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Liu D, Tang D, Xie M, Zhang J, Zhai L, Mao J, Luo C, Lipzen A, Zhang Y, Savage E, Yuan G, Guo HB, Tadesse D, Hu R, Jawdy S, Cheng H, Li L, Yer H, Clark MM, Sun H, Shi J, Budhathoki R, Kumar R, Kamuda T, Li Y, Pennacchio C, Barry K, Schmutz J, Berry R, Muchero W, Chen JG, Li Y, Tuskan GA, Yang X. Agave REVEILLE1 regulates the onset and release of seasonal dormancy in Populus. Plant Physiol 2023; 191:1492-1504. [PMID: 36546733 PMCID: PMC10022617 DOI: 10.1093/plphys/kiac588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Deciduous woody plants like poplar (Populus spp.) have seasonal bud dormancy. It has been challenging to simultaneously delay the onset of bud dormancy in the fall and advance bud break in the spring, as bud dormancy, and bud break were thought to be controlled by different genetic factors. Here, we demonstrate that heterologous expression of the REVEILLE1 gene (named AaRVE1) from Agave (Agave americana) not only delays the onset of bud dormancy but also accelerates bud break in poplar in field trials. AaRVE1 heterologous expression increases poplar biomass yield by 166% in the greenhouse. Furthermore, we reveal that heterologous expression of AaRVE1 increases cytokinin contents, represses multiple dormancy-related genes, and up-regulates bud break-related genes, and that AaRVE1 functions as a transcriptional repressor and regulates the activity of the DORMANCY-ASSOCIATED PROTEIN 1 (DRM1) promoter. Our findings demonstrate that AaRVE1 appears to function as a regulator of bud dormancy and bud break, which has important implications for extending the growing season of deciduous trees in frost-free temperate and subtropical regions to increase crop yield.
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Affiliation(s)
| | | | - Meng Xie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- U.S. DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- U.S. DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Longmei Zhai
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Jiangping Mao
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Chao Luo
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Yu Zhang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Emily Savage
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- U.S. DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Hao-Bo Guo
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, USA
- UES Inc., Dayton, Ohio 45432, USA
| | - Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- U.S. DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Hua Cheng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Linling Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Huseyin Yer
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Miranda M Clark
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- U.S. DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Huayu Sun
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Jiyuan Shi
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Roshani Budhathoki
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Rahul Kumar
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Troy Kamuda
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Yanjun Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Christa Pennacchio
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA
| | - Rajiv Berry
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- U.S. DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- U.S. DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- U.S. DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Guo HB, Perminov A, Bekele S, Kedziora G, Farajollahi S, Varaljay V, Hinkle K, Molinero V, Meister K, Hung C, Dennis P, Kelley-Loughnane N, Berry R. AlphaFold2 models indicate that protein sequence determines both structure and dynamics. Sci Rep 2022; 12:10696. [PMID: 35739160 PMCID: PMC9226352 DOI: 10.1038/s41598-022-14382-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/06/2022] [Indexed: 12/29/2022] Open
Abstract
AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.
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Affiliation(s)
- Hao-Bo Guo
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Alexander Perminov
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- Computer Science Department, Miami University, Oxford, OH, USA
| | - Selemon Bekele
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Gary Kedziora
- General Dynamics Information Technology, Inc., Wright-Patterson Air Force Base, 45433, OH, USA
| | - Sanaz Farajollahi
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
- UES Inc., Dayton, OH, USA
| | - Vanessa Varaljay
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Kevin Hinkle
- Department of Chemical and Materials Engineering, Dayton University, Dayton, OH, USA
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, Salt Lake City, UT, USA
| | - Konrad Meister
- Department of Natural Sciences, University of Alaska Southeast, Juneau, AK, USA
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Chia Hung
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Patrick Dennis
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA
| | - Nancy Kelley-Loughnane
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA.
| | - Rajiv Berry
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, 45433, OH, USA.
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Wei QT, Liu BY, Ji HY, Lan YF, Tang WH, Zhou J, Zhong XY, Lian CL, Huang QZ, Wang CY, Xu YM, Guo HB. Exosome-mediated transfer of MIF confers temozolomide resistance by regulating TIMP3/PI3K/AKT axis in gliomas. Mol Ther Oncolytics 2021; 22:114-128. [PMID: 34514093 PMCID: PMC8413833 DOI: 10.1016/j.omto.2021.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/12/2021] [Indexed: 01/08/2023]
Abstract
Temozolomide (TMZ) resistance is an important cause of clinical treatment failure and poor prognosis in gliomas. Increasing evidence indicates that cancer-derived exosomes contribute to chemoresistance; however, the specific contribution of glioma-derived exosomes remains unclear. The aim of this study was to explore the role and underlying mechanisms of exosomal macrophage migration inhibitory factor (MIF) on TMZ resistance in gliomas. We first demonstrated that MIF was upregulated in the exosomes of TMZ-resistant cells, engendering the transfer of TMZ resistance to sensitive cells. Our results indicated that exosomal MIF conferred TMZ resistance to sensitive cells through the enhancement of cell proliferation and the repression of cell apoptosis upon TMZ exposure. MIF knockdown enhanced TMZ sensitivity in resistant glioma cells by upregulating Metalloproteinase Inhibitor 3 (TIMP3) and subsequently suppressing the PI3K/AKT signaling pathway. Additionally, exosomal MIF promoted tumor growth and TMZ resistance of glioma cells in vivo, while IOS-1 (MIF inhibitor) promotes glioma TMZ sensitive in vivo. Taken together, our study demonstrated that exosome-mediated transfer of MIF enhanced TMZ resistance in glioma through downregulating TIMP3 and further activating the PI3K/AKT signaling pathway, highlighting a prognostic biomarker and promising therapeutic target for TMZ treatment in gliomas.
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Affiliation(s)
- Q T Wei
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China.,Department of Neurosurgery, The First Affiliated Hospital of Shantou University, Shantou 515041, Guangdong, China
| | - B Y Liu
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China
| | - H Y Ji
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China.,Department of Neurosurgery, The First Affiliated Hospital of Shantou University, Shantou 515041, Guangdong, China
| | - Y F Lan
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China
| | - W H Tang
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China
| | - J Zhou
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China
| | - X Y Zhong
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China
| | - C L Lian
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China
| | - Q Z Huang
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China
| | - C Y Wang
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China
| | - Y M Xu
- Department of Neurosurgery, The First Affiliated Hospital of Shantou University, Shantou 515041, Guangdong, China
| | - H B Guo
- Department of Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, 253 Gongye Middle Avenue, Haizhu District, Guangzhou, Guangdong 510280, China
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Sun Y, Yu R, Guo HB, Qin H, Dang W. A quantitative yeast aging proteomics analysis reveals novel aging regulators. GeroScience 2021; 43:2573-2593. [PMID: 34241809 DOI: 10.1007/s11357-021-00412-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 06/23/2021] [Indexed: 11/29/2022] Open
Abstract
Calorie restriction (CR) is the most robust longevity intervention, extending lifespan from yeast to mammals. Numerous conserved pathways regulating aging and mediating CR have been identified; however, the overall proteomic changes during these conditions remain largely unexplored. We compared proteomes between young and replicatively aged yeast cells under normal and CR conditions using the Stable-Isotope Labeling by Amino acids in Cell culture (SILAC) quantitative proteomics and discovered distinct signatures in the aging proteome. We found remarkable proteomic similarities between aged and CR cells, including induction of stress response pathways, providing evidence that CR pathways are engaged in aged cells. These observations also uncovered aberrant changes in mitochondria membrane proteins as well as a proteolytic cellular state in old cells. These proteomics analyses help identify potential genes and pathways that have causal effects on longevity.
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Affiliation(s)
- Yu Sun
- Huffington Center On Aging and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ruofan Yu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hao-Bo Guo
- Department of Computer Science and Engineering, Department of Biology, Geology and Environmental Science, SimCenter, The University of Tennessee At Chattanooga, Chattanooga, TN, 37403, USA
| | - Hong Qin
- Department of Computer Science and Engineering, Department of Biology, Geology and Environmental Science, SimCenter, The University of Tennessee At Chattanooga, Chattanooga, TN, 37403, USA
| | - Weiwei Dang
- Huffington Center On Aging and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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5
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Abstract
We proposed a novel interaction potential landscape approach to map the systems-level profile changes of gene networks during replicative aging in Saccharomyces cerevisiae. This approach enabled us to apply quasi-potentials, the negative logarithm of the probabilities, to calibrate the elevation of the interaction landscapes with young cells as a reference state. Our approach detected opposite landscape changes based on protein abundances from transcript levels, especially for intra-essential gene interactions. We showed that essential proteins play different roles from hub proteins on the age-dependent interaction potential landscapes. We verified that hub proteins tend to avoid other hub proteins, but essential proteins prefer to interact with other essential proteins. Overall, we showed that the interaction potential landscape is promising for inferring network profile change during aging and that the essential hub proteins may play an important role in the uncoupling between protein and transcript levels during replicative aging.
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Affiliation(s)
- Hao-Bo Guo
- Department of Computer Science and Engineering, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- SimCenter, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH, 45433, USA.
| | - Mehran Ghafari
- Department of Computer Science and Engineering, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hong Qin
- Department of Computer Science and Engineering, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- SimCenter, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- Department of Biology, Geology and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
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6
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Ghafari M, Clark J, Guo HB, Yu R, Sun Y, Dang W, Qin H. Complementary performances of convolutional and capsule neural networks on classifying microfluidic images of dividing yeast cells. PLoS One 2021; 16:e0246988. [PMID: 33730031 PMCID: PMC7968698 DOI: 10.1371/journal.pone.0246988] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/19/2021] [Indexed: 01/17/2023] Open
Abstract
Microfluidic-based assays have become effective high-throughput approaches to examining replicative aging of budding yeast cells. Deep learning may offer an efficient way to analyze a large number of images collected from microfluidic experiments. Here, we compare three deep learning architectures to classify microfluidic time-lapse images of dividing yeast cells into categories that represent different stages in the yeast replicative aging process. We found that convolutional neural networks outperformed capsule networks in terms of accuracy, precision, and recall. The capsule networks had the most robust performance in detecting one specific category of cell images. An ensemble of three best-fitted single-architecture models achieves the highest overall accuracy, precision, and recall due to complementary performances. In addition, extending classification classes and data augmentation of the training dataset can improve the predictions of the biological categories in our study. This work lays a useful framework for sophisticated deep-learning processing of microfluidic-based assays of yeast replicative aging.
