Publications by authors named "Ranjit Bahadur"

53 Publications

Unusual RNA binding of FUS RRM studied by molecular dynamics simulation and enhanced sampling method.

Biophys J 2021 05 9;120(9):1765-1776. Epub 2021 Mar 9.

Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India. Electronic address:

Amyotrophic lateral sclerosis (ALS) and frontotemporal lobe degeneration (FTLD) are two inter-related intractable diseases of motor neuron degeneration. Fused in sarcoma (FUS) is found in cytoplasmic accumulation of ALS and FTLD patients, which readily link the protein with the diseases. The RNA recognition motif (RRM) of FUS has the canonical α-β folds along with an unusual lysine-rich loop (KK-loop) between α1 and β2. This KK-loop is highly conserved among FET family proteins. Another contrasting feature of FUS RRM is the absence of critical binding residues, which are otherwise highly conserved in canonical RRMs. These residues in FUS RRM are Thr286, Glu336, Thr338, and Ser367, which are substitutions of lysine, phenylalanine, phenylalanine, and lysine, respectively, in other RRMs. Considering the importance of FUS in RNA regulation and metabolism, and its implication in ALS and FTLD, it is important to elucidate the underlying molecular mechanism of RNA recognition. In this study, we have performed molecular dynamics simulation with enhanced sampling to understand the conformational dynamics of noncanonical FUS RRM and its binding with RNA. We studied two sets of mutations: one with alanine mutation of KK-loop and another with KK-loop mutations along with critical binding residues mutated back to their canonical form. We find that concerted movement of KK-loop and loop between β2 and β3 facilitates the folding of the partner RNA, indicating an induced-fit mechanism of RNA binding. Flexibility of the RRM is highly restricted upon mutating the lysine residues of the KK-loop, resulting in weaker binding with the RNA. Our results also suggest that absence of the canonical residues in FUS RRM along with the KK-loop is equally important in regulating its binding dynamics. This study provides a significant structural insight into the binding of FUS RRM with its cognate RNA, which may further help in designing potential drugs targeting noncanonical RNA recognition.
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http://dx.doi.org/10.1016/j.bpj.2021.03.001DOI Listing
May 2021

DSS1 allosterically regulates the conformation of the tower domain of BRCA2 that has dsDNA binding specificity for homologous recombination.

Int J Biol Macromol 2020 Dec 1;165(Pt A):918-929. Epub 2020 Oct 1.

Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India. Electronic address:

DSS1 is an evolutionary conserved, small intrinsically disordered protein that regulates various cellular functions. Although several studies have elucidated the role of DSS1 in stabilizing BRCA2 and its importance in homologous recombination repair (HRR), yet the structural mechanism behind the stability and HRR remains elusive. In this study, using molecular dynamics simulation we show that DSS1 stabilizes linearly arranged DNA/DSS1 binding domains of BRCA2 with many native contacts. These contacts are absent in the complexes with two missense DSS1 mutants associated with germline breast cancer and somatic mouth carcinoma. Most importantly, our protein energy-based network models show DSS1 allosterically regulates the conformation of the distant tower domain of BRCA2 that has dsDNA binding specificity for HRR. We further postulate that the unique conformation of the tower domain with kinked-helices might be responsible for DNA strand invasion and initiation of HRR. Induced conformation of the tower domain by the kinked-helices is absent in the unbound BRCA2, as well as in the two mutant DSS1-BRCA2 complexes. This suggests that DSS1 allosterically regulates the tower domain conformations of BRCA2 that affects dsDNA binding, essential for HRR. Our results add a new dimension to the function of DSS1 and its role in regulating HRR.
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http://dx.doi.org/10.1016/j.ijbiomac.2020.09.230DOI Listing
December 2020

Do sequence neighbours of intrinsically disordered regions promote structural flexibility in intrinsically disordered proteins?

J Struct Biol 2020 02 20;209(2):107428. Epub 2019 Nov 20.

Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India. Electronic address:

Intrinsically disordered proteins (IDPs) are crucial players in various cellular activities. Several experimental and computational analyses have been conducted to study structural pliability and functional potential of IDPs. In spite of active research in past few decades, what induces structural disorder in IDPs and how is still elusive. Many studies testify that sequential and spatial neighbours often play important roles in determining structural and functional behaviour of proteins. Considering this fact, we assessed sequence neighbours of intrinsically disordered regions (IDRs) to understand if they have any role to play in inducing structural flexibility in IDPs. Our analysis includes 97% eukaryotic IDPs and 3% from bacteria and viruses. Physicochemical and structural parameters including amino acid propensity, hydrophobicity, secondary structure propensity, relative solvent accessibility, B-factor and atomic packing density are used to characterise the neighbouring residues of IDRs (NRIs). We show that NRIs exhibit a unique nature, which makes them stand out from both ordered and disordered residues. They show correlative occurrences of residue pairs like Ser-Thr and Gln-Asn, indicating their tendency to avoid strong biases of order or disorder promoting amino acids. We also find differential preferences of amino acids between N- and C-terminal neighbours, which might indicate a plausible directional effect on the dynamics of adjacent IDRs. We designed an efficient prediction tool using Random Forest to distinguish the NRIs from the ordered residues. Our findings will contribute to understand the behaviour of IDPs, and may provide potential lead in deciphering the role of IDRs in protein folding and assembly.
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http://dx.doi.org/10.1016/j.jsb.2019.107428DOI Listing
February 2020

Residue conservation elucidates the evolution of r-proteins in ribosomal assembly and function.

