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586 results on '"Mahadevan, Radhakrishnan"'

3. Biological and Environmental Research Exascale Requirements Review. An Office of Science review sponsored jointly by Advanced Scientific Computing Research and Biological and Environmental Research, March 28-31, 2016, Rockville, Maryland

Author

Arkin, Adam, Bader, David C, Coffey, Richard, Antypas, Katie, Bard, Deborah, Dart, Eli, Dosanjh, Sudip, Gerber, Richard, Hack, James, Monga, Inder, Papka, Michael E, Riley, Katherine, Rotman, Lauren, Straatsma, Tjerk, Wells, Jack, Aluru, Srinivas, Andersen, Amity, Aprá, Edoardo, Azad, Ariful, Bates, Susan, Blaby, Ian, Blaby-Haas, Crysten, Bonneau, Rich, Bowen, Ben, Bradford, Mark A, Brodie, Eoin, Brown, James Ben, Buluc, Aydin, Bernholdt, David, Bylaska, Eric, Calvin, Kate, Cannon, Bill, Chen, Xingyuan, Cheng, Xiaolin, Cheung, Margaret, Chowdhary, Kenny, Colella, Phillip, Collins, Bill, Compo, Gil, Crowley, Mike, Debusschere, Bert, D’Imperio, Nicholas, Dror, Ron, Egan, Rob, Evans, Katherine, Friedberg, Iddo, Fyke, Jeremy, Gao, Zheng, Georganas, Evangelos, Giraldo, Frank, Gnanakaran, Gnana, Govind, Niri, Grandy, Stuart, Gustafson, Bill, Hammond, Glenn, Hargrove, William, Heroux, Michael, Hoffman, Forrest, Hofmeyr, Steven, Hunke, Elizabeth, Jackson, Charles, Jacob, Rob, Jacobson, Dan, Jacobson, Matt, Jain, Chirag, Johansen, Hans, Johnson, Jeff, Jones, Andy, Jones, Phil, Kalyanaraman, Ananth, Kang, Senghwa, King, Eric, Koanantakool, Penporn, Kollias, Pavlos, Kopera, Michal, Kotamarthi, Rao, Kowalski, Karol, Kumar, Jitendra, Kyrpides, Nikos, Leung, Ruby, Li, Xiaolin, Lin, Wuyin, Link, Robert, Liu, Yangang, Loew, Leslie, Luke, Edward, Ma, Hsi-Yen, Mahadevan, Radhakrishnan, Maranas, Costas, Martin, Daniel, Maslowski, Wieslaw, McCue, Lee Ann, McInnes, Lois Curfman, Mills, Richard, Molins Rafa, Sergi, Morozov, Dmitriy, Mostafavi, Sara, Moulton, David J, Mourao, Zenaida, and Najm, Habib

Published
2022

9. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

Author

Lieven, Christian, Beber, Moritz E, Olivier, Brett G, Bergmann, Frank T, Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A, Blank, Lars M, Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E, Edirisinghe, Janaka N, Faria, José P, Feist, Adam M, Fengos, Georgios, Fleming, Ronan MT, García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S, Hermjakob, Henning, Herrgård, Markus J, Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda, Koehorst, Jasper J, König, Matthias, Lakshmanan, Meiyappan, Lee, Dong-Yup, Lee, Sang Yup, Lee, Sunjae, Lewis, Nathan E, Liu, Filipe, Ma, Hongwu, Machado, Daniel, Mahadevan, Radhakrishnan, Maia, Paulo, Mardinoglu, Adil, Medlock, Gregory L, Monk, Jonathan M, Nielsen, Jens, Nielsen, Lars Keld, Nogales, Juan, Nookaew, Intawat, Palsson, Bernhard O, Papin, Jason A, Patil, Kiran R, Poolman, Mark, Price, Nathan D, Resendis-Antonio, Osbaldo, Richelle, Anne, Rocha, Isabel, Sánchez, Benjamín J, Schaap, Peter J, Sheriff, Rahuman S Malik, Shoaie, Saeed, Sonnenschein, Nikolaus, Teusink, Bas, Vilaça, Paulo, Vik, Jon Olav, Wodke, Judith AH, Xavier, Joana C, Yuan, Qianqian, Zakhartsev, Maksim, and Zhang, Cheng

Subjects
Biological Sciences, Industrial Biotechnology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

21. Functional and structural characterization of an IclR family transcription factor for the development of dicarboxylic acid biosensors.

Author

Pham, Chester, Nasr, Mohamed A., Skarina, Tatiana, Di Leo, Rosa, Kwan, David H., Martin, Vincent J. J., Stogios, Peter J., Mahadevan, Radhakrishnan, and Savchenko, Alexei

Abstract

Prokaryotic transcription factors (TFs) regulate gene expression in response to small molecules, thus representing promising candidates as versatile small molecule‐detecting biosensors valuable for synthetic biology applications. The engineering of such biosensors requires thorough in vitro and in vivo characterization of TF ligand response as well as detailed molecular structure information. In this work, we functionally and structurally characterize the Pca regulon regulatory protein (PcaR) transcription factor belonging to the IclR transcription factor family. Here, we present in vitro functional analysis of the ligand profile of PcaR and the construction of genetic circuits for the characterization of PcaR as an in vivo biosensor in the model eukaryote Saccharomyces cerevisiae. We report the crystal structures of PcaR in the apo state and in complex with one of its ligands, succinate, which suggests the mechanism of dicarboxylic acid recognition by this transcription factor. This work contributes key structural and functional insights enabling the engineering of PcaR for dicarboxylic acid biosensors, in addition to providing more insights into the IclR family of regulators. [ABSTRACT FROM AUTHOR]

Published
2024
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23. Ni(II)‐binding affinity of CcNikZ‐II and its homologs: the role of the HH‐prong and variable loop revealed by structural and mutational studies.

Author

Diep, Patrick, Stogios, Peter J., Evdokimova, Elena, Savchenko, Alexei, Mahadevan, Radhakrishnan, and Yakunin, Alexander F.

Subjects
CRYSTAL structure, MUTAGENESIS, FLUORESCENCE quenching, METALLOPROTEINS
Abstract

Extracytoplasmic Ni(II)‐binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ‐II at 2.38 Å, which revealed a Ni(II)‐binding site comprised of the double His (HH‐)prong (His511, His512) and a short variable (v‐)loop nearby (Thr59‐Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)‐binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH‐prong. Metal‐binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)‐binding affinities. Replacement of the wild type v‐loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering. [ABSTRACT FROM AUTHOR]

Published
2024
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39. Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

Author

Suzuki, Hitoshi, MacDonald, Jacqueline, Syed, Khajamohiddin, Salamov, Asaf, Hori, Chiaki, Aerts, Andrea, Henrissat, Bernard, Wiebenga, Ad, vanKuyk, Patricia A., Barry, Kerrie, Lindquist, Erika, LaButti, Kurt, Lapidus, Alla, Lucas, Susan, Coutinho, Pedro, Gong, Yunchen, Samejima, Masahiro, Mahadevan, Radhakrishnan, Abou-Zaid, Mamdouh, Vries, Ronald P. de, Igarashi, Kiyohiko, Yadav, Jagit S., Grigoriev, Igor V., and Master, Emma R.

Subjects
Phanerochaete carnosa, Comparative genomics, Phanerochaete chrysosporium, softwood degradation
Abstract

BackgroundSoftwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome.ResultsP. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood.ConclusionsThe P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.

Published
2012

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