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Affiliation(s)
- Mehran Ghafari
- SimCenter, Department of Computer Science and Engineering, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
- * E-mail: (MG); (HQ)
| | - Justin Clark
- SimCenter, Department of Computer Science and Engineering, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
| | - Hao-Bo Guo
- SimCenter, Department of Computer Science and Engineering, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
| | - Ruofan Yu
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yu Sun
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas, United States of America
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hong Qin
- SimCenter, Department of Computer Science and Engineering, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
- Department of Computer Science and Engineering, Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
- * E-mail: (MG); (HQ)
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7
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Liu D, Hu R, Zhang J, Guo HB, Cheng H, Li L, Borland AM, Qin H, Chen JG, Muchero W, Tuskan GA, Yang X. Overexpression of an Agave Phospho enolpyruvate Carboxylase Improves Plant Growth and Stress Tolerance. Cells 2021; 10:582. [PMID: 33800849 PMCID: PMC7999111 DOI: 10.3390/cells10030582] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/29/2022] Open
Abstract
It has been challenging to simultaneously improve photosynthesis and stress tolerance in plants. Crassulacean acid metabolism (CAM) is a CO2-concentrating mechanism that facilitates plant adaptation to water-limited environments. We hypothesized that the ectopic expression of a CAM-specific phosphoenolpyruvate carboxylase (PEPC), an enzyme that catalyzes primary CO2 fixation in CAM plants, would enhance both photosynthesis and abiotic stress tolerance. To test this hypothesis, we engineered a CAM-specific PEPC gene (named AaPEPC1) from Agave americana into tobacco. In comparison with wild-type and empty vector controls, transgenic tobacco plants constitutively expressing AaPEPC1 showed a higher photosynthetic rate and biomass production under normal conditions, along with significant carbon metabolism changes in malate accumulation, the carbon isotope ratio δ13C, and the expression of multiple orthologs of CAM-related genes. Furthermore, AaPEPC1 overexpression enhanced proline biosynthesis, and improved salt and drought tolerance in the transgenic plants. Under salt and drought stress conditions, the dry weight of transgenic tobacco plants overexpressing AaPEPC1 was increased by up to 81.8% and 37.2%, respectively, in comparison with wild-type plants. Our findings open a new door to the simultaneous improvement of photosynthesis and stress tolerance in plants.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hao-Bo Guo
- Department of Computer Science and Engineering, SimCenter, University of Tennessee Chattanooga, Chattanooga, TN 37403, USA; (H.-B.G.); (H.Q.)
| | - Hua Cheng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
| | - Linling Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
| | - Anne M. Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Hong Qin
- Department of Computer Science and Engineering, SimCenter, University of Tennessee Chattanooga, Chattanooga, TN 37403, USA; (H.-B.G.); (H.Q.)
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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8
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Danquah MK, Guo HB, Tan KX, Bhakta M. Atomistic probing of aptameric binding of CD19 outer membrane domain reveals an "aptamer walking" mechanism. Biotechnol Prog 2020; 36:e2957. [PMID: 31912987 DOI: 10.1002/btpr.2957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/15/2019] [Accepted: 12/29/2019] [Indexed: 12/16/2022]
Abstract
We propose an integrated structural approach to search potential aptamer molecules for targeting cancer receptor proteins. We used the outer cellular domain of the B-lymphocyte antigen, CD19, as the target for this study. First, using available protein-aptamer structures deposited in the protein data bank as resources, structural annotation was performed to seek the most probable binding aptamer and its potential initial configuration to the CD19 structure. Using this initial structure, molecular dynamics (MD) simulations were performed for adjustment of the aptamer-binding. During this process, we observed an "aptamer walking" mechanism of the binding of the single-stranded RNA-aptamer to CD19: the aptamer molecule gradually adjusts its configurations and shifts toward favorable binding positions. However, the target molecule CD19 maintained a relatively stable conformation during this process. The interface area between the RNA-aptamer and CD19 increased from less than 8 nm2 to over 12 nm2 during a 2-μs MD simulation. Using a stable binding pose as the starting structure, we manually mutated the RNA-aptamer to a DNA-aptamer and found that the interface area was further increased to over 16 nm2 , indicating a stronger affinity compared to the RNA-aptamer. The RNA- and DNA-aptamers and their stable binding-poses to the CD19 molecule may be used as templates in designing potential aptamer molecules that target the B-cell marker molecule CD19 with enhanced specificity and stability.
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Affiliation(s)
- Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga, Tennessee
| | - Hao-Bo Guo
- Department of Computer Science and Engineering, University of Tennessee, Chattanooga, Tennessee.,SimCenter, University of Tennessee, Chattanooga, Tennessee
| | - Kei X Tan
- School of Materials Science & Engineering, Nanyang Technological University, Singapore
| | - Manoo Bhakta
- Pediatric Hematology and Oncology, Children's Hospital at Erlanger, Chattanooga, Tennessee
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9
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Yin H, Guo HB, Weston DJ, Borland AM, Ranjan P, Abraham PE, Jawdy SS, Wachira J, Tuskan GA, Tschaplinski TJ, Wullschleger SD, Guo H, Hettich RL, Gross SM, Wang Z, Visel A, Yang X. Correction to: Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave. BMC Genomics 2019; 20:279. [PMID: 30971209 PMCID: PMC6456932 DOI: 10.1186/s12864-019-5663-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
- Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Present address: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Paul E Abraham
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James Wachira
- Department of Biology, Morgan State University, Baltimore, MD, 21251, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert L Hettich
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stephen M Gross
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Present address: Illumina, Inc., San Diego, CA, 92122, USA
| | - Zhong Wang
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Axel Visel
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. .,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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10
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Zhang T, Guo HB, Li WH, Li W, Zhang XM, Li QL, Zhang XM. [Numerical simulation study of type B aortic dissection using patient-specific reverse engineering and fluid-structure interaction]. Zhonghua Yi Xue Za Zhi 2019; 99:142-147. [PMID: 30669754 DOI: 10.3760/cma.j.issn.0376-2491.2019.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To construct computational fluid model of type B aortic dissection using patient-specific reverse engineering and fluid-structure interaction, and evaluate the application of computational fluid model on aortic remodeling of type B aortic dissection. Methods: Consecutive computed tomographic angiograph data was acquired from a patient with type B aortic dissection at initial diagnosis, 1 week and 6 years after endovascular repair of primary tear entry and 3 months after endovascular repair of distal tear erosion. Three-dimensional model of aortic dissection was reversely reconstructed by Mimics, and then the model was smoothened by Geomagic. Computational fluid dynamic numerical simulation was performed in ANSYS by the means of two-way fluid-structure interaction, and the relation between blood dynamic characteristic and thrombosed remodeling of type B aortic dissection was evaluated. Results: The computational fluid model of type B aortic dissection using patient-specific reverse engineering and fluid-structure interaction method was successfully constructed. Local peak of blood pressure on the convex surface of junction at aortic arch and descending aorta was found. The wall stress was much higher at the false lumen than that at the true lumen, and the peak of wall stress converged on the edge and tear entry of false lumen. After the exclusion of proximal tear entry, the blood streamline was decreased significantly and flowed reversely. Blood flow in the remaining false lumen was retrograded from the entry at left iliac artery and formed turbulence at the top of false lumen, which was benefit for dissection thrombus remodeling. The higher pressure at the false lumen was associated with the new formation of aortic aneurysm at the distal tear. Conclusion: The computational fluid model of aortic dissection based on patient-specific reverse engineering and fluid-structure interaction method can successfully reveal the relatively truly blood dynamic and wall pressure characteristic of type B aortic dissection.
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Affiliation(s)
- T Zhang
- Department of Vascular Surgery, Peking University People's Hospital, Beijing 100044, China
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11
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Badmi R, Payyavula RS, Bali G, Guo HB, Jawdy SS, Gunter LE, Yang X, Winkeler KA, Collins C, Rottmann WH, Yee K, Rodriguez M, Sykes RW, Decker SR, Davis MF, Ragauskas AJ, Tuskan GA, Kalluri UC. A New Calmodulin-Binding Protein Expresses in the Context of Secondary Cell Wall Biosynthesis and Impacts Biomass Properties in Populus. Front Plant Sci 2018; 9:1669. [PMID: 30568662 PMCID: PMC6290091 DOI: 10.3389/fpls.2018.01669] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/26/2018] [Indexed: 05/21/2023]
Abstract
A greater understanding of biosynthesis, signaling and regulatory pathways involved in determining stem growth and secondary cell wall chemistry is important for enabling pathway engineering and genetic optimization of biomass properties. The present study describes a new functional role of PdIQD10, a Populus gene belonging to the IQ67-Domain1 family of IQD genes, in impacting biomass formation and chemistry. Expression studies showed that PdIQD10 has enhanced expression in developing xylem and tension-stressed tissues in Populus deltoides. Molecular dynamics simulation and yeast two-hybrid interaction experiments suggest interactions with two calmodulin proteins, CaM247 and CaM014, supporting the sequence-predicted functional role of the PdIQD10 as a calmodulin-binding protein. PdIQD10 was found to interact with specific Populus isoforms of the Kinesin Light Chain protein family, shown previously to function as microtubule-guided, cargo binding and delivery proteins in Arabidopsis. Subcellular localization studies showed that PdIQD10 localizes in the nucleus and plasma membrane regions. Promoter-binding assays suggest that a known master transcriptional regulator of secondary cell wall biosynthesis (PdWND1B) may be upstream of an HD-ZIP III gene that is in turn upstream of PdIQD10 gene in the transcriptional network. RNAi-mediated downregulation of PdIQD10 expression resulted in plants with altered biomass properties including higher cellulose, wall glucose content and greater biomass quantity. These results present evidence in support of a new functional role for an IQD gene family member, PdIQD10, in secondary cell wall biosynthesis and biomass formation in Populus.
