a reduced amyloidogenic potential while maintaining the major immunogenic epitopes of Abeta is reported. More importantly, this homologue has been shown to be non-toxic, as this peptide failed to exert any observable effect on erythrocytes. The results of the present study suggests that immunization with non-toxic Abeta derivative may offer a safer therapeutic approach to AD, instead of using toxic Abeta fibrils.     

An integrated diagnostic approach to understand drought tolerance in mulberry (Morus indica L.)

Four popular mulberry cultivars (Morus indica L. cvs.V-1, MR-2, S-36 and K-2) were assessed for drought tolerance with an integration of selective approaches. The potted plants were subjected to two watering treatments for 75 days: control pots were watered up to 100% field capacity (FC) and stressed pots were maintained at 25–30% FC. Net photosynthetic rate (P_n), stomatal conductance (g_s), transpiration rate (E) and instantaneous water use efficiency (WUE_i) were the key parameters to assess photosynthetic gas exchange performance. Drought caused marked down-regulation in leaf gas exchange in all cultivars (cvs) except V-1 which maintained better P_n, g_s, E and higher WUE_i under severe water deficit. All the four cvs also showed differential antioxidative responses under water stress. Higher concentrations of carotenoids, ascorbic acid, glutathione, α-tocopherol and proline were observed in the leaf extracts of V-1, while minimum accumulation of those metabolites was recorded with K-2 and S-36. An endogenous loss of α-tocopherol and higher lipid peroxidation were encountered in K-2, S-36 and MR-2, whereas V-1 showed minimum lipid peroxidation under water deficit regimes. Comparative morpho-anatomical analysis revealed a well-developed root system and a better anatomical architecture in V-1 which could further contribute tolerance during drought stress.     

Water deficit as a regulatory switch for legume root responses

Plant roots perceive declining soil water potential as an initial signal which further triggers an array of physiological, morphological and molecular responses in the whole plant. Understanding the root responses with parallel insights on protein level changes has always been an area of interest for stress biologists. In a recent study, we reported drought stress-induced changes among certain structural and functional root proteins involved in reactive oxygen species (ROS) detoxification, primary and secondary metabolite biosynthetic pathways as well as proteins associated with cell signaling in an economically important legume crop Vigna radiata (L.) Wilczek. We also demonstrated photosynthetic gas exchange characteristics and root physiology under varying levels of water-deficit and recovery. In this report, we depict a closer analysis of the expression patterns of the identified proteins which were categorized into five major functional groups. These proteins represent a unique coherence and networking with each other as well as with the overall physiological and metabolic machinery in the plant cell.Key words: drought, legume, plant metabolism, root proteins, signaling, root response     

Effect of Flanking Residues on CA and AA Dinucleotides: Some Rationale

Abstract

Effect of flanking base pairs on CA and AA dinluceotide step-geometry has been studied using molecular dynamics method. Sixteen dodecameric sequences are constructed for each doublet with all possible bases at their 5′ and 3′ positions along with their complementary sequences. Structural parameter, formation of Extra Watson Crick bifurcated hydrogen bonds along or across the strands and effect of sodium ions are studied for these sequences. It is found that geometry of CA doublet step is perturbed by the neighboring base pairs, which might be due to inherent flexibility of the step. Flexible character of CA step is reflected in its low bifurcated hydrogen bond formation capability and lower preference of sodium ions to enter in minor or major grooves. AA step on the other hand is quite rigid according to different structural parameters and respond much less to environmental changes due to formation of strong Extra Watson-Crick hydrogen bonds.     

A powerful method for pleiotropic analysis under composite null hypothesis identifies novel shared loci between Type 2 Diabetes and Prostate Cancer

There is increasing evidence that pleiotropy, the association of multiple traits with the same genetic variants/loci, is a very common phenomenon. Cross-phenotype association tests are often used to jointly analyze multiple traits from a genome-wide association study (GWAS). The underlying methods, however, are often designed to test the global null hypothesis that there is no association of a genetic variant with any of the traits, the rejection of which does not implicate pleiotropy. In this article, we propose a new statistical approach, PLACO, for specifically detecting pleiotropic loci between two traits by considering an underlying composite null hypothesis that a variant is associated with none or only one of the traits. We propose testing the null hypothesis based on the product of the Z-statistics of the genetic variants across two studies and derive a null distribution of the test statistic in the form of a mixture distribution that allows for fractions of variants to be associated with none or only one of the traits. We borrow approaches from the statistical literature on mediation analysis that allow asymptotic approximation of the null distribution avoiding estimation of nuisance parameters related to mixture proportions and variance components. Simulation studies demonstrate that the proposed method can maintain type I error and can achieve major power gain over alternative simpler methods that are typically used for testing pleiotropy. PLACO allows correlation in summary statistics between studies that may arise due to sharing of controls between disease traits. Application of PLACO to publicly available summary data from two large case-control GWAS of Type 2 Diabetes and of Prostate Cancer implicated a number of novel shared genetic regions: 3q23 (ZBTB38), 6q25.3 (RGS17), 9p22.1 (HAUS6), 9p13.3 (UBAP2), 11p11.2 (RAPSN), 14q12 (AKAP6), 15q15 (KNL1) and 18q23 (ZNF236).     

DNA polymerase λ promotes error-free replication through Watson–Crick impairing N1-methyl-deoxyadenosine adduct in conjunction with DNA polymerase ζ

In a previous study, we showed that replication through the N1-methyl-deoxyadenosine (1-MeA) adduct in human cells is mediated via three different Polι/Polθ, Polη, and Polζ-dependent pathways. Based on biochemical studies with these Pols, in the Polι/Polθ pathway, we inferred a role for Polι in the insertion of a nucleotide (nt) opposite 1-MeA and of Polθ in extension of synthesis from the inserted nt; in the Polη pathway, we inferred that this Pol alone would replicate through 1-MeA; in the Polζ pathway, however, the Pol required for inserting an nt opposite 1-MeA had remained unidentified. In this study, we provide biochemical and genetic evidence for a role for Polλ in inserting the correct nt T opposite 1-MeA, from which Polζ would extend synthesis. The high proficiency of purified Polλ for inserting a T opposite 1-MeA implicates a role for Polλ—which normally uses W-C base pairing for DNA synthesis—in accommodating 1-MeA in a syn confirmation and forming a Hoogsteen base pair with T. The potential of Polλ to replicate through DNA lesions by Hoogsteen base pairing adds another novel aspect to Polλ’s role in translesion synthesis in addition to its role as a scaffolding component of Polζ. We discuss how the action mechanisms of Polλ and Polζ could be restrained to inserting a T opposite 1-MeA and extending synthesis thereafter, respectively.