Modeling and analysis of soybean (Glycine max. L) Cu/Zn, Mn and Fe superoxide dismutases

Gopavajhula, V. Ramana; Chaitanya, K. V.; Khan, P. Akbar Ali; Shaik, Jilani Purusottapatnam; Reddy, P. Narasimha; Alanazi, Mohammad

doi:10.1590/s1415-47572013005000023

Cited by 37 publications

(26 citation statements)

References 25 publications

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“…To identify all potential family members of SOD in soybean, the known soybean SOD amino acid sequences were used as queries to establish a Hidden Markov model (Gopavajhula et al, 2013), and searched in soybean genome database by using the HMM profile (build 2.3.2) (Finn, Clements & Eddy, 2011). The Pfam and SMART database were used to remove incomplete domains and overlapping genes (Finn et al, 2016).…”

Section: Identification Of Sod Family Genes In Soybean Genomementioning

confidence: 99%

“…Previous studies revealed that SOD genes were divided into three subfamilies (Kliebenstein, Monde & Last, 1998;Zhou et al, 2017). However, others showed that SOD genes could be classified into four subfamilies: MnSOD, FeSOD, Cu/ZnSOD and NiSOD (Gopavajhula et al, 2013). MnSOD, FeSOD and Cu/ZnSOD occur in almost all plants, whereas Ni-containing SOD was found in Streptomyces (Dupont et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…The photosynthetic rate, sugar production, N metabolism and amino acid production were also significantly inhibited under alkaline stress (at high pH) (Hu et al, 2015). Further, alkaline stress has affected 434 million ha of land and limited the crop productivity worldwide (Chen et al, 2018), although single form of soybean SOD gene has been identified under various stresses (Gopavajhula et al, 2013;Wang et al, 2016). It is necessary to explore the roles of soybean SOD family under environmental stresses, especially under alkaline stress.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Duanmu

Qiao

et al. 2020

PeerJ

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Background Superoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of SOD family genes in regulating alkaline stress response are not fully reported. Methods We identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tree and exon-intron structures were generated by using software MEGA 5.0 and GSDS online server, respectively. Furthermore, the conserved motifs were analyzed by MEME online server. The syntenic analysis was conducted using Circos-0.69. Additionally, the expression levels of soybean SOD genes under alkaline stress were identified by qRT-PCR. Results In this study, we identified 13 potential SOD genes in soybean genome. Phylogenetic analysis suggested that SOD genes could be classified into three subfamilies, including MnSODs (GmMSD1–2), FeSODs (GmFSD1–5) and Cu/ZnSODs (GmCSD1–6). We further investigated the gene structure, chromosomal locations and gene-duplication, conserved domains and promoter cis-elements of the soybean SOD genes. We also explored the expression profiles of soybean SOD genes in different tissues and alkaline, salt and cold stresses, based on the transcriptome data. In addition, we detected their expression patterns in roots and leaves by qRT-PCR under alkaline stress, and found that different SOD subfamily genes may play different roles in response to alkaline stress. These results also confirmed the hypothesis that the great evolutionary divergence may contribute to the potential functional diversity in soybean SOD genes. Taken together, we established a foundation for further functional characterization of soybean SOD genes in response to alkaline stress in the future.

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Section: Identification Of Sod Family Genes In Soybean Genomementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Duanmu

Qiao

et al. 2020

PeerJ

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“…Soon thereafter, it was adopted as a quaternary structure validation and annotation tool for PDB archival depositions. which represents the free energy difference between the associated and dissociated states [36]. Possible oligomeric states yielding positive and negative Gibbs free energy of dissociation score are considered to be chemically stable and unstable quaternary structures, respectively [37].…”

Section: Pisa Predictionmentioning

confidence: 99%

Quaternary structure evaluation tool for protein assemblies

Korkmaz

Duarte

Prlić

et al. 2017

Preprint

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Abstract. CC-BY 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/224196 doi: bioRxiv preprint first posted online Nov. 23, 2017; 2 The Protein Data Bank (PDB) is the single worldwide archive of experimentallydetermined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. For example, it makes a difference if the protein is normally a dimer and not a monomer or a trimer or a tetramer or a hexamer in nature. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier).Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 86% correct, 9% incorrect, and 5% inconclusive predictions, when tested with a well-curated

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“…(Adriano, 1986;Han et al, 1997;Stevenson, 1994). (Gayomba et al, 2013;Gopavajhula et al, 2013;Jung et al, 2015). (Gayomba et al, 2013;Jung et al, 2015).…”

mentioning

confidence: 99%

Effect of Rice Straw Compost on Cadmium Transfer and Metal-ions Distribution at Different Growth Stages of Soybean

Jung

Chae

Maria

et al. 2016

Korean J. Soil. Sci. Fert.

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In soil-to-plant transfer of heavy metals, the amount absorbed and accumulated varies depending on the environment conditions. The absorption rate of cadmium (Cd) in plants differs considerably depending on the bioavailability of Cd in the soil, while usage by various organic matters is also reported to affect absorption patterns. Therefore, this study aimed to identify the difference in the transfer of essential metal ions and Cd to various plant parts when rice straw compost was used to cultivate soybean (Glycine max L. cv. Daepung). In the two-leaf stage of soybean cultivated in a greenhouse, Cd was mixed in the soil, after which the Cd and essential metal ions contents, and physiological changes of soybean seedlings were studied on the 15th and 25th day. The Cd toxicity in the plant was reduced with the use of rice straw compost. Further, the Cd content varied with the plant part, and was higher in young leaves (3rd and 4th leaf) than in the stem. When analyzed by leaf age, the Cd transfer was highest in young leaves (3rd and 4th leaf), followed by mature leaves (1st and 2nd leaf). While there was no significant difference between plant tissues in the absorption rate of copper (Cu) and zinc (Zn) when rice straw compost was used against Cd toxicity, the absorption rate of manganese (Mn) and iron (Fe) showed a significant decline in both the control and rice straw compost treatment conditions, as well as a significant difference between leaf ages. Therefore, these results confirm that the use of rice straw compost against Cd toxicity is effective, and implies that the rate of Cd transfer in the soybean plant varies significantly with leaf age.Key words: Cadmium, Metal-ions distribution, Rice straw compost, SoybeanEffects of the application of rice straw compost on Cd concentrations in stems, mature leaves (1st, 2nd leaf), and young leaves (3rd, 4th leaf) of soybean plants grown on the Cd-contaminated soils for 15 days (A) and 25 days (B).

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Modeling and analysis of soybean (Glycine max. L) Cu/Zn, Mn and Fe superoxide dismutases

Cited by 37 publications

References 25 publications

Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Quaternary structure evaluation tool for protein assemblies

Effect of Rice Straw Compost on Cadmium Transfer and Metal-ions Distribution at Different Growth Stages of Soybean

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