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Chen ZF, Ru JN, Sun GZ, Du Y, Chen J, Zhou YB, Chen M, Ma YZ, Xu ZS, Zhang XH. Genomic-Wide Analysis of the PLC Family and Detection of GmPI-PLC7 Responses to Drought and Salt Stresses in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:631470. [PMID: 33763092 PMCID: PMC7982816 DOI: 10.3389/fpls.2021.631470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/10/2021] [Indexed: 05/12/2023]
Abstract
Phospholipase C (PLC) performs significant functions in a variety of biological processes, including plant growth and development. The PLC family of enzymes principally catalyze the hydrolysis of phospholipids in organisms. This exhaustive exploration of soybean GmPLC members using genome databases resulted in the identification of 15 phosphatidylinositol-specific PLC (GmPI-PLC) and 9 phosphatidylcholine-hydrolyzing PLC (GmNPC) genes. Chromosomal location analysis indicated that GmPLC genes mapped to 10 of the 20 soybean chromosomes. Phylogenetic relationship analysis revealed that GmPLC genes distributed into two groups in soybean, the PI-PLC and NPC groups. The expression patterns and tissue expression analysis showed that GmPLCs were differentially expressed in response to abiotic stresses. GmPI-PLC7 was selected to further explore the role of PLC in soybean response to drought and salt stresses by a series of experiments. Compared with the transgenic empty vector (EV) control lines, over-expression of GmPI-PLC7 (OE) conferred higher drought and salt tolerance in soybean, while the GmPI-PLC7-RNAi (RNAi) lines exhibited the opposite phenotypes. Plant tissue staining and physiological parameters observed from drought- and salt-stressed plants showed that stress increased the contents of chlorophyll, oxygen free radical (O2 -), hydrogen peroxide (H2O2) and NADH oxidase (NOX) to amounts higher than those observed in non-stressed plants. This study provides new insights in the functional analysis of GmPLC genes in response to abiotic stresses.
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Affiliation(s)
- Zhi-Feng Chen
- College of Life Sciences, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Jing-Na Ru
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Guo-Zhong Sun
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yan Du
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Jun Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yong-Bin Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Xiao-Hong Zhang
- College of Life Sciences, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
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Kumar P, Bansal M. Structural and functional analyses of PolyProline-II helices in globular proteins. J Struct Biol 2016; 196:414-425. [PMID: 27637571 DOI: 10.1016/j.jsb.2016.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 11/18/2022]
Abstract
PolyProline-II (PPII) helices are defined as a continuous stretch of a protein chain in which the constituent residues have backbone torsion angle (φ, ψ) values of (-75°, 145°) and take up an extended left handed helical conformation, without any intra-chain hydrogen bonds. They are found to occur quite frequently in protein structures, with their number exceeding that of π-helices, though it is considerably less than that of α-helices and β-strands. A relatively new procedure, ASSP, for the identification of regular secondary structures using Cα trace identifies 3597 PPII-helices in 3582 protein chains, solved at resolution ⩽2.0Å. Taking advantage of this significantly expanded database of PPII-helices, we have analyzed their structural and functional roles as well as determined the amino acid propensity within and around them. Though Pro residues are highly preferred, their presence is not a mandatory requirement for the formation of PPII-helices, since ∼40% PPII-helices were found to contain no Pro residues. Aromatic amino acids are avoided within this helix, while Gly, Asn and Asp residues are preferred in the proximal flanking regions. The PPII-helices range from 3 to 13 residues in length with the average twist and rise being -121.2°±9.2° and 3.0ű0.1Å respectively. A majority (∼72%) of PPII-helices were found to occur in conjunction with α-helices and β-strands, and serve as linkers as well. The analysis of various intra-helical non-bonded interactions revealed frequent presence of CH⋯O H-bonds. PPII-helices participate in maintaining the three-dimensional structure of proteins and are important constituents of binding motifs involved in various biological functions.
