Vertical Profile of Phosphatase Activity in the Sundarban Mangrove Forest,North East Coast of Bay of Bengal,India

Impact of phosphate solubilizing bacteria along with soil phosphatase activity on phosphorous cycle was found to be quiet interesting in the Sundarban mangrove ecosystem. Soil phosphatase activity showed a decreasing pattern with increase in depth [soil phosphatase activity (μg pnp produced g^?1 dry wt of soil) = 906.85 – 5.6316 Depth (cm)] from the deep forest region of the Sundarban forest ecosystem. Soil salinity showed a very little effect on soil phosphatase activity whereas soil temperature and pH was found to show significant impact on the soil phosphatase activity. This ensured that the microbes associated with phosphate mineralization present in the Sundarban forest ecosystem are more tolerant to fluctuation in salinity than that of temperature and pH. A direct correlation was perceptible between the number of phosphate solubilizing bacteria and phosphatase activity in the soil during the study period from 2007 to 2012. Soil phosphate concentration was found to be directly governed by the soil phosphatase activity [The regression equation is: avg PO₄^?3-P (μg g^?1 dry wt of soil) = 0.0311 + 0.000606 soil phosphatase activity (μg pnp produced g^?1 dry wt of soil); R² = 63.2%, p < 0.001, n = 62].     

Rad17 recruits the MRE11‐RAD50‐NBS1 complex to regulate the cellular response to DNA double‐strand breaks

The MRE11‐RAD50‐NBS1 (MRN) complex is essential for the detection of DNA double‐strand breaks (DSBs) and initiation of DNA damage signaling. Here, we show that Rad17, a replication checkpoint protein, is required for the early recruitment of the MRN complex to the DSB site that is independent of MDC1 and contributes to ATM activation. Mechanistically, Rad17 is phosphorylated by ATM at a novel Thr622 site resulting in a direct interaction of Rad17 with NBS1, facilitating recruitment of the MRN complex and ATM to the DSB, thereby enhancing ATM signaling. Repetition of these events creates a positive feedback for Rad17‐dependent activation of MRN/ATM signaling which appears to be a requisite for the activation of MDC1‐dependent MRN complex recruitment. A point mutation of the Thr622 residue of Rad17 leads to a significant reduction in MRN/ATM signaling and homologous recombination repair, suggesting that Thr622 phosphorylation is important for regulation of the MRN/ATM signaling by Rad17. These findings suggest that Rad17 plays a critical role in the cellular response to DNA damage via regulation of the MRN/ATM pathway.     

Autophagy inhibition in early but not in later stages prevents 3T3-L1 differentiation: Effect on mitochondrial remodeling

Autophagy is essential for successful white adipocyte differentiation but the data regarding the timing and relevance of autophagy action during different phases of adipogenesis are limited.     

Scavenger receptor CL-P1 mediates endocytosis by associating with AP-2μ2

Background

Scavenger receptor CL-P1 (collectin placenta 1) has been found recently as a first membrane-type collectin which is mainly expressed in vascular endothelial cells. CL-P1 can endocytose OxLDL as well as microbes but in general, the endocytosis mechanism of a scavenger receptor is not well elucidated.

Methods

We screened a placental cDNA library using a yeast two-hybrid system to detect molecules associated with the cytoplasmic domain of CL-P1. We analyzed the binding and endocytosis of several ligands in CL-P1 transfectants and performed the inhibition study using tyrphostin A23 which is a specific inhibitor of tyrosine kinase, especially in μ2-dependent endocytosis and the site-directed mutagenesis in the endocytosis YXXΦ motif in CL-P1 cytoplasmic region. Furthermore, the SiRNA study of clathrin, adaptor AP-2 and dynamin-2 during the endocytosis of OxLDL in CL-P1 transfectant cells was carried out.

Results

We identified μ2 subunit of the AP-2 adaptor complex as a molecule associated with the cytoplasmic region of CL-P1. We demonstrated that AP-2μ2 was essential for CL-P1 mediated endocytosis of OxLDL in CL-P1 transfectant cells and its endocytosis was also mediated by clathrin, dynamin and adaptin complex molecules.

Conclusions

Tyrosine-based YXXΦ sequences play an important role in CL-P1-mediated OxLDL endocytosis associated with AP-2μ2.

General Significance

This might be the first finding of the clear endocytosis mechanism in scavenger receptor CL-P1.     

Dynamics of α-Hb chain binding to its chaperone AHSP depends on heme coordination and redox state

Background

AHSP is an erythroid molecular chaperone of the α-hemoglobin chains (α-Hb). Upon AHSP binding, native ferric α-Hb undergoes an unprecedented structural rearrangement at the heme site giving rise to a 6th coordination bond with His(E7).

Methods

Recombinant AHSP, WT α-Hb:AHSP and α-Hb^HE7Q:AHSP complexes were expressed in Escherichia coli. Thermal denaturation curves were measured by circular dichroism for the isolated α-Hb and bound to AHSP. Kinetics of ligand binding and redox reactions of α-Hb bound to AHSP as well as α-Hb release from the α-Hb:AHSP complex were measured by time-resolved absorption spectroscopy.

