A secreted chitinase‐like protein (OsCLP) supports root growth through calcium signaling in Oryza sativa

Chitinases belong to a conserved protein family and play multiple roles in defense, development and growth regulation in plants. Here, we identified a secreted chitinase‐like protein, OsCLP, which functions in rice growth. A T‐DNA insertion mutant of OsCLP (osclp) showed significant retardation of root and shoot growth. A comparative proteomic analysis was carried out using root tissue of wild‐type and the osclp mutant to understand the OsCLP‐mediated rice growth retardation. Results obtained revealed that proteins related to glycolysis (phosphoglycerate kinase), stress adaption (chaperonin) and calcium signaling (calreticulin and CDPK1) were differentially regulated in osclp roots. Fura‐2 molecular probe staining, which is an intracellular calcium indicator, and inductively coupled plasma‐mass spectrometry (ICP‐MS) analysis suggested that the intracellular calcium content was significantly lower in roots of osclp as compared with the wild‐type. Exogenous application of Ca²⁺ resulted in successful recovery of both primary and lateral root growth in osclp. Moreover, overexpression of OsCLP resulted in improved growth with modified seed shape and starch structure; however, the overall yield remained unaffected. Taken together, our results highlight the involvement of OsCLP in rice growth by regulating the intracellular calcium concentrations.     

Genetic analysis and mapping of adult plant resistance loci to leaf rust in durum wheat cultivar Bairds

Key message

New leaf rust adult plant resistance (APR) QTL QLr.cim - 6BL was mapped and confirmed the known pleotropic APR gene Lr46 effect on leaf rust in durum wheat line Bairds.

Abstract

CIMMYT-derived durum wheat line Bairds displays an adequate level of adult plant resistance (APR) to leaf rust in Mexican field environments. A recombinant inbred line (RIL) population developed from a cross of Bairds with susceptible parent Atred#1 was phenotyped for leaf rust response at Ciudad Obregon, Mexico, during 2013, 2014, 2015 and 2016 under artificially created epidemics of Puccinia triticina (Pt) race BBG/BP. The RIL population and its parents were genotyped with the 50 K diversity arrays technology (DArT) sequence system and simple sequence repeat (SSR) markers. A genetic map comprising 1150 markers was used to map the resistance loci. Four significant quantitative trait loci (QTLs) were detected on chromosomes 1BL, 2BC (centromere region), 5BL and 6BL. These QTLs, named Lr46, QLr.cim-2BC, QLr.cim-5BL and QLr.cim-6BL, respectively, explained 13.5–60.8%, 9.0–14.3%, 2.8–13.9%, and 11.6–29.4%, respectively, of leaf rust severity variation by the inclusive composite interval mapping method. All of these resistance loci were contributed by the resistant parent Bairds, except for QLr.cim-2BC, which came from susceptible parent Atred#1. Among these, the QTL on chromosome 1BL was the known pleiotropic APR gene Lr46, whereas QLr.cim-6BL, a consistently detected locus, should be a new leaf rust resistance locus in durum wheat. The mean leaf rust severity of RILs carrying all four QTLs ranged from 8.0 to 17.5%, whereas it ranged from 10.9 to 38.5% for three QTLs (Lr46 + 5BL + 6BL) derived from the resistant parent Bairds. Two RILs with four QTLs combinations can be used as sources of complex APR in durum wheat breeding.