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Affiliation(s)
- Raghuram Badmi
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Raja S. Payyavula
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Garima Bali
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Georgia Institute of Technology, Atlanta, GA, United States
| | - Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sara S. Jawdy
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Lee E. Gunter
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xiaohan Yang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | | | | | - Kelsey Yee
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Miguel Rodriguez
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert W. Sykes
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Stephen R. Decker
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Mark F. Davis
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Arthur J. Ragauskas
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Gerald A. Tuskan
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Udaya C. Kalluri
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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12
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Yin H, Guo HB, Weston DJ, Borland AM, Ranjan P, Abraham PE, Jawdy SS, Wachira J, Tuskan GA, Tschaplinski TJ, Wullschleger SD, Guo H, Hettich RL, Gross SM, Wang Z, Visel A, Yang X. Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave. BMC Genomics 2018; 19:588. [PMID: 30081833 PMCID: PMC6090859 DOI: 10.1186/s12864-018-4964-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO2 uptake. CAM has evolved independently in over 35 plant lineages, accounting for ~ 6% of all higher plants. Agave species are highly heat- and drought-tolerant, and have been domesticated as model CAM crops for beverage, fiber, and biofuel production in semi-arid and arid regions. However, the genomic basis of evolutionary innovation of CAM in genus Agave is largely unknown. Results Using an approach that integrated genomics, gene co-expression networks, comparative genomics and protein structure analyses, we investigated the molecular evolution of CAM as exemplified in Agave. Comparative genomics analyses among C3, C4 and CAM species revealed that core metabolic components required for CAM have ancient genomic origins traceable to non-vascular plants while regulatory proteins required for diel re-programming of metabolism have a more recent origin shared among C3, C4 and CAM species. We showed that accelerated evolution of key functional domains in proteins responsible for primary metabolism and signaling, together with a diel re-programming of the transcription of genes involved in carbon fixation, carbohydrate processing, redox homeostasis, and circadian control is required for the evolution of CAM in Agave. Furthermore, we highlighted the potential candidates contributing to the adaptation of CAM functional modules. Conclusions This work provides evidence of adaptive evolution of CAM related pathways. We showed that the core metabolic components required for CAM are shared by non-vascular plants, but regulatory proteins involved in re-reprogramming of carbon fixation and metabolite transportation appeared more recently. We propose that the accelerated evolution of key proteins together with a diel re-programming of gene expression were required for CAM evolution from C3 ancestors in Agave. Electronic supplementary material The online version of this article (10.1186/s12864-018-4964-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Present address: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Hao-Bo Guo
- Department of Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Paul E Abraham
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, TN, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James Wachira
- Department of Biology, Morgan State University, Baltimore, MD, 21251, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Hong Guo
- Department of Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert L Hettich
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, TN, USA
| | - Stephen M Gross
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Present address: Illumina, Inc., San Diego, CA, 92122, USA
| | - Zhong Wang
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Axel Visel
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. .,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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13
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Xie M, Muchero W, Bryan AC, Yee K, Guo HB, Zhang J, Tschaplinski TJ, Singan VR, Lindquist E, Payyavula RS, Barros-Rios J, Dixon R, Engle N, Sykes RW, Davis M, Jawdy SS, Gunter LE, Thompson O, DiFazio SP, Evans LM, Winkeler K, Collins C, Schmutz J, Guo H, Kalluri U, Rodriguez M, Feng K, Chen JG, Tuskan GA. A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus. Plant Cell 2018; 30:1645-1660. [PMID: 29891568 PMCID: PMC6096593 DOI: 10.1105/tpc.18.00168] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/17/2018] [Accepted: 06/05/2018] [Indexed: 05/21/2023]
Abstract
Long-lived perennial plants, with distinctive habits of inter-annual growth, defense, and physiology, are of great economic and ecological importance. However, some biological mechanisms resulting from genome duplication and functional divergence of genes in these systems remain poorly studied. Here, we discovered an association between a poplar (Populus trichocarpa) 5-enolpyruvylshikimate 3-phosphate synthase gene (PtrEPSP) and lignin biosynthesis. Functional characterization of PtrEPSP revealed that this isoform possesses a helix-turn-helix motif in the N terminus and can function as a transcriptional repressor that regulates expression of genes in the phenylpropanoid pathway in addition to performing its canonical biosynthesis function in the shikimate pathway. We demonstrated that this isoform can localize in the nucleus and specifically binds to the promoter and represses the expression of a SLEEPER-like transcriptional regulator, which itself specifically binds to the promoter and represses the expression of PtrMYB021 (known as MYB46 in Arabidopsis thaliana), a master regulator of the phenylpropanoid pathway and lignin biosynthesis. Analyses of overexpression and RNAi lines targeting PtrEPSP confirmed the predicted changes in PtrMYB021 expression patterns. These results demonstrate that PtrEPSP in its regulatory form and PtrhAT form a transcriptional hierarchy regulating phenylpropanoid pathway and lignin biosynthesis in Populus.
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Affiliation(s)
- Meng Xie
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Wellington Muchero
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Anthony C Bryan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Kelsey Yee
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Jin Zhang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Timothy J Tschaplinski
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Vasanth R Singan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Raja S Payyavula
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Jaime Barros-Rios
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203
| | - Richard Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203
| | - Nancy Engle
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Robert W Sykes
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Mark Davis
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Sara S Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Lee E Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Olivia Thompson
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, West Virginia 26506
| | - Luke M Evans
- Department of Biology, West Virginia University, Morgantown, West Virginia 26506
| | | | | | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Udaya Kalluri
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Miguel Rodriguez
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Kai Feng
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Gerald A Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
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14
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Yang X, Hu R, Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Cheol Yim W, Ha J, Heyduk K, Goodstein DM, Guo HB, Moseley RC, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell J, Grimwood J, Abraham PE, Mewalal R, Beltrán JD, Boxall SF, Dever LV, Palla KJ, Albion R, Garcia T, Mayer JA, Don Lim S, Man Wai C, Peluso P, Van Buren R, De Paoli HC, Borland AM, Guo H, Chen JG, Muchero W, Yin Y, Jacobson DA, Tschaplinski TJ, Hettich RL, Ming R, Winter K, Leebens-Mack JH, Smith JAC, Cushman JC, Schmutz J, Tuskan GA. The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nat Commun 2017; 8:1899. [PMID: 29196618 PMCID: PMC5711932 DOI: 10.1038/s41467-017-01491-7] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022] Open
Abstract
Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression data for Kalanchoë fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identify signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock, and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA.
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Deborah A Weighill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jungmin Ha
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Karolina Heyduk
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert C Moseley
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Elisabeth Fitzek
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Zhihao Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Meng Xie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James Hartwell
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Juan D Beltrán
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Susanna F Boxall
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Louisa V Dever
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Rebecca Albion
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Travis Garcia
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jesse A Mayer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Sung Don Lim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Paul Peluso
- Pacific Biosciences, Inc., 940 Hamilton Avenue, Menlo Park, CA, 94025, USA
| | - Robert Van Buren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Henrique Cestari De Paoli
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama
| | | | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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15
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Plett JM, Yin H, Mewalal R, Hu R, Li T, Ranjan P, Jawdy S, De Paoli HC, Butler G, Burch-Smith TM, Guo HB, Ju Chen C, Kohler A, Anderson IC, Labbé JL, Martin F, Tuskan GA, Yang X. Populus trichocarpa encodes small, effector-like secreted proteins that are highly induced during mutualistic symbiosis. Sci Rep 2017; 7:382. [PMID: 28336910 PMCID: PMC5428498 DOI: 10.1038/s41598-017-00400-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 02/27/2017] [Indexed: 11/09/2022] Open
Abstract
During symbiosis, organisms use a range of metabolic and protein-based signals to communicate. Of these protein signals, one class is defined as ‘effectors’, i.e., small secreted proteins (SSPs) that cause phenotypical and physiological changes in another organism. To date, protein-based effectors have been described in aphids, nematodes, fungi and bacteria. Using RNA sequencing of Populus trichocarpa roots in mutualistic symbiosis with the ectomycorrhizal fungus Laccaria bicolor, we sought to determine if host plants also contain genes encoding effector-like proteins. We identified 417 plant-encoded putative SSPs that were significantly regulated during this interaction, including 161 SSPs specific to P. trichocarpa and 15 SSPs exhibiting expansion in Populus and closely related lineages. We demonstrate that a subset of these SSPs can enter L. bicolor hyphae, localize to the nucleus and affect hyphal growth and morphology. We conclude that plants encode proteins that appear to function as effector proteins that may regulate symbiotic associations.