Results

AHSP binding to α-Hb is kinetically controlled to prevail over direct binding with β-chains and is also thermodynamically controlled by the α-Hb redox state and not the liganded state of the ferrous α-Hb. The dramatic instability of isolated ferric α-Hb is greatly decreased upon AHSP binding. Removing the bis-histidyl hexacoordination in α-HbH58(E7)Q:AHSP complex reduces the stabilizing effect of AHSP binding. Once the ferric α-Hb is bound to AHSP, the globin can be more easily reduced by several chemical and enzymatic systems compared to α-Hb within the Hb-tetramer.

Conclusion

α-Hb reduction could trigger its release from AHSP toward its final Hb β-chain partner producing functional ferrous Hb-tetramers. This work indicates a preferred kinetic pathway for Hb-synthesis.

General significance

The cellular redox balance in Hb-synthesis should be considered as important as the relative proportional synthesis of both Hb-subunits and their heme cofactor. The in vivo role of AHSP is discussed in the context of the molecular disorders observed in thalassemia.     

Förster Resonance Energy Transfer — An approach to visualize the spatiotemporal regulation of macromolecular complex formation and compartmentalized cell signaling

Background

Signaling messengers and effector proteins provide an orchestrated molecular machinery to relay extracellular signals to the inside of cells and thereby facilitate distinct cellular behaviors. Formations of intracellular macromolecular complexes and segregation of signaling cascades dynamically regulate the flow of a biological process.

Scope of review

In this review, we provide an overview of the development and application of FRET technology in monitoring cyclic nucleotide-dependent signalings and protein complexes associated with these signalings in real time and space with brief mention of other important signaling messengers and effector proteins involved in compartmentalized signaling.

Major conclusions

The preciseness, rapidity and specificity of cellular responses indicate restricted alterations of signaling messengers, particularly in subcellular compartments rather than globally. Not only the physical confinement and selective depletion, but also the intra- and inter-molecular interactions of signaling effectors modulate the direction of signal transduction in a compartmentalized fashion. To understand the finer details of various intracellular signaling cascades and crosstalk between proteins and other effectors, it is important to visualize these processes in live cells. Förster Resonance Energy Transfer (FRET) has been established as a useful tool to do this, even with its inherent limitations.

General significance

FRET technology remains as an effective tool for unraveling the complex organization and distribution of various endogenous signaling proteins, as well as the spatiotemporal dynamics of second messengers inside a single cell to distinguish the heterogeneity of cell signaling under normal physiological conditions and during pathological events.     

Environmental restoration effects of Ranunculus sceleratus L. in a eutrophic sewage system

This study investigated the environmental restoration effects of Ranunculus sceleratus in a sewage system microcosm trial, including the removal of pollutants and algal inhibition. We compared the removal of pollutants by R. sceleratus in a eutrophic sewage system in the presence and the absence of algae. The rate of removal without algae was 16.2–20.5% of that with algae. ${\text{NH}}_4^{+}–\text{N}$ was removed most readily by R. sceleratus. The effects of R. sceleratus on the growth of Microcystis aeruginosa were also investigated in two allelopathic modes. The level of algal inhibition after the addition of an extract of Ranunculus scleratus was 57.1–78.9% greater than that in a co-culture test. To understand the role of allelopathy interference with algal development, we also determined the total flavonoid contents of plants, which ranged from 3.57 g to 20.19 g per plant. The cell density of Microcystis aeruginosa was negatively correlated with the total flavonoids in R. sceleratus, although aquatic macrophytes may contain other allelochemicals involved with algal inhibition in addition to flavonoid compounds. The environmental effects of R. sceleratus were significantly correlated with its growth stage (or water retention time), plant height, and biomass. This study suggests that R. sceleratus has potential for the low-effort and sustainable management of freshwaters, particularly the removal of nutrient pollutants and the reduction of excessive algal growth, which may be attributable to allelochemicals such as flavonoids. The in situ environmental restoration effects of R. sceleratus require further investigation at the ecosystem level.     

High-throughput sequence analysis of small RNAs in skotomorphogenic seedlings of Brassica rapa ssp. rapa

Skotomorphogenic development is the process by which seedlings adapt to a stressful dark environment. Such metabolic responses to abiotic stresses in plants are known to be regulated in part by microRNAs (miRNAs); however, little is known about the involvement of miRNAs in the regulation of skotomorphogenesis. To identify miRNAs at the genome-wide level in skotomorphogenic seedlings of turnip (Brassica rapa subsp. rapa), an important worldwide root vegetable, we used Solexa sequencing to sequence a small RNA library from seedlings grown in the dark for 4 days. Deep sequencing showed that the small RNAs (sRNAs) were predominantly 21 to 24 nucleotides long. Specifically, 13,319,035 reads produced 359,531 unique sRNAs including rRNA, tRNA, miRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and unannotated sRNAs. Sequence analysis identified 96 conserved miRNAs belonging to 36 miRNA families and 576 novel miRNAs. qRT-PCR confirmed that the miRNAs were expressed during skotomorphogenesis similar to the trends shown by the Solexa sequencing results. A total of 2013 potential targets were predicted, and the targets of BrmiR157, BrmiR159 and BrmiR160 were proved to be regulated by miRNA-guided cleavage. These results show that specific regulatory miRNAs are present in skotomorphogenic seedlings of turnip and may play important roles in growth, development, and response to dark environment.