Int J Biol Macromol 2019 Nov 15;140:323-329. Epub 2019 Aug 15.

Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India. Electronic address:

Ribosomes are the translational machineries having two unequal subunits, small subunit (SSU) and large subunit (LSU) across all the domains of life. Origin and evolution of ribosome are encoded in its structure, and the core of the ribosome is highly conserved. Here, we have used Shannon entropy to analyze the evolution of ribosomal proteins (r-proteins) across the three domains of life. Moreover, we have analyzed the residue conservation at protein-protein (PP) and protein-RNA (PR) interfaces in SSU and LSU. Furthermore, we have studied the evolution of early, intermediate and late binding r-proteins. We show that the r-proteins of Thermus thermophilus are better conserved during the evolution. Furthermore, we find the late binders are better conserved than the early and the intermediate binders. The residues at the interior of the r-proteins are the most conserved followed by those at the interface and the solvent accessible surface. Additionally, we show that the residues at the PP interfaces are better conserved than those at the PR interfaces. However, between PR and PP interfaces, the multi-interface residues at the former are better conserved than those at the latter ones. Our findings may provide insights into the evolution of r-proteins in ribosomal assembly and function.
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http://dx.doi.org/10.1016/j.ijbiomac.2019.08.127DOI Listing
November 2019

A structure-based model for the prediction of protein-RNA binding affinity.

RNA 2019 12 8;25(12):1628-1645. Epub 2019 Aug 8.

Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.

Protein-RNA recognition is highly affinity-driven and regulates a wide array of cellular functions. In this study, we have curated a binding affinity data set of 40 protein-RNA complexes, for which at least one unbound partner is available in the docking benchmark. The data set covers a wide affinity range of eight orders of magnitude as well as four different structural classes. On average, we find the complexes with single-stranded RNA have the highest affinity, whereas the complexes with the duplex RNA have the lowest. Nevertheless, free energy gain upon binding is the highest for the complexes with ribosomal proteins and the lowest for the complexes with tRNA with an average of -5.7 cal/mol/Å in the entire data set. We train regression models to predict the binding affinity from the structural and physicochemical parameters of protein-RNA interfaces. The best fit model with the lowest maximum error is provided with three interface parameters: relative hydrophobicity, conformational change upon binding and relative hydration pattern. This model has been used for predicting the binding affinity on a test data set, generated using mutated structures of yeast aspartyl-tRNA synthetase, for which experimentally determined Δ values of 40 mutations are available. The predicted Δ values highly correlate with the experimental observations. The data set provided in this study should be useful for further development of the binding affinity prediction methods. Moreover, the model developed in this study enhances our understanding on the structural basis of protein-RNA binding affinity and provides a platform to engineer protein-RNA interfaces with desired affinity.
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http://dx.doi.org/10.1261/rna.071779.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859855PMC
December 2019

Dissecting macromolecular recognition sites in ribosome: implication to its self-assembly.

RNA Biol 2019 09 17;16(9):1300-1312. Epub 2019 Jun 17.

a Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur , Kharagpur , India.

Interactions between macromolecules play a crucial role in ribosome assembly that follows a highly coordinated process involving RNA folding and binding of ribosomal proteins (r-proteins). Although extensive studies have been carried out to understand macromolecular interactions in ribosomes, most of them are confined to either large or small ribosomal-subunit of few species. A comparative analysis of macromolecular interactions across different domains is still missing. We have analyzed the structural and physicochemical properties of protein-protein (PP), protein-RNA (PR) and RNA-RNA (RR) interfaces in small and large subunits of ribosomes, as well as in between the two subunits. Additionally, we have also developed Random Forest (RF) classifier to catalog the r-proteins. We find significant differences as well as similarities in macromolecular recognition sites between ribosomal assemblies of prokaryotes and eukaryotes. PR interfaces are substantially larger and have more ionic interactions than PP and RR interfaces in both prokaryotes and eukaryotes. PP, PR and RR interfaces in eukaryotes are well packed compared to those in prokaryotes. However, the packing density between the large and the small subunit interfaces in the entire assembly is strikingly low in both prokaryotes and eukaryotes, indicating the periodic association and dissociation of the two subunits during the translation. The structural and physicochemical properties of PR interfaces are used to predict the r-proteins in the assembly pathway into early, intermediate and late binders using RF classifier with an accuracy of 80%. The results provide new insights into the classification of r-proteins in the assembly pathway.
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http://dx.doi.org/10.1080/15476286.2019.1629767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6693545PMC
September 2019

Dissecting protein-protein interactions in proteasome assembly: Implication to its self-assembly.

J Mol Recognit 2019 09 1;32(9):e2784. Epub 2019 May 1.

Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India.