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Affiliation(s)
- Jonathan M Plett
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280, Champenoux, France.,Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, 2753, NSW, Australia
| | - Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ting Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Henrique C De Paoli
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - George Butler
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tessa Maureen Burch-Smith
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Chun Ju Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Annegret Kohler
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280, Champenoux, France
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, 2753, NSW, Australia
| | - Jessy L Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Francis Martin
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280, Champenoux, France
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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16
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Yang Y, Yoo CG, Guo HB, Rottmann W, Winkeler KA, Collins CM, Gunter LE, Jawdy SS, Yang X, Guo H, Pu Y, Ragauskas AJ, Tuskan GA, Chen JG. Overexpression of a Domain of Unknown Function 266-containing protein results in high cellulose content, reduced recalcitrance, and enhanced plant growth in the bioenergy crop Populus. Biotechnol Biofuels 2017; 10:74. [PMID: 28344649 PMCID: PMC5364563 DOI: 10.1186/s13068-017-0760-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/18/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Domain of Unknown Function 266 (DUF266) is a plant-specific domain. DUF266-containing proteins (DUF266 proteins) have been categorized as 'not classified glycosyltransferases (GTnc)' due to amino acid similarity with GTs. However, little is known about the function of DUF266 proteins. RESULTS Phylogenetic analysis revealed that DUF266 proteins are only present in the land plants including moss and lycophyte. We report the functional characterization of one member of DUF266 proteins in Populus, PdDUF266A. PdDUF266A was ubiquitously expressed with high abundance in the xylem. In Populus transgenic plants overexpressing PdDUF266A (OXPdDUF266A), the glucose and cellulose contents were significantly higher, while the lignin content was lower than that in the wild type. Degree of polymerization of cellulose in OXPdDUF266A transgenic plants was also higher, whereas cellulose crystallinity index remained unchanged. Gene expression analysis indicated that cellulose biosynthesis-related genes such as CESA and SUSY were upregulated in mature leaf and xylem of OXPdDUF266A transgenic plants. Moreover, PdDUF266A overexpression resulted in an increase of biomass production. Their glucose contents and biomass phenotypes were further validated via heterologous expression of PdDUF266A in Arabidopsis. Results from saccharification treatment demonstrated that the rate of sugar release was increased by approximately 38% in the OXPdDUF266A transgenic plants. CONCLUSIONS These results suggest that the overexpression of PdDUF266A can increase cellulose content, reduce recalcitrance, and enhance biomass production, and that PdDUF266A is a promising target for genetic manipulation for biofuel production.
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Affiliation(s)
- Yongil Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
| | | | | | | | - Lee E. Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sara S. Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Hong Guo
- Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
| | - Yunqiao Pu
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering & Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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17
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Qian P, Guo HB, Yue Y, Wang L, Yang X, Guo H. Correction to Understanding the Catalytic Mechanism of Xanthosine Methyltransferase in Caffeine Biosynthesis from QM/MM Molecular Dynamics and Free Energy Simulations. J Chem Inf Model 2016; 56:2280. [PMID: 27790913 DOI: 10.1021/acs.jcim.6b00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Zhang Z, Zhang RF, Legut D, Li DQ, Zhang SH, Fu ZH, Guo HB. Pinning effect of reactive elements on adhesion energy and adhesive strength of incoherent Al2O3/NiAl interface. Phys Chem Chem Phys 2016; 18:22864-73. [PMID: 27480916 DOI: 10.1039/c6cp03609k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The profound effects of reactive elements (REs) on the adhesion energy and adhesive strength of the α-Al2O3/β-NiAl interface in thermal barrier coating (TBC) systems have attracted increasing attention because RE-doping has played a significant role in improving the thermal cycling lifetime of TBCs. However, the fundamental mechanism is, so far, not well understood due to the experimental difficulty and theoretical complexity in interface modelling. For this purpose, in the present study we have performed comprehensive density functional theory calculations and information targeted experiments to underline the origin of the surprising enhancement of interface adhesion, stability and mechanical strength of the α-Al2O3/β-NiAl interface by different RE doping levels. Our results suggest that the interface failure firstly appears within the NiAl layer adjacent to the Al-terminated oxide under mechanical loading, while the formation of O-RE-Ni bond pairs at the interface can effectively hinder the interface de-cohesion, providing a higher mechanical strength. By comparing several typical REs, it is observed that Hf can emerge not only with the highest interface adhesion energy, but also the highest mechanical strength; in agreement with our experimental results. By continuously increasing the dopant concentration, the strengthening effect may increase correspondingly, but is limited by the solute solubility. These results shed light into the effect of REs on the stability and strength of the α-Al2O3/β-NiAl interface, providing theoretical guidance for interface design via a combinational analysis of bond topology and electronic structure.
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Affiliation(s)
- Z Zhang
- School of Materials Science and Engineering, Beihang University, Beijing 100191, P. R. China. and Center for Integrated Computational Engineering, International Research Institute for Multidisciplinary Science, Beihang University, Beijing 100191, P. R. China
| | - R F Zhang
- School of Materials Science and Engineering, Beihang University, Beijing 100191, P. R. China. and Center for Integrated Computational Engineering, International Research Institute for Multidisciplinary Science, Beihang University, Beijing 100191, P. R. China
| | - D Legut
- IT4 Innovations Center, VSB-Technical University of Ostrava, CZ-70833 Ostrava, Czech Republic
| | - D Q Li
- School of Materials Science and Engineering, Beihang University, Beijing 100191, P. R. China.
| | - S H Zhang
- School of Materials Science and Engineering, Beihang University, Beijing 100191, P. R. China. and Center for Integrated Computational Engineering, International Research Institute for Multidisciplinary Science, Beihang University, Beijing 100191, P. R. China
| | - Z H Fu
- School of Materials Science and Engineering, Beihang University, Beijing 100191, P. R. China. and Center for Integrated Computational Engineering, International Research Institute for Multidisciplinary Science, Beihang University, Beijing 100191, P. R. China
| | - H B Guo
- School of Materials Science and Engineering, Beihang University, Beijing 100191, P. R. China.
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19
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Qian P, Guo HB, Yue Y, Wang L, Yang X, Guo H. Understanding the Catalytic Mechanism of Xanthosine Methyltransferase in Caffeine Biosynthesis from QM/MM Molecular Dynamics and Free Energy Simulations. J Chem Inf Model 2016; 56:1755-61. [DOI: 10.1021/acs.jcim.6b00153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ping Qian
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Chemistry
and Material Science Faculty, Shandong Agricultural University, Tai’an 271018, Shandong, People’s Republic of China
| | - Hao-Bo Guo
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Yufei Yue
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Liang Wang
- Chemistry
and Material Science Faculty, Shandong Agricultural University, Tai’an 271018, Shandong, People’s Republic of China
| | - Xiaohan Yang
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hong Guo
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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20
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Borland AM, Guo HB, Yang X, Cushman JC. Orchestration of carbohydrate processing for crassulacean acid metabolism. Curr Opin Plant Biol 2016; 31:118-124. [PMID: 27101569 DOI: 10.1016/j.pbi.2016.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
The production of phosphoenolpyruvate as a substrate for nocturnal CO2 uptake represents a significant sink for carbohydrate in CAM plants which has to be balanced with the provisioning of carbohydrate for growth and maintenance. In starch-storing CAM species, diversification in chloroplast metabolite transporters, and the deployment of both phosphorolytic and hydrolytic routes of starch degradation accommodate a division of labour in directing C-skeletons towards nocturnal carboxylation or production of sucrose for growth. In soluble-sugar storing CAM plants, the vacuole plays a central role in managing carbon homeostasis. The molecular identities of various types of vacuolar sugar transporters have only been identified for C3 species within the last 10 years. The recent availability of CAM genomes enables the identification of putative orthologues of vacuolar sugar transporters which represent strategic targets for orchestrating the diel provisioning of substrate for nocturnal carboxylation and growth.
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Affiliation(s)
- Anne M Borland
- School of Biology, Newcastle University, Newcastle upon Tyne NE17 RU, UK; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6407, USA.
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6407, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV 89557-0330, USA
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21
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Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo HB, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen LY, Shirley N, Lin YR, Liu LY, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JAC, Cushman JC, Paull RE, Yu Q. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 2015; 47:1435-42. [PMID: 26523774 PMCID: PMC4867222 DOI: 10.1038/ng.3435] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/05/2015] [Indexed: 12/21/2022]
Abstract
Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.
