Research Article

Cloning and Bioinformatics Analysis of the EfNAC Gene in Erianthus fulvus  

Shujie Gu* , Xianyue Shen* , Zenfeng Qian , Dan Zeng , Hao Ma , Yining Di , Lilian He , Fusheng Li
College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201
* These authors contributed equally to this work
Author    Correspondence author
Computational Molecular Biology, 2021, Vol. 11, No. 3   doi: 10.5376/cmb.2021.11.0003
Received: 01 Sep., 2020    Accepted: 01 Dec., 2020    Published: 19 Mar., 2021
© 2021 BioPublisher Publishing Platform
This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Gu S.J., Shen X.Y., Qian Z.F., Zeng D., Ma H., Di Y.N., He L.L., and Li F.S., 2021, Cloning and bioinformatics analysis of the EfNAC gene in Erianthus fulvus, Computational Molecular Biology, 11(3): 1-10 (doi: 10.5376/cmb.2021.11.0003)


In order to make better use of the resistance-related genes of sugarcane wild species Erianthus fulvus Ness., and to provide reliable candidate genes for resistance breeding of transgenic sugarcane. In this research, we used electronic cloning and RT-PCR to clone a gene that was induced by drought stress in the wild species of Erianthus fulvus (Kun ming 99-2), and named it FfNAC (GenBank ID: MT499790). Bioinformatics analysis shows that the ORF of the EfNAC is 765 bp in length, encodes 254 amino acids in total, and has a conserved NAM Superfamily. EfNAC protein is mainly composed of random coils and alpha helices, without signal peptide, with multiple phosphorylation sites, and no transmembrane structure. this research provides theoretical basis and technical support for in-depth research of the molecular regulation mechanism of drought stress in the sugarcane and the drought-resistant breeding of transgenic sugarcane.

Sugarcane; Erianthus fulvus; EfNAC gene; Drought resistance

Efianthus fulvus Ness. is a wild species in the genus Efianthus. It has excellent characteristics such as strong stress resistance (Cao et al., 2017; Li et al., 2018), resistance to Puccinia stalk (Li et al., 2005) and strong ecological adaptability (Li et al., 2004). Therefore, the excellent stress resistance related gene source in the Efianthus fulvus e can be used Promote the improvement of sugarcane varieties and the development of related stress-resistant varieties (Lu et al., 2012). In addition, Erianthus fulvus has specific and excellent traits such as few chromosomes, more pollen, and high sag (Li, 2005). At present, there are few researches on Efianthus fulvus at home and abroad, and there are reports on mining Efianthus fulvus cold resistance genes, but there are few reports on sugarcane grass drought resistance genes mining. Drought is one of the main abiotic stress factors that affect the yield and quality of sugarcane. Therefore, studying the genes related to drought resistance of Erianthus fulvus vulgare has important significance and value for sugarcane resistance breeding.


NAC (NAM, ATAF1/2, CUC1/2) is the largest transcription factor family unique to plants, and has been found in grasses such as Arabidopsis thaliana, Oryza sativa, Triticum aestivum, Hordeumvulgare, Zea mays, Saccharum officinarum, etc. Studies have shown that NAC gene can effectively improve the stress resistance of plants. The ZmSNAC1 gene induced by drought stress in maize can significantly improve the dehydration tolerance of maize seedlings (Lu et al., 2013). Overexpression of OsNAC9 gene in rice can change the structure of rice root system, thereby improving the drought resistance and yield of rice (Redillas et al., 2012); The stress-responsive NAC transcription factor SNAC3 in rice improves the heat tolerance and drought tolerance of rice by regulating the types of reactive oxygen species in rice (Fang et al., 2015); Overexpression of tobacco NAC4 gene can improve the drought resistance of medicinal plants (Dai et al., 2018). There is no report on cloning drought-resistant NAC transcription factors in Efianthus fulvus.


In this study, the EfNAC gene was cloned from the Efianthus fulvus by electronic cloning combined with RT-PCR, and the EfNAC gene and the encoded protein were analyzed by bioinformatics. This research aims to dig out the excellent genes related to drought resistance of Efianthus fulvus and provide a scientific basis for sugarcane drought resistance breeding.