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Affiliation(s)
- Prasun Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
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Sousa FL, Martin WF. Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:964-81. [PMID: 24513196 DOI: 10.1016/j.bbabio.2014.02.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/31/2014] [Accepted: 02/03/2014] [Indexed: 12/27/2022]
Abstract
The deep dichotomy of archaea and bacteria is evident in many basic traits including ribosomal protein composition, membrane lipid synthesis, cell wall constituents, and flagellar composition. Here we explore that deep dichotomy further by examining the distribution of genes for the synthesis of the central carriers of one carbon units, tetrahydrofolate (H4F) and tetrahydromethanopterin (H4MPT), in bacteria and archaea. The enzymes underlying those distinct biosynthetic routes are broadly unrelated across the bacterial-archaeal divide, indicating that the corresponding pathways arose independently. That deep divergence in one carbon metabolism is mirrored in the structurally unrelated enzymes and different organic cofactors that methanogens (archaea) and acetogens (bacteria) use to perform methyl synthesis in their H4F- and H4MPT-dependent versions, respectively, of the acetyl-CoA pathway. By contrast, acetyl synthesis in the acetyl-CoA pathway - from a methyl group, CO2 and reduced ferredoxin - is simpler, uniform and conserved across acetogens and methanogens, and involves only transition metals as catalysts. The data suggest that the acetyl-CoA pathway, while being the most ancient of known CO2 assimilation pathways, reflects two phases in early evolution: an ancient phase in a geochemically confined and non-free-living universal common ancestor, in which acetyl thioester synthesis proceeded spontaneously with the help of geochemically supplied methyl groups, and a later phase that reflects the primordial divergence of the bacterial and archaeal stem groups, which independently invented genetically-encoded means to synthesize methyl groups via enzymatic reactions. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Filipa L Sousa
- Institute for Molecular Evolution,University of Düsseldorf, 40225 Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution,University of Düsseldorf, 40225 Düsseldorf, Germany.
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Goncearenco A, Berezovsky IN. Exploring the evolution of protein function in Archaea. BMC Evol Biol 2012; 12:75. [PMID: 22646318 PMCID: PMC3458885 DOI: 10.1186/1471-2148-12-75] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 02/24/2012] [Indexed: 11/21/2022] Open
Abstract
Background Despite recent progress in studies of the evolution of protein function, the questions what were the first functional protein domains and what were their basic building blocks remain unresolved. Previously, we introduced the concept of elementary functional loops (EFLs), which are the functional units of enzymes that provide elementary reactions in biochemical transformations. They are presumably descendants of primordial catalytic peptides. Results We analyzed distant evolutionary connections between protein functions in Archaea based on the EFLs comprising them. We show examples of the involvement of EFLs in new functional domains, as well as reutilization of EFLs and functional domains in building multidomain structures and protein complexes. Conclusions Our analysis of the archaeal superkingdom yields the dominating mechanisms in different periods of protein evolution, which resulted in several levels of the organization of biochemical function. First, functional domains emerged as combinations of prebiotic peptides with the very basic functions, such as nucleotide/phosphate and metal cofactor binding. Second, domain recombination brought to the evolutionary scene the multidomain proteins and complexes. Later, reutilization and de novo design of functional domains and elementary functional loops complemented evolution of protein function.
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Affiliation(s)
- Alexander Goncearenco
- Computational Biology Unit, Uni Research, University of Bergen, N-5008 Bergen, Norway
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Speers AE, Cravatt BF. Ligands in crystal structures that aid in functional characterization. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1306-8. [PMID: 20944226 PMCID: PMC2954220 DOI: 10.1107/s1744309110035748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 09/06/2010] [Indexed: 11/30/2022]
Abstract
Liganded structures can be instrumental in assigning function to uncharacterized proteins by revealing active sites, conserved residues, binding motifs, and substrate specificity. This introduction provides an overview and commentary on the value of liganded structures emerging from the JCSG structural genomics initiative.
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Affiliation(s)
- Anna E. Speers
- The Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, USA
| | - Benjamin F. Cravatt
- The Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, USA
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Kumar A, Chiu HJ, Axelrod HL, Morse A, Elsliger MA, Wilson IA, Deacon A. Ligands in PSI structures. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1309-16. [PMID: 20944227 PMCID: PMC2954221 DOI: 10.1107/s1744309110008092] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 03/03/2010] [Indexed: 11/17/2022]
Abstract
Approximately 65% of PSI structures report some type of ligand(s) that is bound in the crystal structure. Here, a description is given of how such ligands are handled and analyzed at the JCSG and a survey of the types, variety and frequency of ligands that are observed in the PSI structures is also compiled and analyzed, including illustrations of how these bound ligands have provided functional clues for annotation of proteins with little or no previous experimental characterization. Furthermore, a web server was developed as a tool to mine and analyze the PSI structures for bound ligands and other identifying features.
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Affiliation(s)
- Abhinav Kumar
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Andrew Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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