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Affiliation(s)
- Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Robert VanBuren
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Ching Man Wai
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Haibao Tang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- iPlant Collaborative/University of Arizona, Tuscon, AZ 85719, USA
| | | | - John E. Bowers
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Eric Lyons
- iPlant Collaborative/University of Arizona, Tuscon, AZ 85719, USA
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Kunia, HI 96759, USA
| | - Jung Chen
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Eric Biggers
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724, USA
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lixian Huang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lingmao Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Wenjing Miao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jian Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhangyao Ye
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Chenyong Miao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhicong Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Hao Wang
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Hongye Zhou
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Won C. Yim
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | | | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada K1N 6N5
| | - Margaret Woodhouse
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Patrick P. Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Romain Guyot
- IRD, UMR DIADE, EVODYN, BP 64501, 34394 Montpellier Cedex 5, France
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Guangyong Zheng
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ratnesh Singh
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX 75252, USA
| | - Anupma Sharma
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX 75252, USA
| | - Xiangjia Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Hayan Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724, USA
| | - James Gurtowski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724, USA
| | | | - Alex Harkess
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | | | - Zhenyang Liao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jingping Fang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Juan Liu
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaodan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Qing Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Weichang Hu
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yuan Qin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Kai Wang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Neil Shirley
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, South Australia 5064, Australia
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan
| | - Li-Yu Liu
- Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan
| | - Alvaro G. Hernandez
- W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chris L. Wright
- W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Vincent Bulone
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, South Australia 5064, Australia
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Katy Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Francis Zee
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Paul H. Moore
- Hawaii Agriculture Research Center, Kunia, HI 96759, USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA
| | | | - Todd Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada K1N 6N5
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Xinguang Zhu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - J. Andrew C. Smith
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - John C. Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | - Robert E. Paull
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX 75252, USA
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22
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Yang X, Cushman JC, Borland AM, Edwards EJ, Wullschleger SD, Tuskan GA, Owen NA, Griffiths H, Smith JAC, De Paoli HC, Weston DJ, Cottingham R, Hartwell J, Davis SC, Silvera K, Ming R, Schlauch K, Abraham P, Stewart JR, Guo HB, Albion R, Ha J, Lim SD, Wone BWM, Yim WC, Garcia T, Mayer JA, Petereit J, Nair SS, Casey E, Hettich RL, Ceusters J, Ranjan P, Palla KJ, Yin H, Reyes-García C, Andrade JL, Freschi L, Beltrán JD, Dever LV, Boxall SF, Waller J, Davies J, Bupphada P, Kadu N, Winter K, Sage RF, Aguilar CN, Schmutz J, Jenkins J, Holtum JAM. A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world. New Phytol 2015; 207:491-504. [PMID: 26153373 DOI: 10.1111/nph.13393] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that features nocturnal CO2 uptake, facilitates increased water-use efficiency (WUE), and enables CAM plants to inhabit water-limited environments such as semi-arid deserts or seasonally dry forests. Human population growth and global climate change now present challenges for agricultural production systems to increase food, feed, forage, fiber, and fuel production. One approach to meet these challenges is to increase reliance on CAM crops, such as Agave and Opuntia, for biomass production on semi-arid, abandoned, marginal, or degraded agricultural lands. Major research efforts are now underway to assess the productivity of CAM crop species and to harness the WUE of CAM by engineering this pathway into existing food, feed, and bioenergy crops. An improved understanding of CAM has potential for high returns on research investment. To exploit the potential of CAM crops and CAM bioengineering, it will be necessary to elucidate the evolution, genomic features, and regulatory mechanisms of CAM. Field trials and predictive models will be required to assess the productivity of CAM crops, while new synthetic biology approaches need to be developed for CAM engineering. Infrastructure will be needed for CAM model systems, field trials, mutant collections, and data management.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, Providence, RI, 02912, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Nick A Owen
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Henrique C De Paoli
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Robert Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - James Hartwell
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Sarah C Davis
- Voinovich School of Leadership and Public Affairs and Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - Katia Silvera
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancon, Republic of Panama
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Karen Schlauch
- Nevada Center for Bioinformatics, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Paul Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - J Ryan Stewart
- Department of Plant and Wildlife Sciences, Brigham Young University, 4105 Life Sciences Building, Provo, UT, 84602, USA
| | - Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Rebecca Albion
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Jungmin Ha
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Sung Don Lim
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Bernard W M Wone
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Travis Garcia
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Jesse A Mayer
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Juli Petereit
- Nevada Center for Bioinformatics, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Sujithkumar S Nair
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
| | - Erin Casey
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Johan Ceusters
- Department of M²S, Faculty of Engineering Technology, TC Bioengineering Technology, KU Leuven, Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Hengfu Yin
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400, China
| | - Casandra Reyes-García
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP 97200, Mérida, México
| | - José Luis Andrade
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP 97200, Mérida, México
| | - Luciano Freschi
- Department of Botany, University of São Paulo, São Paulo, 05508-090, Brazil
| | - Juan D Beltrán
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Louisa V Dever
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Susanna F Boxall
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jade Waller
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jack Davies
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Phaitun Bupphada
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Nirja Kadu
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancon, Republic of Panama
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S3B2, Canada
| | - Cristobal N Aguilar
- Department of Food Research, School of Chemistry, Universidad Autónoma de Coahuila, Saltillo, México
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Joseph A M Holtum
- College of Marine and Environmental Sciences, James Cook University, Townsville, 4811, QLD, Australia
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23
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Lian P, Guo HB, Riccardi D, Dong A, Parks JM, Xu Q, Pai EF, Miller SM, Wei DQ, Smith JC, Guo H. X-ray structure of a Hg2+ complex of mercuric reductase (MerA) and quantum mechanical/molecular mechanical study of Hg2+ transfer between the C-terminal and buried catalytic site cysteine pairs. Biochemistry 2014; 53:7211-22. [PMID: 25343681 PMCID: PMC4245977 DOI: 10.1021/bi500608u] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Mercuric reductase, MerA, is a key
enzyme in bacterial mercury
resistance. This homodimeric enzyme captures and reduces toxic Hg2+ to Hg0, which is relatively unreactive and can
exit the cell passively. Prior to reduction, the Hg2+ is
transferred from a pair of cysteines (C558′ and C559′
using Tn501 numbering) at the C-terminus of one monomer
to another pair of cysteines (C136 and C141) in the catalytic site
of the other monomer. Here, we present the X-ray structure of the
C-terminal Hg2+ complex of the C136A/C141A double mutant
of the Tn501 MerA catalytic core and explore the
molecular mechanism of this Hg transfer with quantum mechanical/molecular
mechanical (QM/MM) calculations. The transfer is found to be nearly
thermoneutral and to pass through a stable tricoordinated intermediate
that is marginally less stable than the two end states. For the overall
process, Hg2+ is always paired with at least two thiolates
and thus is present at both the C-terminal and catalytic binding sites
as a neutral complex. Prior to Hg2+ transfer, C141 is negatively
charged. As Hg2+ is transferred into the catalytic site,
a proton is transferred from C136 to C559′ while C558′
becomes negatively charged, resulting in the net transfer of a negative
charge over a distance of ∼7.5 Å. Thus, the transport
of this soft divalent cation is made energetically feasible by pairing
a competition between multiple Cys thiols and/or thiolates for Hg2+ with a competition between the Hg2+ and protons
for the thiolates.
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Affiliation(s)
- Peng Lian
- The State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
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24
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Abstract
Nelumbo nucifera is widely used as food, as an ornamental, in medicine, and as packing material; it is also reported to have anti-HIV effects and antioxidant capacity. We sought an improved method for extracting high-quality total RNA from different tissues of N. nucifera. Four methods for RNA extraction were assessed for their ability to recover high-quality RNA applicable for evaluation of polyphenol oxidase (PPO) gene expression profiles. The recovery and quality of the RNA obtained from five different tissues by the best CTAB-LiCl method were evaluated through UV light absorbance. Both A(260)/A(280) and A(260)/A(230) absorbance ratios were more than 2.0; the yield ranged from 59.87 to 163.75 μg/g fresh weight. The brightness of the 28S band was approximately twice that of 18S; the latter was also considered as high-quality RNA. The PPO gene fragment (606 bp) was successfully amplified by RT-PCR, demonstrating the integrity of the isolated RNA. The relative expression levels of the PPO gene based on RT-PCR in five tissues of lotus were: rhizome buds (2.66), young leaves (2.42), fresh cut rhizome (2.02), petals (1.80), and petiole (1.65), using housekeeping gene β-actin as an internal control. We concluded that the total RNA isolated by this protocol is of sufficient quality for molecular applications.
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Affiliation(s)
- Y J Zhang
- Shaanxi Key Laboratory of Molecular Biology in Agriculture, College of Life Sciences, Northwest A & F University, Yangling, PR China
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25
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Riccardi D, Guo HB, Parks JM, Gu B, Liang L, Smith JC. Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations. J Chem Theory Comput 2012; 9:555-69. [DOI: 10.1021/ct300296k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Demian Riccardi
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville,
Tennessee 37996, United States
| | - Hao-Bo Guo
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
| | - Baohua Gu
- Environmental Science Division,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Liyuan Liang
- Environmental Science Division,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville,
Tennessee 37996, United States
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26
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Guo HB, He F, Gu B, Liang L, Smith JC. Time-dependent density functional theory assessment of UV absorption of benzoic acid derivatives. J Phys Chem A 2012; 116:11870-9. [PMID: 23134517 DOI: 10.1021/jp3084293] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Benzoic acid (BA) derivatives of environmental relevance exhibit various photophysical and photochemical characteristics. Here, time-dependent density functional theory (TDDFT) is used to calculate photoexcitations of eight selected BAs and the results are compared with UV spectra determined experimentally. High-level gas-phase EOM-CCSD calculations and experimental aqueous-phase spectra were used as the references for the gas-phase and aqueous-phase TDDFT results, respectively. A cluster-continuum model was used in the aqueous-phase calculations. Among the 15 exchange-correlation (XC) functionals assessed, five functionals, including the meta-GGA hybrid M06-2X, double hybrid B2PLYPD, and range-separated functionals CAM-B3LYP, ωB97XD, and LC-ωPBE, were found to be in excellent agreement with the EOM-CCSD gas-phase calculations. These functionals furnished excitation energies consistent with the pH dependence of the experimental spectra with a standard deviation (STDEV) of ∼0.20 eV. A molecular orbital analysis revealed a πσ* feature of the low-lying transitions of the BAs. The CAM-B3LYP functional showed the best overall performance and therefore shows promise for TDDFT calculations of processes involving photoexcitations of benzoic acid derivatives.
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Affiliation(s)
- Hao-Bo Guo
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Tennessee 37831, United States
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27
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Guo HB, Johs A, Parks JM, Olliff L, Miller SM, Summers AO, Liang L, Smith JC. Structure and conformational dynamics of the metalloregulator MerR upon binding of Hg(II). J Mol Biol 2010; 398:555-68. [PMID: 20303978 DOI: 10.1016/j.jmb.2010.03.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 03/10/2010] [Accepted: 03/11/2010] [Indexed: 11/29/2022]
Abstract
The bacterial metalloregulator MerR is the index case of an eponymous family of regulatory proteins, which controls the transcription of a set of genes (the mer operon) conferring mercury resistance in many bacteria. Homodimeric MerR represses transcription in the absence of mercury and activates transcription upon Hg(II) binding. Here, the average structures of the apo and Hg(II)-bound forms of MerR in aqueous solution are examined using small-angle X-ray scattering, indicating an extended conformation of the metal-bound protein and revealing the existence of a novel compact conformation in the absence of Hg(II). Molecular dynamics (MD) simulations are performed to characterize the conformational dynamics of the Hg(II)-bound form. In both small-angle X-ray scattering and MD, the average torsional angle between DNA-binding domains is approximately 65 degrees. Furthermore, in MD, interdomain motions on a timescale of approximately 10 ns involving large-amplitude (approximately 20 A) domain opening-and-closing, coupled to approximately 40 degrees variations of interdomain torsional angle, are revealed. This correlated domain motion may propagate allosteric changes from the metal-binding site to the DNA-binding site while maintaining DNA contacts required to initiate DNA underwinding.
