Genome-Wide Investigation and Expression Analysis of the Catalase Gene Family in Oat Plants (Avena sativa L.)

Abstract

Through the degradation of reactive oxygen species (ROS), different antioxidant enzymes, such as catalase (CAT), defend organisms against oxidative stress. These enzymes are crucial to numerous biological functions, like plant development and defense against several biotic and abiotic stresses. However, despite the major economic importance of Avena sativa around the globe, little is known about the CAT gene's structure and organization in this crop. Thus, a genome-wide investigation of the CAT gene family in oat plants has been carried out to characterize the potential roles of those genes under different stressors. Bioinformatic approaches were used in this study to predict the AvCAT gene's structure, secondary and tertiary protein structures, physicochemical properties, phylogenetic tree, and expression profiling under diverse developmental and biological conditions. A local Saudi oat variety (AlShinen) was used in this work. Here, ten AvCAT genes that belong to three groups (Groups I-III) were identified. All identified CATs harbor the two conserved domains (pfam00199 and pfam06628), a heme-binding domain, and a catalase activity motif. Moreover, identified AvCAT proteins were located in different compartments in the cell, such as the peroxisome, mitochondrion, and cytoplasm. By analyzing their promoters, different cis-elements were identified as being related to plant development, maturation, and response to different environmental stresses. Gene expression analysis revealed that three different AvCAT genes belonging to three different subgroups showed noticeable modifications in response to various stresses, such as mannitol, salt, and ABA. As far as we know, this is the first report describing the genome-wide analysis of the oat catalase gene family, and these data will help further study the roles of catalase genes during stress responses, leading to crop improvement.

Keywords: Avena sativa L.; antioxidant enzymes; bioinformatic analysis; catalase; cis-elements regulators; oxidative stress.

Figure 1

Bioinformatic analysis of AvCAT genes/proteins visualized by Tbtools. (A) A phylogenetic tree produced by MEGA 11 shows the phylogenetic relationship between the identified genes. (B) Identification of conserved catalase domains (catalase-like superfamily and catalase-related superfamily) present in AvCAT proteins as revealed by CDD online tool. (C) Representation of conserved motifs of AvCAT proteins as revealed by MEME server. (D) AvCAT gene’s structure. The abscissa in B, C, and D represent the length of the different proteins or genes. The blue rectangle in D represents the CDS of the genes, and the green boxes represent the UTR regions.

Figure 2

The phylogenetic tree of catalase proteins identified in different species: A. sativa L. (AVESA.00001b.r3.1Dg0003456.1; AVESA.00001b.r3.4Ag0002488.4; AVESA.00001b.r3.4Cg0001036.2; AVESA.00001b.r3.7Dg0000025.2; AVESA.00001b.r3.7Dg0002783.2; AVESA.00001b.r3.7Dg0002783.1; AVESA.00001b.r3.6Cg0000037.1; AVESA.00001b.r3.2Dg0000518.1; AVESA.00001b.r3.1Ag0002627.3; AVESA.00001b.r3.6Cg0001322.3); T. turgidum ssp durum (WDD45561.1; VAI41949.1; VAI53367.1; VAI53366.1; VAI10245.1; VAI53365.1); O. sativa ssp japonica (OsCATA: XP_015625395; OsCATB: XP_015643077; OsCATC: Q10S82.1; OsCATD XP_015636098.1), A. thaliana (AtCAT1: AAQ56816.1; AtCAT2: AAL66998.1; AtCAT3: NP_564120.1), N. plumbaginifolia (NpCAT1: P49315.1; NpCAT2: P49316.1; NpCAT3: P49317.1), and T. aestivum (TaCAT1-B: TraesCS4B02G325800; TaCAT1-D: TraesCS4D02G322700; TaCAT1-A: TraesCS5A02G498000; TaCAT2-A: TraesCS6A02G04170; TaCAT2-B: TraesCS6B02G056800; TaCAT2-D: TraesCS6D02G048300; TaCAT3-A1: TraesCS7A02G549800; TaCAT3-A2: TraesCS7A02G549900; TaCAT3-B: TraesCS7B02G473400; TaCAT3-U: TraesCSU02G105300) was constructed with test maximum likelihood with 1000 bootstraps by MEGA 11.

Figure 3

Chromosome localization of AvCAT genes. Prediction of AvCAT genes chromosomal localization in A. sativa genome using MG2C v2.0 online tool. The classification was based on their groups I, II, and III. Gene IDs are colored in blue, pink, and green, respectively.

Figure 4

The predicted 3D structures of AvCAT were built using the SWISS-MODEL web server, and prediction of the binding pocket of catalase protein in Avena sativa was generated by the CASTp 3.0 online tool. Pockets were visualized from the largest to the smallest pocket with pink, purple, and green colors, respectively.

Figure 5

Prediction of subcellular localization of AvCAT proteins using Wolf PSORT online server and visualization via Tbtools software v1.123.

Figure 6

Go ontology prediction of catalase proteins of A. sativa plant realized by PANNZER2 webtool.

Figure 7

Frequency of the cis-elements in AvCAT promoters as revealed by Plantcare.

Figure 8

RT-qPCR expression analysis of AvCAT genes under normal conditions. AvCAT gene expression of groups 1 (A), 2 (B), and 3 (C) was analyzed under normal conditions using tissues from roots, leaves, and stems.

Figure 9

RT-qPCR expression analysis of AvCAT2, AvCAT4, and AvCAT8 genes under heat (A–C) and cold (D–F) stress conditions and using tissues from roots, leaves, and stems. ** Indicates values significantly different from the control. Statistical significance was assessed by applying the Student’s t-test at p < 0.05.

Figure 10

RT-qPCR expression analysis of AvCAT2 (A), AvCAT4 (B), and AvCAT8 (C) genes under ABA stress treatment in different tissues isolated from roots, leaves, and stems. ** Indicates values significantly different from the control. Statistical significance was assessed by applying the Student’s t-test at p < 0.05.