Profiling of Phenylpropanoid Monomers in Developing Xylem
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Domain Analysis and Isolation of Coniferyl Alcohol Dehydrogenase Gene from Pseudomonas Nitroreducens Jin1
British Biotechnology Journal 4(6): 684-695, 2014 SCIENCEDOMAIN international www.sciencedomain.org Domain Analysis and Isolation of Coniferyl Alcohol Dehydrogenase Gene from Pseudomonas nitroreducens Jin1 Praveen P. Balgir1 and Dinesh Kalra1* 1Department of Biotechnology, Punjabi University, Patiala - 147002, India. Authors’ contributions This work was carried out in collaboration between both authors. Author PPB designed the study. Author DK analyzed the data. Both authors contributed equally to the study. Both authors read and approved the final manuscript. Received 14th November 2013 th Short Research Article Accepted 20 April 2014 Published 7th June 2014 ABSTRACT Aim: The Aim of present study is to analyse conserved functional Short Dehydrogenase Reductase (SDR) domain from bacteria. Based on the domain analysis selection of coniferyl alcohol dehydrogenase gene for isolation from Pseudomonas nitroreducens Jin1. Place and Duration of Study: Department of Biotechnology, Punjabi University, Patiala. From July, 2012 to November, 2012. Methodology: Bioinformatics tools were used to analyse various calA genes from bacteria based on the presence of conserved domain in members of SDR family. Based on insilico analysis, Pseudomonas nitroreducens Jin1 calA was selected. PCR was used for amplification of the gene from the genome of Pseudomonas nitroreducens Jin1. Result: Multiple sequence alignment results for conserved domains amongst members of SDR family identified presence of all domains of Short Dehydrogenase Reductase members in Pseudomonas nitroreducens Jin1 calA gene. Amongst the various sequences compared the P. nitroreducens Jin1, calA was found to be the smallest in size. The locus of calA in the genome resides at 103513-104280 bases. It was amplified from the genome of Pseudomonas nitroreducens Jin1. -
University of Oklahoma Graduate College Systems
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE SYSTEMS ANALYSIS OF GRASS CELL WALL BIOSYNTHESIS FOR BIOFUEL PRODUCTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By FAN LIN Norman, Oklahoma 2017 SYSTEMS ANALYSIS OF GRASS CELL WALL BIOSYNTHESIS FOR BIOFUEL PRODUCTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Laura E. Bartley, Chair ______________________________ Dr. Ben F. Holt III ______________________________ Dr. Scott D. Russell ______________________________ Dr. Marc Libault ______________________________ Dr. Randall S. Hewes © Copyright by FAN LIN 2017 All Rights Reserved. Acknowledgements I would like to express my deepest appreciation to my supervisor, Dr. Laura Bartley, for her guidance and advice throughout all projects. She is always encouraging and willing to help me with patience. By working with her, I learned more than anything I learned in a classroom. I would like to acknowledge my collaborators, their significant contributions to the data collection process and their useful discussion were essential for the completion of these projects. Especially thanks to Dr. Lobban, Dr. Mallinson and Dr. Waters for working together as an excellent interdisciplinary team on the thermal conversion project. I enjoy the useful meetings and discussions. I also would like to thank my committee members, Dr. Holt, Dr. Libault, Dr. Russell and Dr. Hewes. They spent their valuable time to meet with me and discuss about these projects. I also thank members of the Bartley lab, Russell lab, and Libault lab for useful discussions. Especially thanks to Dr. Zhao for the discussion on statistical analysis and network analysis. -
Research Article Comparative RNA-Sequence Transcriptome Analysis of Phenolic Acid Metabolism in Salvia Miltiorrhiza, a Traditional Chinese Medicine Model Plant
Hindawi International Journal of Genomics Volume 2017, Article ID 9364594, 10 pages https://doi.org/10.1155/2017/9364594 Research Article Comparative RNA-Sequence Transcriptome Analysis of Phenolic Acid Metabolism in Salvia miltiorrhiza, a Traditional Chinese Medicine Model Plant Zhenqiao Song,1,2 Linlin Guo,1 Tian Liu,1 Caicai Lin,2 Jianhua Wang,1,2 andXingfengLi1,2 1 Agronomy College, Shandong Agricultural University, Tai’an, Shandong 271028, China 2State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai’an, Shandong 271018, China Correspondence should be addressed to Xingfeng Li; [email protected] Received 1 July 2016; Revised 26 October 2016; Accepted 27 November 2016; Published 17 January 2017 Academic Editor: Mohamed Salem