The 26S proteasome is a multi-catalytic ATP-dependent protease complex that recognizes and cleaves damaged or misfolded proteins to maintain cellular homeostasis. The 26S subunit consists of 20S core and 19S regulatory particles. 20S core particle consists of a stack of heptameric alpha and beta subunits. To elucidate the structure-function relationship, we have dissected protein-protein interfaces of 20S core particle and analyzed structural and physiochemical properties of intra-alpha, intra-beta, inter-beta, and alpha-beta interfaces. Furthermore, we have studied the evolutionary conservation of 20S core particle. We find the size of intra-alpha interfaces is significantly larger and is more hydrophobic compared with other interfaces. Inter-beta interfaces are well packed, more polar, and have higher salt-bridge density than other interfaces. In proteasome assembly, residues in beta subunits are better conserved than alpha subunits, while multi-interface residues are the most conserved. Among all the residues at the interfaces of both alpha and beta subunits, Gly is highly conserved. The largest size of intra-alpha interfaces complies with the hypothesis that large interfaces form first during the 20S assembly. The tight packing of inter-beta interfaces makes the core particle impenetrable from outer wall of the cylinder. Comparing the three domains, eukaryotes have large and well-packed interfaces followed by archaea and bacteria. Our findings provide a structural basis of assembly of 20S core particle in all the three domains of life.
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http://dx.doi.org/10.1002/jmr.2784DOI Listing
September 2019

Identification and characterization of differentially expressed Phaseolus vulgaris miRNAs and their targets during mungbean yellow mosaic India virus infection reveals new insight into Phaseolus-MYMIV interaction.

Genomics 2019 12 17;111(6):1333-1342. Epub 2018 Sep 17.

Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan 731235, India. Electronic address:

Phaseolus vulgaris is an economically important legume in tropical and subtropical regions of Asia, Africa, Latin-America and parts of USA and Europe. However, its production gets severely affected by mungbean yellow mosaic India virus (MYMIV). We aim to identify and characterize differentially expressed miRNAs during MYMIV-infection in P. vulgaris. A total of 422 miRNAs are identified of which 292 are expressed in both MYMIV-treated and mock-treated samples, 109 are expressed only in MYMIV-treated and 21 are expressed only in mock-treated samples. Selected up- and down-regulated miRNAs are validated by RT-qPCR. 3367 target ORFs are identified for 270 miRNAs. Selected targets are validated by 5' RLM-RACE. Differentially expressed miRNAs regulate transcription factors and are involved in improving stress tolerance to MYMIV. These findings will provide an insight into the role of miRNAs during MYMIV infection in P. vulgaris in particular and during any biotic stress conditions in Leguminosae family in general.
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http://dx.doi.org/10.1016/j.ygeno.2018.09.005DOI Listing
December 2019

An account of solvent accessibility in protein-RNA recognition.

Sci Rep 2018 Jul 12;8(1):10546. Epub 2018 Jul 12.

Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.

Protein-RNA recognition often induces conformational changes in binding partners. Consequently, the solvent accessible surface area (SASA) buried in contact estimated from the co-crystal structures may differ from that calculated using their unbound forms. To evaluate the change in accessibility upon binding, we compare SASA of 126 protein-RNA complexes between bound and unbound forms. We observe, in majority of cases the interface of both the binding partners gain accessibility upon binding, which is often associated with either large domain movements or secondary structural transitions in RNA-binding proteins (RBPs), and binding-induced conformational changes in RNAs. At the non-interface region, majority of RNAs lose accessibility upon binding, however, no such preference is observed for RBPs. Side chains of RBPs have major contribution in change in accessibility. In case of flexible binding, we find a moderate correlation between the binding free energy and change in accessibility at the interface. Finally, we introduce a parameter, the ratio of gain to loss of accessibility upon binding, which can be used to identify the native solution among the flexible docking models. Our findings provide fundamental insights into the relationship between flexibility and solvent accessibility, and advance our understanding on binding induced folding in protein-RNA recognition.
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http://dx.doi.org/10.1038/s41598-018-28373-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6043566PMC
July 2018

Dissecting water binding sites at protein-protein interfaces: a lesson from the atomic structures in the Protein Data Bank.

J Biomol Struct Dyn 2019 Mar 4;37(5):1204-1219. Epub 2018 Apr 4.

a Computational Structural Biology Lab, Department of Biotechnology , Indian Institute of Technology Kharagpur , Kharagpur , India.

We dissect the protein-protein interfaces into water preservation (WP), water hydration (WH) and water dehydration (WD) sites by comparing the water-mediated hydrogen bonds (H-bond) in the bound and unbound states of the interacting subunits. Upon subunit complexation, if a H-bond between an interface water and a protein polar group is retained, we assign it as WP site; if it is lost, we assign it as WD site and if a new H-bond is created, we assign it as WH site. We find that the density of WD sites is highest followed by WH and WP sites except in antigen and (or) antibody complexes, where the density of WH sites is highest followed by WD and WP sites. Furthermore, we find that WP sites are the most conserved followed by WD and WH sites in all class of complexes except in antigen and (or) antibody complexes, where WD sites are the most conserved followed by WH and WP sites. A significant number of WP and WH sites are involved in water bridges that stabilize the subunit interactions. At WH sites, the residues involved in water bridges are significantly better conserved than the other residues. However, no such difference is observed at WP sites. Interestingly, WD sites are generally replaced with direct H-bonds upon subunit complexation. Significantly, we observe many water-mediated H-bonds remain preserved in spite of large conformational changes upon subunit complexation. These findings have implications in predicting and engineering water binding sites at protein-protein interfaces.
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http://dx.doi.org/10.1080/07391102.2018.1453379DOI Listing
March 2019

Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan.

BMC Genomics 2017 Nov 15;18(1):878. Epub 2017 Nov 15.

Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India.

