Binding to syntenin-1 protein defines a new mode of ubiquitin-based interactions regulated by phosphorylation

Syntenin-1 is a PDZ domain-containing adaptor that controls trafficking of transmembrane proteins including those associated with tetraspanin-enriched microdomains. We describe the interaction of syntenin-1 with ubiquitin through a novel binding site spanning the C terminus of ubiquitin, centered on Arg(72), Leu(73), and Arg(74). A conserved LYPSL sequence in the N terminus, as well as the C-terminal region of syntenin-1, are essential for binding to ubiquitin. We present evidence for the regulation of this interaction through syntenin-1 dimerization. We have also established that syntenin-1 is phosphorylated downstream of Ulk1, a serine/threonine kinase that plays a critical role in autophagy and regulates endocytic trafficking. Importantly, Ulk1-dependent phosphorylation of Ser(6) in the LYPSL prevents the interaction of syntenin-1 with ubiquitin. These results define an unprecedented ubiquitin-dependent pathway involving syntenin-1 that is regulated by Ulk1.     

Effect of Arsenic on Nodulation and Nitrogen Fixation of Blackgram (<Emphasis Type="Italic">Vigna mungo</Emphasis>)

Rhizobium–legume symbiotic interaction is an efficient model system for soil remediation and reclamation. We earlier isolated an arsenic (As) (2.8 mM arsenate) tolerant and symbiotically effective Rhizobium strain, VMA301 from Vigna mungo and in this study we further characterized its efficacy for arsenic removal from the soil and its nitrogen fixation capacity. Although nodule formation is delayed in plants with As-treated composite when the inoculum was prepared without arsenic in culture medium, whereas it attains the significant number of nodules compare to plant grown in As-free soil when the inoculum was prepared with arsenic supplemented medium. Arsenic accumulation was higher in roots than root nodules. Nitrogenase activity is reduced to almost 2 fold in plants with As-treated soil but not abolished. These results suggest that this strain, VMA301, has been able to establish an effective symbiotic interaction in V. mungo in As-contaminated soil and can perform dual role of arsenic bioremediation as well as soil nitrogen improvement.     

Relationship between glycerol-3-phosphate dehydrogenase,fatty acid synthase and fatty acid binding proteins in developing human placenta

The activities of the enzymes glycerol-3-phosphate dehydrogenase and fatty acid synthase are inhibited by palmitoyl-coenzyme A and oleate. The two isoforms of fatty acid binding proteins (PI 6.9 and PI 5.4) enhance the activities of glycerol-3-phosphate dehydrogenase and fatty acid synthase in the absence of palmitoyl-coenzyme A or oleate and also protect them against palmitoyl-coenzyme A or oleate inhibition. Levels of fatty acid binding proteins, the activities of the enzymes fatty acid synthase and glycerol-3-phosphate dehydrogenase increase with gestation showing a peak at term. However, the activity of fatty acid synthase showed the same trend up to the 30th week of gestation and then declined slightly at term. With the advancement of pregnancy when more lipids are required for the developing placenta, fatty acid binding proteins supply more fatty acids and glycerol-3-phosphate for the synthesis of lipids. Thus a correlation exists between glycerol-3-phosphate dehydrogenase, fatty acid synthase and fatty acid binding proteins in developing human placenta.     

Benzyl prolinate derivatives as novel selective KCC2 blockers

The discovery and optimization of a novel class of selective submicromolar KCC2 blockers is described. Details of synthesis and SAR are given together with ADME properties of selected compounds. A methylsulfone residue on the R¹ phenyl group improved the overall general profile of these prolinate derivatives.     

Introduction of bacterial blight resistance into Triguna,a high yielding,mid-early duration rice variety

Bacterial blight (BB) is a serious disease of rice in India. We have used molecular marker-assisted selection in a backcross breeding program to introgress three genes (Xa21, xa13, and xa5) for BB resistance into Triguna, a mid-early duration, high yielding rice variety that is susceptible to BB. At each generation in the backcross program, molecular markers were used to select plants possessing these resistance genes and to select plants that have maximum contribution from the Triguna genome. A selected BC3F1 plant was selfed to generate homozygous BC₃F₂ plants with different combinations of BB resistance genes. Plants containing the two-gene combination, Xa21 and xa13, were found to exhibit excellent resistance against BB. Single plant selections for superior agronomic characteristics were performed on the progeny of these plants, from BC₃F₃ generation onwards. The selected plants were subjected to yield trials at the BC₃F₈ generation and were found to have a significant yield advantage over Triguna. The newly developed lines are being entered into national multi-location field trials. This work represents a successful example of the application of molecular marker-assisted selection for BB resistance breeding in rice.     

A classification model for distinguishing copy number variants from cancer-related alterations

Background  

Both somatic copy number alterations (CNAs) and germline copy number variants (CNVs) that are prevalent in healthy individuals can appear as recurrent changes in comparative genomic hybridization (CGH) analyses of tumors. In order to identify important cancer genes CNAs and CNVs must be distinguished. Although the Database of Genomic Variants (DGV) contains a list of all known CNVs, there is no standard methodology to use the database effectively.     

Seco diterpenoids from Excoecaria agallocha L

Chemical examination of the ethyl acetate solubles of the CH(3)OH:CH(2)Cl(2) (1:1) extract of the roots of Excoecaria agallocha L. collected from Godavary estuary resulted in the isolation of three more new diterpenoids, agallochins M-O (1-3). The structures of the new diterpenoids were elucidated by a study of their physical and spectral data as methyl ent-13-epi-8,13-epoxy-4,6alpha-dihydroxy-3,4-secolabd-14-en-3-oate (1), methyl ent-13-epi-8,13-epoxy-2,3-secolabd-14-en-2,11-olid-3-oate (2), and methyl ent-17-hydroxy-3,4-secokaura-4(19),15-dien-3-oate (3).     

Applicability of CoA/acetyl-CoA manipulation system to enhance isoamyl acetate production in Escherichia coli

Coenzyme A (CoA) and its thioester derivatives are important precursor molecules for many industrially useful compounds such as esters, PHBs, lycopene and polyketides. Previously, in our lab we could increase the intracellular levels of CoA and acetyl-Coenzyme A (acetyl-CoA) by overexpressing one of the upstream rate-controlling enzymes pantothenate kinase with a concomitant supplementation of the precursor pantothenic acid to the cell culture medium. In this study, we showed that the CoA/acetyl-CoA manipulation system could be used to increase the productivity of industrially useful compounds derived from acetyl-CoA. We chose the production of isoamyl acetate as a model system. Isoamyl acetate is an important flavor component of sake yeast and holds a great commercial value. Alcohol acetyl transferase (AAT) condenses isoamyl alcohol and acetyl-CoA to produce isoamyl acetate. The gene ATF2, coding for this AAT was cloned and expressed in Escherichia coli. This genetic engineered E. coli produces isoamyl acetate, an ester, from intracellular acetyl-CoA when isoamyl alcohol is added externally to the cell culture medium. In the current study, we showed that in a strain bearing ATF2 gene, an increase in intracellular CoA/acetyl-CoA by overexpressing panK leads to an increase in isoamyl acetate production. Additionally, the cofactor manipulation technique was combined with more traditional approach of competing pathway deletions to further increase isoamyl acetate production. The acetate production pathway competes with isoamyl acetate production for the common intracellular metabolite acetyl-CoA. Earlier we have shown that acetate pathway deletion (ackA-pta) increases isoamyl acetate production. The acetate production pathway was inactivated under elevated CoA/acetyl-CoA conditions, which lead to a further increase in isoamyl acetate production.