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Affiliation(s)
- Hao-Bo Guo
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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28
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Xu Q, Chu YZ, Guo HB, Smith JC, Guo H. Energy triplets for writing epigenetic marks: insights from QM/MM free-energy simulations of protein lysine methyltransferases. Chemistry 2010; 15:12596-9. [PMID: 19882600 DOI: 10.1002/chem.200902297] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qin Xu
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
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29
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Smolin N, Lindner B, Guo HB, Smith JC. Integration of Computer Simulation and Neutron Scattering in the Characterization of Protein Dynamics. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.1282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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30
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Guo HB, Guo H. Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity. Proc Natl Acad Sci U S A 2007; 104:8797-802. [PMID: 17517655 PMCID: PMC1885582 DOI: 10.1073/pnas.0702981104] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Methylation of certain lysine residues in the N-terminal tails of core histone proteins in nucleosome is of fundamental importance in the regulation of chromatin structure and gene expression. Such histone modification is catalyzed by protein lysine methyltransferases (PKMTs). PKMTs contain a conserved SET domain in almost all of the cases and may transfer one to three methyl groups from S-adenosyl-L-methionine (AdoMet) to the epsilon-amino group of the target lysine residue. Here, quantum mechanical/molecular mechanical molecular dynamics and free-energy simulations are performed on human PKMT SET7/9 and its mutants to understand two outstanding questions for the reaction catalyzed by PKMTs: the mechanism for deprotonation of positively charged methyl lysine (lysine) and origin of product specificity. The results of the simulations suggest that Tyr-335 (an absolute conserved residue in PKMTs) may play the role as the general base for the deprotonation after dissociation of AdoHcy (S-adenosyl-L-homocysteine) and before binding of AdoMet. It is shown that conformational changes could bring Y335 to the target methyl lysine (lysine) for proton abstraction. This mechanism provides an explanation why methyl transfers could be catalyzed by PKMTs processively. The free-energy profiles for methyl transfers are reported and analyzed for wild type and certain mutants (Y305F and Y335F) and the active-site interactions that are of importance for the enzyme's function are discussed. The results of the simulations provide important insights into the catalytic process and lead to a better understanding of experimental observations concerning the origin of product specificity for PKMTs.
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Affiliation(s)
- Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, Center of Excellence in Structural Biology, University of Tennessee, Knoxville, TN 37996-0840
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, Center of Excellence in Structural Biology, University of Tennessee, Knoxville, TN 37996-0840
- To whom correspondence should be addressed. E-mail:
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31
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Xu Q, Guo HB, Wlodawer A, Nakayama T, Guo H. The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As. Biochemistry 2007; 46:3784-92. [PMID: 17326662 PMCID: PMC2533263 DOI: 10.1021/bi061737p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum mechanical/molecular mechanical molecular dynamics and free energy simulations are performed to study the acylation reaction catalyzed by kumamolisin-As, a serine-carboxyl peptidase, and to elucidate the catalytic mechanism and the origin of substrate specificity. It is demonstrated that the nucleophilic attack by the serine residue on the substrate may not be the rate-limiting step for the acylation of the GPH*FF substrate. The present study also confirms the earlier suggestions that Asp164 acts as a general acid during the catalysis and that the electrostatic oxyanion hole interactions may not be sufficient to lead a stable tetrahedral intermediate along the reaction pathway. Moreover, Asp164 is found to act as a general base during the formation of the acyl-enzyme from the tetrahedral intermediate. The role of dynamic substrate assisted catalysis (DSAC) involving His at the P1 site of the substrate is examined for the acylation reaction. It is demonstrated that the bond-breaking and -making events at each stage of the reaction trigger a change of the position for the His side chain and lead to the formation of the alternative hydrogen bonds. The back and forth movements of the His side chain between the C=O group of Pro at P2 and Odelta2 of Asp164 in a ping-pong-like mechanism and the formation of the alternative hydrogen bonds effectively lower the free energy barriers for both the nucleophilic attack and the acyl-enzyme formation and may therefore contribute to the relatively high activity of kumamolisin-As toward the substrates with His at the P1 site.
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Affiliation(s)
- Qin Xu
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11, Aoba-yama, Sendai 980-8579, Japan
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
- To whom correspondence should be addressed. E-mail: . Telephone: (865)974-3610. Fax: (865)974-6306
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32
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Kong Y, Guo HB, Yan HF, Liu BX. Nonequilibrium Solid Phase Formation Studied by Lattice Dynamics Calculation and Ion Beam Mixing in an Immiscible Co−Ag System. J Phys Chem B 2005; 109:9362-7. [PMID: 16852121 DOI: 10.1021/jp044449g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For the equilibrium immiscible Co-Ag system, a proven realistic ab initio derived n-body potential is applied to study the nonequilibrium solid phase formation at three chemical stoichiometries of Co/Ag = 1:3, 1:1, and 3:1. To predict the structural stability, the elastic constants and the phonon spectra are calculated at the chosen stoichiometries with a total of eight hypothetical crystalline structures. The calculated results suggest that four compounds, that is, D0(3) CoAg3, B1 CoAg, B2 CoAg, and D0(3) Co3Ag, are unstable, as they all feature negative elastic constants as well as imaginary phonons, and that another four compounds of both fcc-type L1(2) and hcp-type D0(19) structures at chemical stoichiometries of Co/Ag = 1:3 and 3:1, respectively, may elastically be favored and therefore obtainable under some specific conditions. It is also found that all the calculated elastic constants and phonon spectra are coincident within the framework of the elastic theory. Moreover, the calculated elastic constants are in good agreement with those acquired directly from ab initio calculations, lending support to the validity of the ab initio derived n-body Co-Ag potential as well as its resultant elastic constants and the phonon spectra. Interestingly, some of the predicted nonequilibrium solid phases, that is, two hcp-type compounds at chemical stoichiometries of Co/Ag = 1:3 and 3:1, respectively, are indeed obtained in ion beam mixing experiments and their lattice constants determined by diffraction analysis are in good agreement with those from calculations.
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Affiliation(s)
- Y Kong
- Advanced Materials Laboratory, Department of Materials Science and Engineering, Tsinghua University, Beijing 100084, China
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Guo P, Wang QY, Guo HB, Shen ZH, Chen HL. N-acetylglucosaminyltransferase V modifies the signaling pathway of epidermal growth factor receptor. Cell Mol Life Sci 2004; 61:1795-804. [PMID: 15241555 DOI: 10.1007/s00018-004-4122-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Transfection of sense cDNA of N-acetylglucosamyltransferase V (GnTV-S) into human H7721 hepatocarcinoma cells resulted in an increase in the N-acetylglucosaminebeta1,6mannosealpha1,3- branch (GnT-V product) on the N-glycans of epidermal growth factor (EGF) receptor (EGFR), and promotion of its EGF binding and tyrosine autophosphorylation, but showed little effect on the expression of EGFR protein. The phosphorylation at T308, S473 and tyrosine residue(s) and the activity of protein kinase B (Akt/PKB) as well as the phosphorylation of p42/44 mitogen-activated protein kinase (MAPK) and MAPK kinase (MEK) before and after EGF stimulation were concomitantly increased. Conversely, in the antisense GnT-V (GnTV-AS)-transfected H7721 cells, all the results were the reverse of those with GnTV-S-transfected cells. After the cells were treated with 1-deoxymannojirimycin, an inhibitor of N-glycan processing at high mannose, or antibody against the extracellular glycan domain of EGFR, the differences in PKB activity, p42/44 MAPK and MEK phosphorylation among GnTV-S-, GnTV-AS- and mock-transfected cells were significantly attenuated. These findings indicate that the altered expression of GnT-V will change the glycan structure and function of EGFR, which may modify downstream signal transduction.
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Affiliation(s)
- P Guo
- Key Laboratory of Glycoconjugate Research, Ministry of Health, Department of Biochemistry, Shanghai Medical College, Fudan University, 200032, China
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Guo HB, Zhang Y, Chen HL. Relationship between metastasis-associated phenotypes and N-glycan structure of surface glycoproteins in human hepatocarcinoma cells. J Cancer Res Clin Oncol 2001; 127:231-6. [PMID: 11315257 DOI: 10.1007/s004320000186] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
PURPOSE To study the relation of N-glycan structure on cell surface glycoproteins to the metastatic phenotypes. METHODS Two human hepatocarcinoma 7721 cell lines transfected with sense or antisense cDNA of GnT-V, named GnT-V/7721 and GnT-V-AS/7721, respectively, were adopted, because GnT-V can change the antennary number and the content of the beta 1,6 GlcNAc branch in N-glycans. The effects of over- and under-expression of GnT-V on the metastasis-associated phenotype of the transfected cells were investigated and compared with the cells mock-transfected with the plasmid vector. RESULTS In GnT-V/7721 cells, GnT-V activity was increased by 92% compared with the mock cells. HRP-labeled lectin staining of transfected cells showed elevated intensity with HRP-L-PHA and reduced intensity with HRP-ConA, suggesting the increased antennary number and content of the beta 1,6 GlcNAc branch in N-glycans. Analysis of the N-glycan structure of [3H]-labeled glycopeptides prepared from cell-surface [3H] glycoproteins using DSA-affinity chromatography also revealed the above change of the N-glycan structure in a more quantitative manner. GnT-V/7721 cells showed a suppressed cell attachment to fibronectin (Fn) or laminin (Ln), and increased cell migration and invasion through matrigel. In contrast, GnT-V-AS/7721 cells showed reduction of both GnT-V activity and content of the beta 1,6 branch in N-linked glycans, elevation of cell attachment to Fn or Ln, and decline of cell migration and invasion through matrigel. These changes were just the opposite to those in GnT-V/7721 cells. CONCLUSIONS The alteration of N-glycan structure in surface glycoproteins resulting from the activity change of GnT-V contributes to the alterations in metastasis-associated phenotypes. The product of GnT-V, the beta 1,6 GlcNAc branch in N-linked glycans, is a structural factor of adhesion inhibition and invasion promotion. GnT-V is, therefore, closely related to cancer metastasis and its over-expression is an important molecular mechanism of metastasis.