Background: Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negatively regulate gene expression at the levels of messenger RNAs stability and translation inhibition, on the other hand, long ncRNAs (lncRNAs) are a large and diverse class of transcribed non-protein coding RNA molecules (> 200nt) that play both up-regulatory as well as down-regulatory roles at the transcriptional level. Cajanus cajan, a leguminosae pulse crop grown in tropical and subtropical areas of the world, is a source of high value protein to vegetarians or very poor populations globally. Hence, genome-wide identification of miRNAs and lncRNAs in C. cajan is extremely important to understand their role in PTGR with a possible implication to generate improve variety of crops.

Results: We have identified 616 mature miRNAs in C. cajan belonging to 118 families, of which 578 are novel and not reported in MirBase21. A total of 1373 target sequences were identified for 180 miRNAs. Of these, 298 targets were characterized at the protein level. Besides, we have also predicted 3919 lncRNAs. Additionally, we have identified 87 of the predicted lncRNAs to be targeted by 66 miRNAs.

Conclusions: miRNA and lncRNAs in plants are known to control a variety of traits including yield, quality and stress tolerance. Owing to its agricultural importance and medicinal value, the identified miRNA, lncRNA and their targets in C. cajan may be useful for genome editing to improve better quality crop. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of C. cajan agricultural traits.
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http://dx.doi.org/10.1186/s12864-017-4232-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5688659PMC
November 2017

A non-redundant protein-RNA docking benchmark version 2.0.

Proteins 2017 02 2;85(2):256-267. Epub 2016 Dec 2.

Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India.

We present an updated version of the protein-RNA docking benchmark, which we first published four years back. The non-redundant protein-RNA docking benchmark version 2.0 consists of 126 test cases, a threefold increase in number compared to its previous version. The present version consists of 21 unbound-unbound cases, of which, in 12 cases, the unbound RNAs are taken from another complex. It also consists of 95 unbound-bound cases where only the protein is available in the unbound state. Besides, we introduce 10 new bound-unbound cases where only the RNA is found in the unbound state. Based on the degree of conformational change of the interface residues upon complex formation the benchmark is classified into 72 rigid-body cases, 25 semiflexible cases and 19 full flexible cases. It also covers a wide range of conformational flexibility including small side chain movement to large domain swapping in protein structures as well as flipping and restacking in RNA bases. This benchmark should provide the docking community with more test cases for evaluating rigid-body as well as flexible docking algorithms. Besides, it will also facilitate the development of new algorithms that require large number of training set. The protein-RNA docking benchmark version 2.0 can be freely downloaded from http://www.csb.iitkgp.ernet.in/applications/PRDBv2. Proteins 2017; 85:256-267. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/prot.25211DOI Listing
February 2017

A structural perspective of RNA recognition by intrinsically disordered proteins.

Cell Mol Life Sci 2016 11 26;73(21):4075-84. Epub 2016 May 26.

Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.

Protein-RNA recognition is essential for gene expression and its regulation, which is indispensable for the survival of the living organism at one hand, on the other hand, misregulation of this recognition may lead to their extinction. Polymorphic conformation of both the interacting partners is a characteristic feature of such molecular recognition that promotes the assembly. Many RNA binding proteins (RBP) or regions in them are found to be intrinsically disordered, and this property helps them to play a central role in the regulatory processes. Sequence composition and the length of the flexible linkers between RNA binding domains in RBPs are crucial in making significant contacts with its partner RNA. Polymorphic conformations of RBPs can provide thermodynamic advantage to its binding partner while acting as a chaperone. Prolonged extensions of the disordered regions in RBPs also contribute to the stability of the large cellular machines including ribosome and viral assemblies. The involvement of these disordered regions in most of the significant cellular processes makes RBPs highly associated with various human diseases that arise due to their misregulation.
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http://dx.doi.org/10.1007/s00018-016-2283-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079799PMC
November 2016

Layers: A molecular surface peeling algorithm and its applications to analyze protein structures.

Sci Rep 2015 Nov 10;5:16141. Epub 2015 Nov 10.

Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India.

We present an algorithm 'Layers' to peel the atoms of proteins as layers. Using Layers we show an efficient way to transform protein structures into 2D pattern, named residue transition pattern (RTP), which is independent of molecular orientations. RTP explains the folding patterns of proteins and hence identification of similarity between proteins is simple and reliable using RTP than with the standard sequence or structure based methods. Moreover, Layers generates a fine-tunable coarse model for the molecular surface by using non-random sampling. The coarse model can be used for shape comparison, protein recognition and ligand design. Additionally, Layers can be used to develop biased initial configuration of molecules for protein folding simulations. We have developed a random forest classifier to predict the RTP of a given polypeptide sequence. Layers is a standalone application; however, it can be merged with other applications to reduce the computational load when working with large datasets of protein structures. Layers is available freely at http://www.csb.iitkgp.ernet.in/applications/mol_layers/main.
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http://dx.doi.org/10.1038/srep16141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4639851PMC
November 2015

Probing binding hot spots at protein-RNA recognition sites.

Nucleic Acids Res 2016 Jan 13;44(2):e9. Epub 2015 Sep 13.

Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur-721302, India

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity.
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http://dx.doi.org/10.1093/nar/gkv876DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737170PMC
January 2016

Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures.

BMC Plant Biol 2015 Jun 12;15:140. Epub 2015 Jun 12.

Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, India.

Background: MicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information of P. vulgaris miRNAs and their expression patterns prompted us to identify new miRNAs in P. vulgaris by computational methods. Besides conventional approaches, we have used the simple sequence repeat (SSR) signatures as one of the prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, normalized base pairing index and normalized base-pair distance, instead of taking a fixed cut-off value, we have used 99% probability range derived from the available data.