     

The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study

Retroviral integrases are reported to form alternate dimer assemblies like the core–core dimer and reaching dimer. The core–core dimer is stabilized predominantly by an extensive interface between two catalytic core domains. The reaching dimer is stabilized by N-terminal domains that reach to form intermolecular interfaces with the other subunit’s core and C-terminal domains (CTD), as well as CTD–CTD interactions. In this study, molecular dynamics (MD), Brownian dynamics (BD) simulations, and free energy analyses, were performed to elucidate determinants for the stability of the reaching dimer forms of full-length Avian Sarcoma Virus (ASV) and Human Immunodeficiency Virus (HIV) IN, and to examine the role of the C-tails (the last ~16–18 residues at the C-termini) in their structural dynamics. The dynamics of an HIV reaching dimer derived from small angle X-ray scattering and protein crosslinking data, was compared with the dynamics of a core–core dimer model derived from combining the crystal structures of two-domain fragments. The results showed that the core domains in the ASV reaching dimer express free dynamics, whereas those in the HIV reaching dimer are highly stable. BD simulations suggest a higher rate of association for the HIV core–core dimer than the reaching dimer. The predicted stability of these dimers was therefore ranked in the following order: ASV reaching dimer < HIV reaching dimer < composite core–core dimer. Analyses of MD trajectories have suggested residues that are critical for intermolecular contacts in each reaching dimer. Tests of these predictions and insights gained from these analyses could reveal a potential pathway for the association and dissociation of full-length IN multimers.     

Evolution of a multi‐step phosphorelay signal transduction system in Ensifer: recruitment of the sigma factor RpoN and a novel enhancer‐binding protein triggers acid‐activated gene expression

Most Ensifer strains are comparatively acid sensitive, compromising their persistence in low pH soils. In the acid‐tolerant strain Ensifer medicae WSM419, the acid‐activated expression of lpiA is essential for enhancing survival in lethal acidic conditions. Here we characterise a multi‐step phosphorelay signal transduction pathway consisting of TcsA, TcrA, FsrR, RpoN and its cognate enhancer‐binding protein EbpA, which is required for the induction of lpiA and the downstream acvB gene. The fsrR, tcrA, tcsA and rpoN genes were constitutively expressed, whereas lpiA and acvB were strongly acid‐induced. RACE mapping revealed that lpiA/acvB were co‐transcribed as an operon from an RpoN promoter. In most Ensifer species, lpiA/acvB is located on the chromosome and the sequence upstream of lpiA lacks an RpoN‐binding site. Nearly all Ensifer meliloti strains completely lack ebpA, tcrA, tcsA and fsrR regulatory loci. In contrast, E. medicae strains have lpiA/acvB and ebpA/tcrA/tcsA/fsrR co‐located on the pSymA megaplasmid, with lpiA/acvB expression coupled to an RpoN promoter. Here we provide a model for the expression of lpiA/acvB in E. medicae. This unique acid‐activated regulatory system provides insights into an evolutionary process which may assist the adaptation of E. medicae to acidic environmental niches.     

Osmoregulatory capacity,health status and growth as functions of moult stages from various weight classes in marron (Cherax cainii) and yabbies (Cherax destructor)

The study investigated the relationship between five moult stages and the osmoregulatory capacities (OC), moisture content of hepatopancreas (HM%), hepatosomatic indices (HI_wet, HI_dry) and growth of 6 weight classes of 235 marron (Cherax cainii) and 235 yabbies (Cherax destructor) under laboratory conditions. In each moult stage, OC increased linearly with the increase in wet body weight. Intermoult stage C showed the highest OC significantly lower than premoult stages D₀, D₁, D₂ and postmoult stage AB in every weight class in both crayfish. HM% decreased from AB to D₂, while both HI_wet and HI_dry reduced from C to D₂. Percentage dry matter of whole body carcass was highest in stage C and lowest during the AB stage with a significant difference between the two species. Larger than 15-g marron and yabbies differ with each other in OC, HI_wet, and HI_dry, moult intervals and growth rates.     