Copyright © 2017 Zhenqiao Song et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Salvia miltiorrhiza Bunge is an important traditional Chinese medicine (TCM). In this study, two S. miltiorrhiza genotypes (BH18 and ZH23) with different phenolic acid concentrations were used for de novo RNA sequencing (RNA-seq). A total of 170,787 transcripts and 56,216 unigenes were obtained. There were 670 differentially expressed genes (DEGs) identified between BH18and ZH23, 250 of which were upregulated in ZH23, with genes involved in the phenylpropanoid biosynthesis pathway being the most upregulated genes. Nine genes involved in the lignin biosynthesis pathway were upregulated in BH18 and thus result in higher lignin content in BH18. However, expression profiles of most genes involved in the core common upstream phenylpropanoid biosynthesis pathway were higher in ZH23 than that in BH18. -
Flux Modeling for Monolignol Biosynthesis
Available online at www.sciencedirect.com ScienceDirect Flux modeling for monolignol biosynthesis 1,2 3 4,5 Jack P Wang , Megan L Matthews , Punith P Naik , 3 5 2 Cranos M Williams , Joel J Ducoste , Ronald R Sederoff and 1,2 Vincent L Chiang The pathway of monolignol biosynthesis involves many coniferyl, and 4-coumaryl alcohols that are incorporated components interacting in a metabolic grid to regulate the into the polymer resulting in syringyl (S), guaiacyl (G), supply and ratios of monolignols for lignification. The and p-hydroxyphenyl (H) units, respectively [3,4]. complexity of the pathway challenges any intuitive prediction of the output without mathematical modeling. Several models The biosynthetic pathway (Figure 1) for lignin has been have been presented to quantify the metabolic flux for studied extensively because of its fundamental role in the monolignol biosynthesis and the regulation of lignin content, regulation of plant secondary cell wall formation and the composition, and structure in plant cell walls. Constraint-based consequent determination of wood chemical and physical models using data from transgenic plants were formulated to properties [5,6 ,7–9]. Lignin content, composition, and describe steady-state flux distribution in the pathway. Kinetic- structure are predominantly controlled by the metabolic based models using enzyme reaction and inhibition constants flux that regulates the supply and ratio of monolignols for were developed to predict flux dynamics for monolignol lignification [10]. Monolignols are biosynthesized from biosynthesis in wood-forming cells. This review summarizes phenylalanine (or tyrosine in grasses [11,12]) through a the recent progress in flux modeling and its application to lignin metabolic grid consisting of up to 11 enzyme families and engineering for improved plant development and utilization. -
Biochemical Control Aspects in Lignin Polymerization
Biochemical Control Aspects in Lignin Polymerization Anders Holmgren Doctoral Thesis Royal Institute of Technology School of Chemical Sciences and Engineering Department of Fibre and Polymer Technology Division of Wood Chemistry and Pulp Technology Stockholm 2008 Biochemical Control Aspects in Lignin Polymerization Supervisors: Professor Gunnar Henriksson and Dr Liming Zhang AKADEMISK AVHANDLING som med tillstånd av Kungliga Tekniska Högskolan i Stockholm framlägges till offentlig granskning för avläggande av teknologie doktorsexamen fredagen den 29 februari 2008, kl 10:00 i STFI-salen, STFI-Packforsk, Drottning Kristinas Väg 61. Avhandlingen försvaras på engelska. © Anders Holmgren 2008 Paper I Reproduced by permission of The Royal Society of Chemistry TRITA-CHE-Report 2008:10 ISSN 1654-1081 ISBN 978-91-7178-864-1 Abstract Lignins are produced by all vascular plants and they represent one of the most abundant groups of biopolymers in nature. Lignin chemistry research, which has been of great importance for the progress of pulping technologies, has been plagued by the difficulties of its isolation and characterization. The pioneering work of Karl Freudenberg in the 1950’s with synthetic models of lignin paved the way for a detailed structural characterization of many lignin substructures. His work with the so-called “synthetic lignins” or dehydrogenative polymers (DHP) also laid a foundation for understanding how different lignin substructures are formed, reinforcing the already existing theory of lignin polymerization. However, subsequent structural characterizations of DHPs and lignins have repeatedly put this theory to the test. In the past decade, even a new radically different hypothesis for lignin polymerization has emerged and is sustained by a few researchers in the field.