Results: We have identified 208 mature miRNAs in P. vulgaris belonging to 118 families, of which 201 are novel. 97 of the predicted miRNAs in P. vulgaris were validated with the sequencing data obtained from the small RNA sequencing of P. vulgaris. Randomly selected predicted miRNAs were also validated using qRT-PCR. A total of 1305 target sequences were identified for 130 predicted miRNAs. Using 80% sequence identity cut-off, proteins coded by 563 targets were identified. The computational method developed in this study was also validated by predicting 229 miRNAs of A. thaliana and 462 miRNAs of G. max, of which 213 for A. thaliana and 397 for G. max are existing in miRBase 20.

Conclusions: There is no universal SSR that is conserved among all precursors of Viridiplantae, but conserved SSR exists within a miRNA family and is used as a signature in our prediction method. Prediction of known miRNAs of A. thaliana and G. max validates the accuracy of our method. Our findings will contribute to the present knowledge of miRNAs and their targets in P. vulgaris. This computational method can be applied to any species of Viridiplantae for the successful prediction of miRNAs and their targets.
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http://dx.doi.org/10.1186/s12870-015-0516-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4464996PMC
June 2015

A repressor activator protein1 homologue from an oleaginous strain of Candida tropicalis increases storage lipid production in Saccharomyces cerevisiae.

FEMS Yeast Res 2015 Jun 23;15(4):fov013. Epub 2015 Mar 23.

Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India Adv. Lab. for Plant Genetic Engineering, Advanced Technology Development Center, Indian Institute of Technology Kharagpur, Kharagpur 721302, India

The repressor activator protein1 (Rap1) has been studied over the years as a multifunctional regulator in Saccharomyces cerevisiae. However, its role in storage lipid accumulation has not been investigated. This report documents the identification and isolation of a putative transcription factor CtRap1 gene from an oleaginous strain of Candida tropicalis, and establishes the direct effect of its expression on the storage lipid accumulation in S. cerevisiae, usually a non-oleaginous yeast. In silico analysis revealed that the CtRap1 polypeptide binds relatively more strongly to the promoter of fatty acid synthase1 (FAS1) gene of S. cerevisiae than ScRap1. The expression level of CtRap1 transcript in vivo was found to correlate directly with the amount of lipid produced in oleaginous native host C. tropicalis. Heterologous expression of the CtRap1 gene resulted in ∼ 4-fold enhancement of storage lipid content (57.3%) in S. cerevisiae. We also showed that the functionally active CtRap1 upregulates the endogenous ScFAS1 and ScDGAT genes of S. cerevisiae, and this, in turn, might be responsible for the increased lipid production in the transformed yeast. Our findings pave the way for the possible utility of the CtRap1 gene in suitable microorganisms to increase their storage lipid content through transcription factor engineering.
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http://dx.doi.org/10.1093/femsyr/fov013DOI Listing
June 2015

Reductions in indoor black carbon concentrations from improved biomass stoves in rural India.

Environ Sci Technol 2015 Apr 20;49(7):4749-56. Epub 2015 Mar 20.

§Scripps Institute of Oceanography, University of California, San Diego 92093, United States.

Deployment of improved biomass burning cookstoves is recognized as a black carbon (BC) mitigation measure that has the potential to achieve health benefits and climate cobenefits. Yet, few field based studies document BC concentration reductions (and resulting human exposure) resulting from improved stove usage. In this paper, data are presented from 277 real-world cooking sessions collected during two field studies to document the impacts on indoor BC concentrations inside village kitchens as a result of switching from traditional stoves to improved forced draft (FD) stoves. Data collection utilized new low-cost cellphone methods to monitor BC, cooking duration, and fuel consumption. A cross sectional study recorded a reduction of 36% in BC during cooking sessions. An independent paired sample study demonstrated a statistically significant reduction of 40% in 24 h BC concentrations when traditional stoves were replaced with FD stoves. Reductions observed in these field studies differ from emission factor reductions (up to 99%) observed under controlled conditions in laboratory studies. Other nonstove sources (e.g., kerosene lamps, ambient concentrations) likely offset the reductions. Health exposure studies should utilize reductions determined by field measurements inside village kitchens, in conjunction with laboratory data, to assess the health impacts of new cooking technologies.
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http://dx.doi.org/10.1021/es506208xDOI Listing
April 2015

Molecular architecture of protein-RNA recognition sites.

J Biomol Struct Dyn 2015 11;33(12):2738-51. Epub 2015 Feb 11.

a Computational Structural Biology Laboratory, Department of Biotechnology , Indian Institute of Technology Kharagpur , Kharagpur , India.

The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is smaller than an average protein-DNA interface but larger than an average protein-protein interface. Among the different classes of protein-RNA complexes, interfaces with tRNA are the largest, while the interfaces with the single-stranded RNA are the smallest. Significantly, RNA contributes more to the interface area than its partner protein. Moreover, unlike protein-protein interfaces where the side chain contributes less to the interface area compared to the main chain, the main chain and side chain contributions flipped in protein-RNA interfaces. We find that the protein surface in contact with the RNA in protein-RNA complexes is better packed than that in contact with the DNA in protein-DNA complexes, but loosely packed than that in contact with the protein in protein-protein complexes. Shape complementarity and electrostatic potential are the two major factors that determine the specificity of the protein-RNA interaction. We find that the H-bond density at the protein-RNA interfaces is similar with that of protein-DNA interfaces but higher than the protein-protein interfaces. Unlike protein-DNA interfaces where the deoxyribose has little role in intermolecular H-bonds, due to the presence of an oxygen atom at the 2' position, the ribose in RNA plays significant role in protein-RNA H-bonds. We find that besides H-bonds, salt bridges and stacking interactions also play significant role in stabilizing protein-nucleic acids interfaces; however, their contribution at the protein-protein interfaces is insignificant.
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http://dx.doi.org/10.1080/07391102.2015.1004652DOI Listing
October 2016

Hydration of protein-RNA recognition sites.