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Affiliation(s)
- H B Guo
- Key Laboratory of Glycoconjugate Research, Ministry of Health, Department of Biochemistry, Shanghai Medical University, Shanghai, 200032, PR China
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Guo HB, Liu F, Zhao JH, Chen HL. Down-regulation of N-acetylglucosaminyltransferase V by tumorigenesis- or metastasis-suppressor gene and its relation to metastatic potential of human hepatocarcinoma cells. J Cell Biochem 2000; 79:370-85. [PMID: 10972975 DOI: 10.1002/1097-4644(20001201)79:3<370::aid-jcb30>3.0.co;2-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The effects of transfection of the metastasis suppressor gene nm23-H1 and cell-cycle related tumor-suppressor gene p16 on the activity of N-acetylglucosaminyltransferase V (GnT-V) and their relations to cancer metastatic potential were investigated. After transfection of nm23-H1 into 7721 human hepatocarcinoma cells and A549 human lung cancer cells, the activities of GnT-V were decreased by 28%-42% in the cells. In contrast, when p16 was transfected into these two cell lines, the decrease of GnT-V activity was only observed in A549 cells. This was probably to be due to the obvious expression of p16 gene in parental 7721 cells and the deletion of p16 in A549 cells. The decrease of GnT-V mRNA was only observed in nm23-H1-transfected cells, but not in p16-transfected A549 cells, suggesting that these two genes regulated GnT-V via different mechanisms. Horseradish peroxidase (HRP)-lectin staining showed that the 7721 cells transfected with nm23-H1 or the A549 cells transfected with p16 displayed a decreased intensity with HRP-leucoagglutinating phytohemagglutinin and increased intensity with HRP-concanavalin A, indicating the decline of beta1,6 N-acetylglucosamine branching structure on the asparagine-linked glycans of cell-surface and intracellular glycoproteins. The nm23-H1 transfected 7721 cells also displayed some changes in metastasis-related phenotypes, including the increase in cell adhesion to fibronectin (Fn), the decline in cell adhesion to laminin (Ln), and the decreased cell migration and invasion through matrigel. Transfection of antisense GnT-V cDNA into 7721 cells resulted in a decrease of GnT-V activity, an increase of cell adhesion to Fn or Ln, and a decrease in cell migration and invasion through matrigel. These phenotypes bore similarity to those of the 7721 cells transfected with nm23-H1. Our findings indicate that the down-regulation of GnT-V by nm23-H1 contributes to the alterations in metastasis-related phenotypes, and is an important molecular mechanism of metastasis suppression mediated by nm23-H1.
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MESH Headings
- Adenocarcinoma/enzymology
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Asparagine/chemistry
- Carbohydrate Conformation
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Cell Adhesion
- Cell Movement
- Collagen
- Cyclin-Dependent Kinase Inhibitor p16/physiology
- Drug Combinations
- Enzyme Induction/genetics
- Fibronectins/chemistry
- Gene Expression Regulation, Neoplastic/genetics
- Genes, Tumor Suppressor
- Genes, p16
- Glycoproteins/metabolism
- Humans
- Laminin/chemistry
- Liver Neoplasms/enzymology
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Lung Neoplasms/enzymology
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Monomeric GTP-Binding Proteins/genetics
- Monomeric GTP-Binding Proteins/physiology
- N-Acetylglucosaminyltransferases/biosynthesis
- N-Acetylglucosaminyltransferases/genetics
- NM23 Nucleoside Diphosphate Kinases
- Neoplasm Invasiveness/genetics
- Neoplasm Metastasis/genetics
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Nucleoside-Diphosphate Kinase
- Phenotype
- Polysaccharides/metabolism
- Proteoglycans
- RNA, Messenger/biosynthesis
- RNA, Neoplasm/biosynthesis
- Recombinant Fusion Proteins/physiology
- Transcription Factors/genetics
- Transcription Factors/physiology
- Transfection
- Tumor Cells, Cultured/enzymology
- Tumor Cells, Cultured/pathology
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Affiliation(s)
- H B Guo
- Key Laboratory of Glycoconjugate Research, Ministry of Health, Department of Biochemistry, Shanghai Medical University, Shanghai, People's Republic of China
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Guo HB, Shen ZH, Huang CX, Ma J, Huang Y, Chen HL. Modulation of the basal activity of phosphatidylinositol-3-kinase/protein kinase B signaling pathway in human hepatocarcinoma cells. Glycoconj J 2000; 17:315-22. [PMID: 11261840 DOI: 10.1023/a:1007177806496] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The modulation of GnT-V activity by signaling molecules in PI-3-K/PKB pathway in human hepatocarcinoma cell line 7721 was studied. GnT-V activity was determined after the transfection of sense or antisense cDNA of PKB into the cells, as well as the addition of activators, specific inhibitors, and the antibodies to the enzyme assay system or culture medium. It was found that the basal activity of GnT-V was up regulated by the sense and down regulated by the antisense cDNA of PKB transfected into 7721 cells. GnT-V was activated by PIP2, PIP3 or GTPgamma[S] added to the assay system, and the activation of PIP2 or GTPgamma[S] was abolished by LY2940002, a specific inhibitor of PI-3-K, but the activation of PIP3 was not attenuated by LY2940002. In addition, GnT-V activity in cultured parental or H-ras transfected cells was inhibited by the antibody against PKB or PI-3-K. These findings demonstrated the involvement of PI-3-K/PKB signaling pathway in the regulation of GnT-V. Moreover, ET18-OCH3, an inhibitor of Raf translocation and PI-PLC enzyme, which produces the activator of PKC, as well as the antibodies against Raf-1 or MEK also inhibited GnT-V activity in the parental and H-ras transfected cells. The inhibitory rates, however, were less in the transfected cells than those in the parental cells. These results reveal that in parental and H-ras transfected 7721 cells, the basal activity of GnT-V is also regulated by the Ras/Raf-1/MEK/MAPK cascade in addition to PI-3-K/PKB signaling pathway. The significance of these two pathways in the regulation of GnT-V and their relations to the activation of PKC previously reported by our laboratory (Ju TZ et al., 1995 Glyconjugate J 12, 767-772) was discussed.
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Affiliation(s)
- H B Guo
- Key Laboratory of Glycoconjugate Research, Ministry of Health, Shanghai Medical University, China
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Guo HB, Zhang QS, Chen HL. Effects of H-ras and v-sis overexpression on N-acetylglucosaminyltransferase V and metastasis-related phenotypes in human hepatocarcinoma cells. J Cancer Res Clin Oncol 2000; 126:263-70. [PMID: 10815761 DOI: 10.1007/s004320050341] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Oncogenes and N-acetylglucosaminyltransferase (GnT-V) are both commonly associated with carcinogenesis and metastasis. In order to elucidate the relationship between oncogenes and GnT-V, two oncogenes, H-ras and v-sis/PDGF (platelet-derived growth factor), were selected, and the effects of their overexpression on GnT-V in 7721 human hepatocarcinoma cells were investigated. The results showed that the over expression of H-ras or v-sis/PDGF-B up-regulated the activities of GnT-V to various degrees in the transfected cells. In H-ras- and PDGF-B-overexpressing cells, the activity of GnT-V was up-regulated to double the normal value. The transient expression of v-sis, which produces a protein almost identical to PDGF-B, stimulated the GnT-V activity by 80.3%, and the effect was more pronounced (increased by 182.5%) in 7721 cells with stable expression of v-sis. The stimulating effect was entirely abolished by treatment with PDGF-B antibody. The staining of asparagine-linked glycans (N-glycans) in the H-ras- and v-sis-overexpressing 7721 cells was intensified when horseradish peroxidase-labeled leucoagglutinating phytohemogglutinin was used as a probe, indicating the increased content of beta1,6GlcNAc branching on the N-glycans. The enhancement of GnT-V mRNA expression was also observed in H-ras- and v-sis- overexpressing cells, indicating that H-ras and v-sis regulated GnT-V via the transcription of GnT-V mRNA and the synthesis of GnT-V protein. The cells overexpressing H-ras and v-sis displayed some changes in metastasis-related phenotypes, including acceleration of cell growth, decline of cell adhesion to fibronectin, and an increase of cell adhesion to laminin, as well as increased invasiveness through Matrigel. These results indicated that the alteration of cell adhesion and invasion induced by oncogenes is closely related to the up-regulation of GnT-V activity and its product, beta1,6GlcNAc branching in N-glycans on the cell surface.