Comprehensive physiological analyses and reactive oxygen species profiling in drought tolerant rice genotypes under salinity stress

Rice being a staple cereal is extremely susceptible towards abiotic stresses. Drought and salinity are two vital factors limiting rice cultivation in Eastern Indo-Gangetic Plains (EIGP). Present study has intended to evaluate the consequences of salinity stress on selected drought tolerant rice genotypes at the most susceptible seedling stage with an aim to identify the potential multi-stress (drought and salt) tolerant rice genotype of this region. Genotypic variation was obvious in all traits related to drought and salt susceptibility. IR84895-B-127-CRA-5-1-1, one of the rice genotypes studied, exhibited exceptional drought and salinity tolerance. IR83373-B-B-25-3-B-B-25-3 also displayed enhanced drought and salt tolerance following IR84895-B-127-CRA-5-1-1. Variations were perceptible in different factors involving photosynthetic performance, proline content, lipid peroxidation, K⁺/Na⁺ ratio. Accumulation of reactive oxygen species (ROS) disintegrated cellular and sub-cellular membrane leading to decreased photosynthetic activities. Therefore, accumulation and detoxification of reactive oxygen species was also considered as a major determinant of salt tolerance. IR84895-B-127-CRA-5-1-1 showed improved ROS detoxification mediated by antioxidant enzymes. IR84895-B-127-CRA-5-1-1 seedlings also displayed significant recovery after removal of salt stress. The results established a direct association of ROS scavenging with improved physiological activities and salt tolerance. The study also recommended IR84895-B-127-CRA-5-1-1 for improved crop performance in both drought and saline environments of EIGP. These contrasting rice genotypes may assist in understanding the multiple stress associated factors in concurrent drought and salt tolerant rice genotypes.     

Role of the hepatocyte growth factor receptor, c-Met, in oncogenesis and potential for therapeutic inhibition.

Receptor tyrosine kinases have become important therapeutic targets for anti-neoplastic molecularly targeted therapies. c-Met is a receptor tyrosine kinase shown to be over-expressed and mutated in a variety of malignancies. Stimulation of c-Met via its ligand hepatocyte growth factor also known as scatter factor (HGF/SF), leads to a plethora of biological and biochemical effects in the cell. There has been considerable knowledge gained on the role of c-Met-HGF/SF axis in normal and malignant cells. This review summarizes the structure of c-Met and HGF/SF and their family members. Since there are known mutations of c-Met in solid tumors, particularly in papillary renal cell carcinoma, we have summarized the various mutations and over-expression of c-Met known thus far. Stimulation of c-Met can lead to scattering, angiogenesis, proliferation, enhanced cell motility, invasion, and eventual metastasis. The biological functions altered by c-Met are quite unique and described in detail. Along with biological functions, various signal transduction pathways, including the cytoskeleton are altered with the activation of c-Met-HGF/SF loop. We have recently shown the phosphorylation of focal adhesion proteins, such as paxillin and p125FAK in response to c-Met stimulation in lung cancer cells, and this is detailed here. Finally, c-Met when mutated or over-expressed in malignant cells serves as an important therapeutic target and the most recent data in terms of inhibition of c-Met and downstream signal transduction pathways is summarized.     

Epistasis Creates Invariant Sites and Modulates the Rate of Molecular Evolution

Invariant sites are a common feature of amino acid sequence evolution. The presence of invariant sites is frequently attributed to the need to preserve function through site-specific conservation of amino acid residues. Amino acid substitution models without a provision for invariant sites often fit the data significantly worse than those that allow for an excess of invariant sites beyond those predicted by models that only incorporate rate variation among sites (e.g., a Gamma distribution). An alternative is epistasis between sites to preserve residue interactions that can create invariant sites. Through computer-simulated sequence evolution, we evaluated the relative effects of site-specific preferences and site-site couplings in the generation of invariant sites and the modulation of the rate of molecular evolution. In an analysis of ten major families of protein domains with diverse sequence and functional properties, we find that the negative selection imposed by epistasis creates many more invariant sites than site-specific residue preferences alone. Further, epistasis plays an increasingly larger role in creating invariant sites over longer evolutionary periods. Epistasis also dictates rates of domain evolution over time by exerting significant additional purifying selection to preserve site couplings. These patterns illuminate the mechanistic role of epistasis in the processes underlying observed site invariance and evolutionary rates.