Nucleic Acids Res 2014 Sep 11;42(15):10148-60. Epub 2014 Aug 11.

Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India

We investigate the role of water molecules in 89 protein-RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein-RNA interfaces are hydrated less than protein-DNA interfaces, but more than protein-protein interfaces. Majority of the waters at protein-RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively 'dry' than interfaces with tRNA and duplex RNA. In contrast to protein-DNA interfaces, mainly due to the presence of the 2'OH, the ribose in protein-RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein-RNA interfaces is hydrated more than the major groove, while in protein-DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein-RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein-RNA recognition and should be carefully treated while engineering protein-RNA interfaces.
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http://dx.doi.org/10.1093/nar/gku679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150782PMC
September 2014

Molecular modeling of protein-protein interaction to decipher the structural mechanism of nonhost resistance in rice.

J Biomol Struct Dyn 2014 Apr 10;32(4):669-81. Epub 2013 May 10.

a Department of Biotechnology , Indian Institute of Technology , Kharagpur , 721302 , India .

Nonhost resistance (NHR) is the most common and durable form of plant resistance to disease-causing organisms. A successful example of NHR is the cloning of a maize R gene Rxo1 in rice and validating its function in conferring bacterial streak resistance in transgenic rice lines. In order to understand the structural mechanism of NHR in rice, we built the model of the protein-protein interaction between the encoded Rxo1 (RXO1) and AvrRXO1 (avirulence protein of rice pathogen, Xanthomonas oryzae pv. oryzicola). Interestingly, although a RXO1 homolog in rice (RHR) is present, it does not interact with AvrRXO1 in nature. We have confirmed that the specificity of RXO1-AvrRXO1 interaction originates from the structured leucine rich repeat (LRR) domain of RXO1, facilitating the recognition process, while the absence of such ordered LRR region makes RHR unfavorable to recognize AvrRXO1. We postulate that the RXO1-AvrRXO1 complex formation is a three step process where electrostatic interactions, shape complementarity and short-range interactions play an important role. The presence of the structural and physicochemical properties essential for the protein-protein recognition process empowers RXO1 to mediate NHR, which the host protein RHR lacks and consequently loses its specificity to bind with AvrRXO1. To the best of our knowledge, this is the first report on the understanding of NHR in rice from the structural perspective of protein-protein interaction.
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http://dx.doi.org/10.1080/07391102.2013.787370DOI Listing
April 2014

Solar absorption by elemental and brown carbon determined from spectral observations.

Proc Natl Acad Sci U S A 2012 Oct 8;109(43):17366-71. Epub 2012 Oct 8.

Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0221, USA.

Black carbon (BC) is functionally defined as the absorbing component of atmospheric total carbonaceous aerosols (TC) and is typically dominated by soot-like elemental carbon (EC). However, organic carbon (OC) has also been shown to absorb strongly at visible to UV wavelengths and the absorbing organics are referred to as brown carbon (BrC), which is typically not represented in climate models. We propose an observationally based analytical method for rigorously partitioning measured absorption aerosol optical depths (AAOD) and single scattering albedo (SSA) among EC and BrC, using multiwavelength measurements of total (EC, OC, and dust) absorption. EC is found to be strongly absorbing (SSA of 0.38) whereas the BrC SSA varies globally between 0.77 and 0.85. The method is applied to the California region. We find TC (EC + BrC) contributes 81% of the total absorption at 675 nm and 84% at 440 nm. The BrC absorption at 440 nm is about 40% of the EC, whereas at 675 nm it is less than 10% of EC. We find an enhanced absorption due to OC in the summer months and in southern California (related to forest fires and secondary OC). The fractions and trends are broadly consistent with aerosol chemical-transport models as well as with regional emission inventories, implying that we have obtained a representative estimate for BrC absorption. The results demonstrate that current climate models that treat OC as nonabsorbing are underestimating the total warming effect of carbonaceous aerosols by neglecting part of the atmospheric heating, particularly over biomass-burning regions that emit BrC.
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http://dx.doi.org/10.1073/pnas.1205910109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491478PMC
October 2012

Protein-DNA docking with a coarse-grained force field.

BMC Bioinformatics 2012 Sep 11;13:228. Epub 2012 Sep 11.

Physics Department T38, Technical University Munich, James Franck Str. 1, 85748 Garching, Germany.

Background: Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the prediction of complex architecture given detailed structures of its constituents. They are becoming an increasingly important tool in the field of macromolecular assemblies, complementing particularly demanding protein-nucleic acids X ray crystallography and providing means for the refinement and integration of low resolution data coming from rapidly advancing methods such as cryoelectron microscopy.

Results: We present a new coarse-grained force field suitable for protein-DNA docking. The force field is an extension of previously developed parameter sets for protein-RNA and protein-protein interactions. The docking is based on potential energy minimization in translational and orientational degrees of freedom of the binding partners. It allows for fast and efficient systematic search for native-like complex geometry without any prior knowledge regarding binding site location.