1 Results and Analysis

1.1 RNA extraction and EfNAC gene cloning

Total RNA was extracted from the leaves of Efianthus fulvus 99-2, and the electrophoresis detection band was clear (Figure 1). The measured OD260/280 was between 1.6 and 1.8, which can be used for reverse transcription as a cDNA template, and then PCR amplification in the amplification test, after the amplification, the PCR product was detected by 1% agarose TAE gel electrophoresis (Figure 2). There is a clear band at about 990 bp, which is inferred to be the target fragment.


Figure 1 Total RNA in leaves

Note: M: DL2000 DNA Mark; 1,2,3,4,5,6: Total RNA of Efianthus fulvus 99-2



Figure 2 EfNAC PCR cloning

Note: M: DL2000 DNA Mark

1.2 ORF and conservative domain prediction of EfNAC gene

The sequencing results were analyzed on the NCBI Open ORF (Open reading frame), the results showed that there are 6 ORFs, of which the longest ORF encodes 254 amino acids, and the CDS (Coding sequencing, coding sequence) 765 bp (Figure 3). The protein encoded by the EfNAC gene was then predicted for conserved domains (Figure 4). This protein has a typical NAM domain.


Figure 3 EfNAC gene of nucleic acid and deduce amino acid sequence



Figure 4 EfNAC protein conserved domain prediction


1.3 Analysis of the physical and chemical properties of EfNAC encoded protein

Using ProtParam and CFSSP software to analyze the protein encoded by the EfNAC gene, the results showed that: the molecular formula of the protein is C1166H1833N373O344S10, the relative molecular mass is 26.9 kD, and it is composed of C, H, N, O, and S atoms, with a total of 3 726 atoms, Theoretical isoelectric point pI: 9.06; the most encoded amino acid is alanine (37), followed by glycine (31) and arginine (28). The EfNAC protein has an unstable coefficient of 55.40, a fat coefficient of 64.72, and a GRAVY value of -0.446. It is a class of unstable proteins; using the ProScale online software to analyze the hydrophilicity and hydrophobicity (Figure 5), the area with a score less than 0 is significantly greater than the area with a score greater than 0 Dense, combined with the GRAVY value, it can be predicted that the protein is a hydrophilic protein. SOPMA software analysis results show that the protein is composed of alpha helix (Alpha helix, 14.96%), extended strand (13.78%), beta turn (Beta turn, 5.12%) and random coil (Random coil, 66.14%) Composition, in general, the main secondary structure of EfNAC protein is random coils, followed by α helix (Figure 6). Use SWISS-MODEL to model the tertiary structure of EfNAC protein, mainly with random coils and α-helices (Figure 7).



Figure 5 Hydrophobic/hydrophilic analysis of EfNAC amino acid sequence



Figure 6 Predicted secondary structure of EfNAC protein



Figure 7 Three-dimensional structure of EfNAC encoding protein


1.4 The signal peptide, phosphorylation site and transmembrane structure prediction of EfNAC protein

Using SignalP5.0 online tool to predict the signal peptide of EfNAC protein, the results showed (Figure 8) that the protein doesn’t contain signal peptide, and it is a relatively stable and not easily degraded protein. Using NetPhos 3.1 Server software to detect the phosphorylation sites of EfNAC protein, it was found (Figure 9) that there are multiple phosphorylation sites (>0.5) on threonine (Thr) and serine (Ser) in the polypeptide chain encoded by EfNAC. TMHMM Server v.2.0 software was used to detect the transmembrane structure of the protein encoded by the EfNAC gene, and the results showed that the EfNAC protein doesn’t have a transmembrane structure and belongs to an extra-membrane protein (Figure 10).



Figure 8 Prediction of EfNAC coding protein signal peptide



Figure 9 Phosphorylation site detection of EfNAC protein



Figure 10 Transmembrane structure of EfNAC protein


1.5 EfNAC homologous protein analysis and phylogenetic tree construction

Using protein database Uniprot analysis, the protein sequences with high homology and similarity to EfNAC protein sequence are Sorghum bicolor, Zea mays, Panicum miliaceum, Setaria italica, Setaria viridis, Oryza punctata, Eragrostis curvula, Oryza brachyantha, Triticum aestivum, Aegilops tauschii subspsp. Strangulata, Oryza sativa subsp. Indica, the similarity is 87.9%, 87.9%, 77.2%, 73.1%, 73.1%, 60.9%, 62.3%, 59.3%, 57.5%, 57.5%, 56.5%, respectively. Use DNAMAN 7.0 to compare the EfNAC gene with the above homologous proteins (Figure 11). The phylogenetic tree was constructed with MEGA-X software, and the results showed that the EfNAC protein was closely related to the sorghum NAC protein (Figure 12).