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Affiliation(s)
- H B Guo
- Key Laboratory of Glycoconjugate Research, Ministry of Health, Shanghai Medical University, China
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Guo HB, Jiang AL, Ju TZ, Chen HL. Opposing changes in N-acetylglucosaminyltransferase-V and -III during the cell cycle and all-trans retinoic acid treatment of hepatocarcinoma cell line. Biochim Biophys Acta 2000; 1495:297-307. [PMID: 10699467 DOI: 10.1016/s0167-4889(99)00157-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The changes in N-acetylglucosaminyltransferase-V and -III (GnT-V, GnT-III) during the cell-cycle of synchronized 7721 human hepatocarcinoma cell line were investigated. Using an HPLC method to assay GnT and flow cytometry (FCM) for cell cycle analysis, it was found that GnT-V showed the highest activity, but GnT-III reached the lowest activity when G(2)/M cells were most abundant. In contrast, GnT-V declined to the minimum while GnT-III elevated to maximum when G(0)/G(1) cells were most predominant. The opposing changes were more obvious when the activities of GnT-V and GnT-III were expressed as relative activities (activity of GnT-V or GnT-III/the sum of activities of GnT-V plus GnT-IV plus GnT-III). These opposing changes of GnT-V and GnT-III during the cell cycle might result from the different regulatory mechanisms of GnT-V and GnT-III expression in the cell cycle. The alterations in the structures of cell surface N-glycans were compatible with the changes of the activities of GnTs. The results from immunocytochemistry and Northern blot showed that the protein and mRNA contents of GnT-V were not significantly changed during the cell cycle. The activity of a cell cycle regulating protein kinase, p34(cdc2) kinase, correlated to the activity of GnT-V. These findings suggested that the change of GnT-V activity in cell cycle was not the consequence of the alteration of gene transcription or enzyme protein synthesis, but might be caused by the post-translational regulation. The decrease in GnT-V and the corresponding increase in GnT-III activities were also found after the cells were treated with all-trans retinoic acid (ATRA), and the mechanism of this might be different from that in the cell cycle.
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Affiliation(s)
- H B Guo
- Key Laboratory of Glycoconjugate Research, Ministry of Health, Department of Biochemistry, Shanghai Medical University, Shanghai, PR China
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Guo HB, Liu F, Chen HL. Increased susceptibility to apoptosis of human hepatocarcinoma cells transfected with antisense N-acetylglucosaminyltransferase V cDNA. Biochem Biophys Res Commun 1999; 264:509-17. [PMID: 10529394 DOI: 10.1006/bbrc.1999.1303] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The antisense cDNA of N-acetylglucosaminyltransferase V (GnT-V, EC 2. 4.1.155) was constructed as pcDNA3/GnT-V-AS plasmid and transfected into 7721 cells, a human hepatocarcinoma cell line. The transfection was confirmed with Northern blot. By using HPLC and HRP-lectin staining, it was found that the cells transfected with pcDNA3/GnT-V-AS (GnT-V-AS/7721) expressed less GnT-V activity and beta-1,6-GlcNAc branching in the cell glycoproteins compared with the cells mock-transfected with the vector pcDNA3 (pcDNA3/7721). The growth rate of GnT-V-AS/7721 was decreased in serum-containing medium, while the cell death was accelerated in serum-free medium. The GnT-V-AS/7721 cells were more susceptible to the apoptosis induced by ATRA than the mock-transfected cells. This was evidenced by the obvious appearance of a hypoploid sub-G(1) fraction in the DNA histogram using FCM analysis, the more condensed new moon-type nuclei under morphological observation, and the more intensive TUNEL reaction for assaying the fragmented DNA. At the same time as GnT-V down-regulation by GnT-V-AS, an increase of another N-aceylglusaminyltransferase, GnT-III (EC 2.4.1.144), was observed, and the biological significance of this finding was discussed.
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Affiliation(s)
- H B Guo
- Ministry of Health, Shanghai Medical University, Shanghai, 200032, China
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Guo HB, Jiang AL, Chen HL. [Changes with cell cycle of N-acetylglucosaminyl transferase III, IV and V in 7721 human hepatocarcinoma cells]. Shi Yan Sheng Wu Xue Bao 1998; 31:383-91. [PMID: 12016961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
In order to investigate the changes of N-acetylglucosaminyl transferase (GlcNAc-T) III, IV and V in cell cycle, the synchronization of 7721 human hepatocellular carcinoma cells was performed using serum hunger method. The percentages of cells in different phases during cell cycle were measured by flow cytometry (FCM) and the cell cycle was checked by determining the activity of cellular p34cdc2 kinase. It was found that the activities of GlcNAc-T III increased in G0/G1 cell peak phase and had correlation with the cell percentage of G0/G1 phase (r = 0.760, P < 0.05), while GlcNAc-T V showed the highest activity when G2/M cells were most abundant and had an apparent correlation with the cell percentage of G2/M phase (r = 0.868, P < 0.001). The changes of GlcNAc-T IV activity seemed not related to the cell cycle. The changes in opposite directions of relative activities (percentage of total GlcNAc-T III, IV, V) of GlcNAc-T III and GlcNAc-T V were observed during cell cycle (r = -0.951, P < 0.001), suggesting that these two enzymes might be regulated differently and functioned oppositely in the cells: GlcNAc-T V may be related to the proliferation of 7721 cells, while GlcNAc-T III may be related to the non-mitotic silence phase of the cells, or, it may be a factor against proliferation. Immunohistochemical results showed that the protein content of GlcNAc-T V was not significantly changed during cell cycle, and had no correlation with the activity of GlcNAc-T V, suggesting that the changes of GlcNAc-T V activity in cell cycle might not be resulted from the alteration of enzyme protein synthesis. The correlation between the activities of GlcNAc-T V and p34cdc2 kinase (r = 0.752, P < 0.05) was observed in cell cycle, implicating that GlcNAc-T V might possibly be regulated by p34cdc2 kinase.
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Affiliation(s)
- H B Guo
- Key Laboratory of Glycoconjugate Research, Ministry of Public Health, Shanghai, China
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Abstract
The clinical significance of serum S100 was assessed in comparison to neuron-specific enolase (NSE) in 126 patients with malignant melanoma: 80 patients with clinical stage I/II, 23 patients with stage III and 23 patients with stage IV according to the criteria of the American Joint Committee on Cancer (AJCC). Using cut-off values of 0.15 microgram/l for S100 and 12.5 micrograms/l for NSE, the sensitivity was found to be 1.3% (1/80) for S100 and 8.75% (7/80) for NSE in patients with stage I/II, 8.7% (2/23) for S100 and 13% (8/23) for NSE in patients with stage III, and 73.9% (17/23) for S100 and 34.8% (8/23) for NSE in patients with stage IV disease (P < 0.05). In 6 patients with stage III/IV tumours, serial measurement of serum S100 and NSE was performed. A rise of serum S100 indicated progression of the disease; a decline indicated response to treatment. Our preliminary results support the value of serum S100 as an adjunct to the clinical staging and monitoring of metastatic malignant melanoma.
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Affiliation(s)
- H B Guo
- Department of Clinical Biochemistry, University of Bonn, Germany
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Abstract
The clinical significance of serum S100 was assessed in comparison to neuron-specific enolase (NSE) in 126 patients with malignant melanoma: 80 patients with clinical stage I/II, 23 patients with stage III and 23 patients with stage IV according to the criteria of the American Joint Committee on Cancer (AJCC). Using cut-off values of 0.15 micrograms/l for S100 and 12.5 micrograms/l for NSE, the sensitivity was found to be 1.3% (1/80) for S100 and 8.75% (7/80) for NSE in patients with stage I/II, 8.7% (2/23) for S100 and 13% (8/23) for NSE in patients with stage III, and 73.9% (17/23) for S100 and 34.8% (8/23) for NSE in patients with stage IV disease (P < 0.05). In 6 patients with stage III/IV tumours, serial measurement of serum S100 and NSE was performed. A rise of serum S100 indicated progression of the disease; a decline indicated response to treatment. Our preliminary results support the value of serum S100 as an adjunct to the clinical staging and monitoring of metastatic malignant melanoma.
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Affiliation(s)
- H B Guo
- Department of Clinical Biochemistry, University of Bonn, Germany
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Guo HB, Stoffel-Wagner B, Brennemann W, Springer W, Klingmüller D. [Neuron-specific enolase: a serum marker of clinical progression for metastatic malignant melanoma]. J Tongji Med Univ 1995; 15:19-25. [PMID: 7783258 DOI: 10.1007/bf02887879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- H B Guo
- Abteilung für Klinische Biochemie, Bengbu Medizinische Institut
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Wu GH, Guo HB, Yu MM. [Leptotrombidium (L.) scutellare as the transmitting vector of tsutsugamushi disease of autumn-winter type in Jiangsu Province]. Zhonghua Yi Xue Za Zhi 1994; 74:94-6, 127. [PMID: 8069730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In 1986, epidemic of tsutsugamushi disease of autumn-winter type was found in Jiangsu province. To clarify the vector of this disease, we carried out a series of studies in 1986-1992. Leptotrombidium (L.) scutellare was found to be a dominant species of chigger mite on rats in the endemic areas and its seasonal distribution was correlated with the incidence of tsutsugamushi disease in inhabitants. This mite could naturally be infected by Rickettsia tsutsugamushi, and R. tsutsugamushi could be transmitted via biting and transovarial transmission. Specific antibodies could be detected in the sera of mice bitten by the mites or inoculated with the suspension of mites. Serological typing of the sera of mice was of Gilliam type. The above results demonstrate that L. (L.) scutellare can serve as transmitting vector of tsutsugamushi disease of autumn-winter type.
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Affiliation(s)
- G H Wu
- Institute of Military Medicine, Nanjing Command
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Bu XK, Ying MD, Guo HB, Cao Z. Audiologic investigation of autosomal dominant hereditary sensory hearing loss in a family of 507 members in 6 generations. Ann N Y Acad Sci 1991; 630:310-2. [PMID: 1952617 DOI: 10.1111/j.1749-6632.1991.tb19617.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- X K Bu
- ENT Department, People's Hospital of Jiangsu Province, Nanjing, China
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Li JZ, Li PY, Niu QT, Wang S, Jiang L, Zhao SH, Guo HB, Gao H, Zhang ZM, Fang XZ. Serum-lipid and lipoprotein patterns of Beijing populations from birth to senescence. Chin Med J (Engl) 1988; 101:659-64. [PMID: 3148409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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