Conclusions: We find that the force field gives very good results for bound docking. The quality of predictions in the case of unbound docking varies, depending on the level of structural deviation from bound geometries. We analyze the role of specific protein-DNA interactions on force field performance, both with respect to complex structure prediction, and the reproduction of experimental binding affinities. We find that such direct, specific interactions only partially contribute to protein-DNA recognition, indicating an important role of shape complementarity and sequence-dependent DNA internal energy, in line with the concept of indirect protein-DNA readout mechanism.
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http://dx.doi.org/10.1186/1471-2105-13-228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522568PMC
September 2012

The DNA-binding activity of an AP2 protein is involved in transcriptional regulation of a stress-responsive gene, SiWD40, in foxtail millet.

Genomics 2012 Oct 4;100(4):252-63. Epub 2012 Jul 4.

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India.

A differentially expressed transcript, encoding a putative WD protein (Setaria italica WD40; SiWD40), was identified in foxtail millet. Tertiary structure modeling revealed that its C-terminus possesses eight blade β-propeller architecture. Its N-terminal has three α-helices and two 3(10)-helices and was highly induced by different abiotic stresses. The SiWD40:GFP fusion protein was nuclear localized. Promoter analysis showed the presence of many cis-acting elements, including two dehydration responsive elements (DRE). A stress-responsive SiAP2 domain containing protein could specifically bind to these elements in the SiWD40 promoter. Thus, for the first time, we report that DREs probably regulate expression of SiWD40 during environmental stress. Molecular docking analysis revealed that the circumference of the β-propeller structure was involved in an interaction with a SiCullin4 protein, supporting the adaptability of SiWD40 to act as a scaffold. Our study thus provides a vital clue for near future research on the stress-regulation of WD proteins.
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http://dx.doi.org/10.1016/j.ygeno.2012.06.012DOI Listing
October 2012

PRince: a web server for structural and physicochemical analysis of protein-RNA interface.

Nucleic Acids Res 2012 Jul 11;40(Web Server issue):W440-4. Epub 2012 Jun 11.

Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, India.

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein-RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein-RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein-RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.
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http://dx.doi.org/10.1093/nar/gks535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394290PMC
July 2012

A protein-RNA docking benchmark (I): nonredundant cases.

Proteins 2012 Jul 10;80(7):1866-71. Epub 2012 May 10.

Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, India.

We have developed a nonredundant protein-RNA docking benchmark dataset, which is derived from the available bound and unbound structures in the Protein Data Bank involving polypeptide and nucleic acid chains. It consists of nine unbound-unbound cases where both the protein and the RNA are available in the free form. The other 36 cases are of unbound-bound type where only the protein is available in the free form. The conformational change upon complex formation is calculated by a distance matrix alignment method, and based on that, complexes are classified into rigid, semi-flexible, and full flexible. Although in the rigid body category, no significant conformational change accompanies complex formation, the fully flexible test cases show large domain movements, RNA base flips, etc. The benchmark covers four major groups of RNA, namely, t-RNA, ribosomal RNA, duplex RNA, and single-stranded RNA. We find that RNA is generally more flexible than the protein in the complexes, and the interface region is as flexible as the molecule as a whole. The structural diversity of the complexes in the benchmark set should provide a common ground for the development and comparison of the protein-RNA docking methods. The benchmark can be freely downloaded from the internet.
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http://dx.doi.org/10.1002/prot.24083DOI Listing
July 2012

Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)].

J Exp Bot 2011 Jun 17;62(10):3387-401. Epub 2011 Mar 17.

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India.

The DREB genes code for important plant transcription factors involved in the abiotic stress response and signal transduction. Characterization of DREB genes and development of functional markers for effective alleles is important for marker-assisted selection in foxtail millet. Here the characterization of a cDNA (SiDREB2) encoding a putative dehydration-responsive element-binding protein 2 from foxtail millet and the development of an allele-specific marker (ASM) for dehydration tolerance is reported. A cDNA clone (GenBank accession no. GT090998) coding for a putative DREB2 protein was isolated as a differentially expressed gene from a 6 h dehydration stress SSH library. A 5' RACE (rapid amplification of cDNA ends) was carried out to obtain the full-length cDNA, and sequence analysis showed that SiDREB2 encoded a polypeptide of 234 amino acids with a predicted mol. wt of 25.72 kDa and a theoretical pI of 5.14. A theoretical model of the tertiary structure shows that it has a highly conserved GCC-box-binding N-terminal domain, and an acidic C-terminus that acts as an activation domain for transcription. Based on its similarity to AP2 domains, SiDREB2 was classified into the A-2 subgroup of the DREB subfamily. Quantitative real-time PCR analysis showed significant up-regulation of SiDREB2 by dehydration (polyethylene glycol) and salinity (NaCl), while its expression was less affected by other stresses. A synonymous single nucleotide polymorphism (SNP) associated with dehydration tolerance was detected at the 558th base pair (an A/G transition) in the SiDREB2 gene in a core set of 45 foxtail millet accessions used. Based on the identified SNP, three primers were designed to develop an ASM for dehydration tolerance. The ASM produced a 261 bp fragment in all the tolerant accessions and produced no amplification in the sensitive accessions. The use of this ASM might be faster, cheaper, and more reproducible than other SNP genotyping methods, and thus will enable marker-aided breeding of foxtail millet for dehydration tolerance.
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http://dx.doi.org/10.1093/jxb/err016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130168PMC
June 2011

Identifying organic aerosol sources by comparing functional group composition in chamber and atmospheric particles.