Figure 11 Comparison of EfNAC protein homology between listed species

Note: Different colors represent the similarity between sequences, where black indicates 100%; Pink indicates greater than 75%; Blue indicates greater than 50%; Yellow indicates greater than 33%



Figure 12 The phylogenetic tree of protein encoded by EfNAC gene and NAC protein of listed plants


1.6 Fluorescence quantitative expression analysis of EfNAC gene under drought stress

Total RNA was extracted from the seedling leaves of Dian-sugarcane 01-58, Erianthus fulvus 99-2, and Yacheng 89-9 and reverse transcribed into cDNA. RT-qPCR analysis of EfNAC gene was performed using cDNA as a template, and the RT-qPCR results It shows (Figure 13): After drought stress, the up-regulated fold of this gene is the highest in Erianthus fulvus 99-2, which is about 76 times that of the control group, Dian-sugarcane 01-58 is 23 times, and Yacheng 89-9 is about 41 times. The results of the analysis of variance showed that there were extremely significant differences between the treatment group and the control group, and the differences between the three materials were extremely significant. Therefore, we can determine that the EfNAC gene is induced by drought stress based on the above evidence, and we can infer that this gene functions as one of the drought stress regulatory elements.



Figure 13 Expression of EfNAC in different materials at seedling stage

Note: Lowercase letters represent significant differences in gene expression of different varieties under different treatments (p<0.05); Written letters represent differences in gene expression of different varieties under different treatments (p<0.01); CK: Control; DT: Drought treatment


2 Discussion

After being exposed to drought and other abiotic stresses, plants first transmit competent signals to the relevant transcription factors that respond to the stress. The transcription factors respond quickly and begin to encode rRNA, and then rRNA begins to encode amino acid synthesis protein, which can be detected in about 3 minutes. To related proteins, this process is very accurate and rapid, and it is also a very effective means of resisting stress for plants. Therefore, studying transcription factors that regulate drought stress is an important part of studying drought tolerance of sugarcane. The NAC transcription factor was first discovered in petunia (Souer et al., 1996). Studies have shown that it not only participates in plant growth and development, but also participates in plant abiotic stress and metabolism, so it has been studied by many scholars. Wang et al. (2020a) used drought-resistant maize inbred line Y882 as the test material, used PEG (Polyethylene glycol) to simulate drought after rehydration, and obtained 87 NAC transcription factors in maize through transcriptome analysis. The NAC transcription factor in maize plays an important role in the regulation of drought stress response. In this study, the expression of EfNAC induced by drought stress is basically consistent with the results of the study, but there may be other NAC family genes induced by drought stress in Erianthus fulvus. Zhang et al. (2017) also cloned a member of the NAC family ZmNAC99 from different drought-resistant maize inbred lines, and further revealed that the promoter of the ZmNAC99 gene contains two drought-responsive cis-elements MBS and MBS through cis-element analysis. 1 low temperature response element LTR. Wang et al. (2020b) isolated a new stress-responsive NAC transcription factor gene LpNAC13 from lily bulbs, and found that drought stress, salt stress, cold stress and ABA treatment can all induce the expression of LpNAC13, indicating that the LpNAC13 gene is not only in It plays a role in drought resistance and also plays an important role in other stress resistance processes. In this study, the drought-induced expression gene EfNAC was cloned from the transcriptome. It is not clear whether other stress conditions can induce the expression of this gene in Erianthus fulvus. Min et al. (2019) obtained transgenic yeast by transferring 113 NAC transcription factors (MsNAC001~MsNAC113) in alfalfa into yeast. In transgenic yeast, the overexpression of MsNAC058 increased the tolerance to drought stress (MsNAC058).


