Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L

Abstract

Background: The filamentous temperature-sensitive H protease (ftsH) gene family plays an important role in plant growth and development. FtsH proteins belong to the AAA protease family. Studies have shown that it is a key gene for plant chloroplast development and photosynthesis regulation. In addition, the ftsH gene is also involved in plant response to stress. At present, the research and analysis of the ftsH gene family are conducted in microorganisms such as Escherichia coli and Oenococcus and various plants such as Arabidopsis, pear, rice, and corn. However, analysis reports on ftsH genes from tobacco (Nicotiana tabacum L.), an important model plant, are still lacking. Since ftsH genes regulate plant growth and development, it has become necessary to systematically study this gene in an economically important plant like tobacco.

Results: This is the first study to analyze the ftsH gene from Nicotiana tabacum L. K326 (NtftsH). We identified 20 ftsH genes from the whole genome sequence, renamed them according to their chromosomal locations, and divided them into eight subfamilies. These 20 NtftsH genes were unevenly distributed across the 24 chromosomes. We found four pairs of fragment duplications. We further investigated the collinearity between these genes and related genes in five other species. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis identified differential expression patterns of NtftsH in different tissues and under various abiotic stress conditions.

Conclusions: This study provides a comprehensive analysis of the NtftsH gene family. The exon-intron structure and motif composition are highly similar in NtftsH genes that belong to the same evolutionary tree branch. Homology analysis and phylogenetic comparison of ftsH genes from several different plants provide valuable clues for studying the evolutionary characteristics of NtftsH genes. The NtftsH genes play important roles in plant growth and development, revealed by their expression levels in different tissues as well as under different stress conditions. Gene expression and phylogenetic analyses will provide the basis for the functional analysis of NtftsH genes. These results provide a valuable resource for a better understanding of the biological role of the ftsH genes in the tobacco plant.

Keywords: Abiotic stress; FtsH family; Gene expression patterns.

Fig. 1

The rootless phylogenetic tree was constructed based on the gene sequences of ftsH from Arabidopsis, tobacco, and rice; each arc represents a group (a total of 8 groups). The circles represent the AtftsH gene, the rectangles represent the NtftsH gene, and the triangles represent the ftsH gene from the rice plant. ftsH: filamentous temperature-sensitive H

Fig. 2

Phylogenetic relationships, gene structure analysis, and motif distributions of Nicotiana tabacum L. ftsH. ftsH: filamentous temperature-sensitive H. A Phylogenetic tree constructed by the neighbour-joining method, with 1000 replicates on each node. B Exons and introns are indicated by yellow rectangles, and black lines, respectively. C Conserved domain of ftsH gene. D Amino acid motifs in the ftsH proteins (1–10) are represented by coloured boxes. Black lines indicate relative protein lengths

Fig. 3

Schematic diagram of the chromosomal distribution and segmental duplication of the NtftsH genes. Grey lines represent all colinear blocks in the tobacco genome, and red lines represent duplicated ftsH gene pairs

Fig. 4

Analysis of the 2000 bp upstream cis-acting element of NtftsH gene, Diferent colors represent diferent types of cis-acting elements

Fig. 5

Syntenic analysis of ftsH genes between tobacco and five representative plant species. Gray lines in the background indicate the collinear blocks within the tobacco and other plant genomes, while the blue lines highlight the syntenic ftsH gene pairs

Fig. 6

GO annotation analysis of 20 ftsH genes from tobacco; Green represents a molecular function, bright blue represents a cellular component, and orange represents a biological process

Fig. 7

Expression patterns of nine NtftsH genes in different tissues of the tobacco plant; Expression patterns of 9 Nicotiana tabacum L. ftsH in the calyx, petal, anther, stigma, leaf, stem, fruit, and root organs, as examined by qRT-PCR. Error bars represent standard error. Lowercase letters above bars indicate a significant difference (P < 0.05, least significant difference test) among the treatments. ftsH: filamentous temperature-sensitive H; qRT-PCR: Real-time quantitative PCR

Fig. 8

Expression of 3 Nicotiana tabacum L. ftsH in plants subjected to abiotic stresses (NaCl, strong light, PEG6000, UV, 38 °C, 4 °C, and hormones (100 μmol/L IAA, SA, GA3)) at the seedling stage. ftsH: filamentous temperature-sensitive H; qRT-PCR: Real-time quantitative PCR. Expression patterns of 3 NtftsH in root, stem, and leaf organs were examined by qRT-PCR. Error bars represent standard error. Lowercase letters above bars indicate a significant difference (P < 0.05, LSD) among the treatments