Proc Natl Acad Sci U S A 2011 Mar 11;108(9):3516-21. Epub 2011 Feb 11.

Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA.

Measurements of submicron particles by Fourier transform infrared spectroscopy in 14 campaigns in North America, Asia, South America, and Europe were used to identify characteristic organic functional group compositions of fuel combustion, terrestrial vegetation, and ocean bubble bursting sources, each of which often accounts for more than a third of organic mass (OM), and some of which is secondary organic aerosol (SOA) from gas-phase precursors. The majority of the OM consists of alkane, carboxylic acid, hydroxyl, and carbonyl groups. The organic functional groups formed from combustion and vegetation emissions are similar to the secondary products identified in chamber studies. The near absence of carbonyl groups in the observed SOA associated with combustion is consistent with alkane rather than aromatic precursors, and the absence of organonitrate groups can be explained by their hydrolysis in humid ambient conditions. The remote forest observations have ratios of carboxylic acid, organic hydroxyl, and nonacid carbonyl groups similar to those observed for isoprene and monoterpene chamber studies, but in biogenic aerosols transported downwind of urban areas the formation of esters replaces the acid and hydroxyl groups and leaves only nonacid carbonyl groups. The carbonyl groups in SOA associated with vegetation emissions provides striking evidence for the mechanism of esterification as the pathway for possible oligomerization reactions in the atmosphere. Forest fires include biogenic emissions that produce SOA with organic components similar to isoprene and monoterpene chamber studies, also resulting in nonacid carbonyl groups in SOA.
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http://dx.doi.org/10.1073/pnas.1006461108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048156PMC
March 2011

Molecular cloning and characterization of a membrane associated NAC family gene, SiNAC from foxtail millet [Setaria italica (L.) P. Beauv].

Mol Biotechnol 2011 Oct;49(2):138-50

National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.

The plant-specific NAC (NAM, ATAF, and CUC) transcription factors have diverse role in development and stress regulation. A transcript encoding NAC protein, termed SiNAC was identified from a salt stress subtractive cDNA library of S. italica seedling (Puranik et al., J Plant Physiol 168:280-287, 2011). This single/low copy gene containing four exons and four introns within the genomic-sequence encoded a protein of 462 amino acids. Structural analysis revealed that highly divergent C terminus contains a transmembrane domain. The NAC domain consisted of a twisted antiparallel beta-sheet packing against N terminal alpha helix on one side and a shorter helix on the other side. The domain was predicted to homodimerize and control DNA-binding specificity. The physicochemical features of the SiNAC homodimer interface justified the dimeric form of the predicted model. A 1539 bp fragment upstream to the start codon of SiNAC gene was cloned and in silico analysis revealed several putative cis-acting regulatory elements within the promoter sequence. Transactivation analysis indicated that SiNAC activated expression of reporter gene and the activation domain lied at the C terminal. The SiNAC:GFP was detected in the nucleus and cytoplasm while SiNAC ΔC(1-158):GFP was nuclear localized in onion epidermal cells. SiNAC transcripts mostly accumulated in young spikes and were strongly induced by dehydration, salinity, ethephon, and methyl jasmonate. These results suggest that SiNAC encodes a membrane associated NAC-domain protein that may function as a transcriptional activator in response to stress and developmental regulation in plants.
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http://dx.doi.org/10.1007/s12033-011-9385-7DOI Listing
October 2011

Phenol groups in northeastern U.S. submicrometer aerosol particles produced from seawater sources.

Environ Sci Technol 2010 Apr;44(7):2542-8

Scripps Institution of Oceanography, University of California San Diego, La Jolla California 92093-0221, USA.

Atmospheric particles collected during the ICARTT 2004 field experiment at ground based sites at Appledore Island (AI), New Hampshire, Chebogue Point (CP), Nova Scotia, and aboard the R/V Ronald Brown (RB) were analyzed using Fourier transform infrared (FTIR) spectroscopy to quantify organic mass (OM) and organic functional groups. Several of these spectra contain a unique absorbance peak at 3500 cm(-1). Laboratory calibrations identify this peak with phenol functional groups. The phenol groups are associated with seawater-derived emissions based on correlations with tracer volatile organic compounds (VOCs) and ions, and potential source contribution function (PSCF) analysis. On the basis of the measured absorptivities, the project average phenol group concentrations are 0.24 +/- 0.18 microg m(-3) (4% of the total OM) at AI, 0.10 +/- 0.6 microg m(-3) (5% of the total OM) at CP, and 0.08 +/- 0.09 microg m(-3) (2% of the total OM) on board the RB, with detection limits typically between 0.06 and 0.11 microg m(-3). The spectra were partitioned into three primary factors using positive matrix factorization (PMF) sufficient to explain more than 95% of the measured OM. The fossil fuel combustion factor contributed 40% (AI), 34% (CP), and 43% (RB) of the total OM; the terrestrial biogenic factor contributed 20% (AI), 30% (CP), and 27% (RB). The seawater-derived factor contributed 40% (AI), 36% (CP) and 29% (RB) of the OM and showed similar correlations to tracers as the phenol group.
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http://dx.doi.org/10.1021/es9032277DOI Listing
April 2010