The overexpression of ANAC019ANAC055 and ANAC072 in Arabidopsis can significantly improve the drought resistance of Arabidopsis (Tran et al., 2004). Yang et al. (2019) transferred the heterologous gene HaNAC1 to potatoes and found that transgenic potatoes can resist drought by regulating the expression levels of different hormones. Wang et al. (2019) transferred the GhSNAC1 gene cloned from upland cotton to tobacco, and found that overexpression of GhSNAC1 can significantly improve the drought resistance of transgenic tobacco by stressing transgenic tobacco seedlings. A large number of studies have shown that the NAC gene transfer can effectively improve the drought resistance of plants. In this study, the NAC gene cloned from Erianthus fulvus for the first time can be used for subsequent drought-resistant sugarcane transgenic breeding. At present, our research group is engaged in this aspect of research. Sugarcane cultivars are polyploid plants and rarely bloom. Conventional breeding is very difficult. Molecular breeding can effectively shorten the breeding period and avoid problems such as non-orientation of conventional sugarcane breeding, improve breeding efficiency and quality, and accelerate the promotion of sugarcane industry However, at present, there is no genetically modified sugarcane in China. Therefore, more scientific research personnel are needed to overcome this problem in rushing genetically modified breeding. Through further phylogenetic tree analysis, it is found that the EfNAC protein has the highest homology similarity with the NAC protein of maize and sorghum, and a multiple sequence alignment is carried out. It is found that the EfNAC gene has a typical conserved NAM domain. In addition, it was also found that after drought stress, the expression of EfNAC gene in Erianthus fulvus increased by 76 times, further indicating that EfNAC is a gene induced by drought stress and has a certain regulatory effect on drought stress. Whether genes will participate in other stress regulation needs further verification.


In this study, a new NAC gene was cloned from Erianthus fulvus for the first time through the method of electronic cloning and RT-PCR, and named it EfNAC, which not only enriched the gene information of the NAC family and the sugarcane genome database, but also provided theoretical basis and technical support for in-depth study The molecular regulation mechanism of the drought stress and the transgenic breeding of drought-resistant sugarcane.


3 Materials and Methods

3.1 Planting and processing of materials

The test materials were provided by Sugarcane Research Institute of Yunnan Agricultural University. The wild species "Sucrose 99-2" with strong drought resistance was selected for gene cloning, and the materials were all the +1 leaf of the plant (the first fully expanded leaf at the top). The materials used in the fluorescence quantitative PCR are "Erianthus fulvus 99-2" (with strong stress resistance), "Dian-sugarcane 01-58" (the progeny of the hybridization of Erianthus fulvus and sugarcane), and "Yacheng 89-9" (the progeny of the hybridization of Erianthus fulvus and sugarcane). After the stress treatment, the +1 leaves of the corresponding materials were taken and placed in liquid nitrogen. The excess materials were stored at -80℃ in time for later use.


The budded cane stems of the tested varieties (lines) were taken from the resource nursery of the Sugarcane Research Institute of Yunnan Agricultural University, and the surfaces were disinfected, sprouted and transplanted. Plant 10 pots of each material, place them in the greenhouse of the Sugarcane Research Institute of Yunnan Agricultural University, and conduct reasonable field management. Finally, 6 pots with the same growth for each material are selected for follow-up tests, and the selected 6 pots are divided into two groups. Group 3 pots, one group as treatment and one group as control. Treatment is carried out at the seedling stage, the control (CK) is normal water supply, and the treatment (DT) is drought stress: the relative water content of the soil in the pot is measured by the weighing method (drying method), and it is reached when the relative water content of the soil is less than 30% Severe drought (9 days of drought stress). The leaves of 3 materials of the control group (CK) and the treatment group (DT) were collected, and the biological replicates were repeated twice. The samples were used to extract total RNA from the leaves.


3.2 Extraction of total RNA and synthesis of cDNA

The leaves of 3 kinds of materials (Erianthus fulvus 99-2, Dian-sugarcane 01-58, Yacheng 89-9) under normal watering and drought stress were retrieved and then extracted with TRNaol Universal to extract total RNA. The extracted total RNA Dry on a clean bench for about 3 minutes, add 30 μL RNase-Free ddH2O and mix well; check the quality of RNA by electrophoresis to determine whether there is degradation and contamination; check the quality of RNA by spectrophotometry to further determine the concentration and quality of RNA. The results showed that the OD260/280 of most RNA was between 1.6 and 1.8, indicating that the RNA was of high purity and could be used for subsequent reverse transcription.


Use FastKing one-step reverse transcription to synthesize cDNA, the total system is 20 μL. (The formula for calculating RNA concentration is: A[260]×40×100÷1000). 5×FastKing-RT SuperMⅸ× and RNase-Free ddH2O are thawed at room temperature, and quickly placed on ice after thawing. Before use, mix each solution thoroughly by vertexing. The operation steps are all performed on ice. In order to ensure the accuracy of the preparation of the reaction solution, Mix is first prepared in the preparation of the reaction system, and then the same amount is loaded into each reaction tube. Reverse transcription reaction system: 5×FastKing-RT SuperMⅸ 4 μL, total RNA 1 μg, and finally make up to 20 μL with ddH2O without RNase. The cDNA obtained by reverse transcription is stored in a refrigerator at -20°C for later use.


3.3 Primer design and amplification of EfNAC gene

According to the sequence of the EfNAC gene, use the NCBI online software Home-ORF Finder to find the open reading frame of the gene, and then design the amplification primers of the target gene through NCBI's Primer-BLAST. The primers were synthesized by Shanghai Shenggong (Table 1) using TaKaRa's PrimerSTAR Max DNA Polymerase high-fidelity enzyme for amplification. The total PCR reaction system is 25 μL (Table 2), the PCR instrument is provided by the Yunnan Agricultural University, and the PCR reaction program for gene amplification (Table 3). After the PCR reaction is completed, store at 4°C or on ice. Then take 5 μL of the reactant, perform gel agarose electrophoresis detection, use the gel imaging system to take pictures and observe, and get clear bands. For the recovery of the target fragment and the ligation of the cloning vector, use TIANGEN's gel recovery kit (DP209) and pLB Vector kit (VT205), respectively. Refer to the instructions. Finally, use a pipette to place the mixture on the LB agarose plate for transformation, and then perform colony detection to obtain the target strain, and carry out the enrichment culture of the target strain, and send the bacterial solution to Sangon Biotech (Shanghai) for sequencing.



Table 1 EfNAC Gene amplification primer sequences



Table 2 Reaction system



Table 3 PCR reaction program


3.4 Bioinformatics analysis of EfNAC gene

Use Protparam online software to predict the amino acid composition, theoretical molecular weight and theoretical isoelectric point of EfNAC protein; use ProtScale ( online software to predict the hydrophilicity and hydrophobicity of EfNAC protein; to predict EfNAC The prediction of protein domains uses the Conserved Domain Database in NCBI; the prediction of signal peptide, transmembrane structure and phosphorylation site of EfNAC protein uses SignalP, TMHMM Server v.2.0 and NetPhos 2.0 Server, respectively; the CFSSP online software is used to Secondary structure prediction. Use SWISS-MODEL to model the Tertiary structure of EfNAC protein; use SOPMA software to analyze EfNAC protein; use the BLAST function of the protein database UniProt to find homologous sequences, and then use DNAMAN6.0 to analyze the selected homologous sequences, and use MEGA -X builds a phylogenetic tree.


3.5 Real-time fluorescence quantitative expression analysis of EfNAC gene

RT-qPCR uses Primer 5.0 to design its primers, and use the Primer-BLAST function on NCBI to evaluate the quality of the primers. The internal reference gene used the 25S primer sequence designed by Que et al. (2009) (Table 4). The FastKing one-step method was used to generate cDNA, and the cDNA was used for fluorescence quantitative PCR with EvaGreen 2×qPCR MasterMix produced by abm. The reaction system is as shown in (Table 5). Set 3 replicates for each sample, and take the average of the results.



Table 4 Premer of RT-PCR



Table 5 Gene real time fluorescence quantitative RT-PCR reaction system


Authors’ contributions

Gu Shujie and Shen Xianyue were the experiment designers and the executives of the experiment and completed the writing of the first draft of the paper; Qian Zhenfeng, Zeng Dan, Ma Hao, and Di Yining participated in the analysis of the experiment results; He Lilian and Li Fusheng were the project designers, and the person in charge, guide experiment design, data analysis, thesis writing and revision. All authors read and approved the final manuscript.



This research was co-funded by the National Natural Science Foundation of China (31960451, 31560417), a sub-project of the National Key Research and Development Program (2018YFD1000503), and the Key Project of the Applied Basic Research Program of Yunnan Province (2015FA024)).



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