Genome-wide identification and multiple abiotic stress transcript profiling of potassium transport gene homologs in Sorghum bicolor

Abstract

Potassium (K⁺) is the most abundant cation that plays a crucial role in various cellular processes in plants. Plants have developed an efficient mechanism for the acquisition of K⁺ when grown in K⁺ deficient or saline soils. A total of 47 K⁺ transport gene homologs (27 HAKs, 4 HKTs, 2 KEAs, 9 AKTs, 2 KATs, 2 TPCs, and 1 VDPC) have been identified in Sorghum bicolor. Of 47 homologs, 33 were identified as K⁺ transporters and the remaining 14 as K⁺ channels. Chromosome 2 has been found as the hotspot of K⁺ transporters with 9 genes. Phylogenetic analysis revealed the conservation of sorghum K⁺ transport genes akin to Oryza sativa. Analysis of regulatory elements indicates the key roles that K⁺ transport genes play under different biotic and abiotic stress conditions. Digital expression data of different developmental stages disclosed that expressions were higher in milk, flowering, and tillering stages. Expression levels of the genes SbHAK27 and SbKEA2 were higher during milk, SbHAK17, SbHAK11, SbHAK18, and SbHAK7 during flowering, SbHAK18, SbHAK10, and 23 other gene expressions were elevated during tillering inferring the important role that K⁺ transport genes play during plant growth and development. Differential transcript expression was observed in different tissues like root, stem, and leaf under abiotic stresses such as salt, drought, heat, and cold stresses. Collectively, the in-depth genome-wide analysis and differential transcript profiling of K⁺ transport genes elucidate their role in ion homeostasis and stress tolerance mechanisms.

Keywords: HAK/KT/KUP; K+ channels; K+ transporters; KEA; Sorghum; Trk/HKT.

FIGURE 1

Characterization of K⁺ transporter gene homologs. Exons are represented as red boxes and introns as black lines. Sb, Sorghum bicolor; HAK, high affinity potassium; KEA, K⁺ efflux antiporter; VDPC, voltage-dependent potassium channel; TPC, two-pore channels.

FIGURE 2

Conserved motif analysis of K⁺ transporter (HAK, HKT, and KEA) and channel (AKT, KAT, VDPC, and TPC) proteins. The consensus motif GVVYGDLGTSPLY was identified in all the HAK transporters except HAK5, HAK12, and HAK22. The motifs, VEMEDFSSAQLLVLTLLM, FSVFTTVSTFSNCGFLPTNE, GEKLVNALFMAVNSRHAGE, and LSTLASAILVLYVLMMYLP were observed in all the sorghum HKT transport proteins. The KEA family displayed FFMTVGMSIDPKLLJREWP and KAFPNVKIFVRAKDLDH motifs. All the channel proteins displayed the motif YWSITTLTTVGYGDLHAENP. Sb, Sorghum bicolor; HAK, high affinity potassium; KEA, K⁺ efflux antiporter; VDPC, voltage-dependent potassium channel; TPC, two-pore channels.

FIGURE 3

Conserved putative cis-acting elements of sorghum K⁺ transport gene homologs. DRE, dehydration-responsive elements; CRT, low-temperature responsive element; CCAAT, promoter of heat shock protein; MYB, responsive to drought and ABA; MYC, response to drought, cold and ABA; LTRE, low temperature and cold-responsive; CBFHV, dehydration-responsive element; IBOX, light regulation; WBOX, transcriptional repressor ERF3 gene; ABRE, early responsive to dehydration; WRKY, transcriptional repressor of the gibberellin; DPBF, ABA; AAR1, cytokinin-regulated transcription factor; GARE, gibberellic acid-responsive elements.

FIGURE 4

Structural analysis of 47 modeled sorghum K⁺ transport proteins. Sb, Sorghum bicolor; HAK, high affinity potassium; KEA, K⁺ efflux antiporter; VDPC, voltage-dependent potassium channel; TPC, two-pore channels.

FIGURE 5

String analysis of sorghum K⁺ transport homologs. All the proteins displayed the interacting partners except SbHAK15 and SbVDPC1. Sb, Sorghum bicolor; HAK, high affinity potassium; KEA, K⁺ efflux antiporter; VDPC, voltage-dependent potassium channel; TPC, two-pore channels.

FIGURE 6

Phylogenetic tree of K⁺ transport proteins between Sorghum bicolor (Sb), Oryza sativa (Os), and Arabidopsis thaliana (At). Predicted amino acid sequences were used for construction of the tree. The tree was constructed by the Neighbor Joining method using MEGA-X. Values indicate the number of times (as a percentage) that each branch topology was found during bootstrap analysis. Sb, Sorghum bicolor; HAK, high affinity potassium; KEA, K⁺ efflux antiporter; VDPC, voltage-dependent potassium channel; TPC, two-pore channels.

FIGURE 7

Physical mapping of sorghum K⁺ transport gene homologs. The 9 paralog gene pairs are represented in blue color. Of the 9 paralogs, 8 have been identified as segmental (SbHAK24 and SbHKT4, SbHAK6 and SbHAK13, SbHAK7 and SbKEA1, SbHAK18 and SbHAK20, SbHAK21 and SbKAT2, SbHKT2 and SbHKT3, SbAKT7 and SbAKT9, and SbAKT8 and SbAKT5) represented as lines and 1 as regional (SbHAK3 and SbHAK26) represented as box. Sb, Sorghum bicolor; HAK, high affinity potassium; KEA, K⁺ efflux antiporter; VDPC, voltage-dependent potassium channel; TPC, two-pore channels.

FIGURE 8

Synteny analysis of K⁺ transporter genes in Sorghum bicolor and Oryza sativa. The map was built with TB tools software. Sb, Sorghum bicolor; Os, Oryza sativa; HAK, high affinity K⁺; KEA, K⁺ efflux antiporter; VDPC, voltage-dependent K⁺ channel; TPC, two-pore channels.

FIGURE 9

Digital expression profile of sorghum K⁺ transport genes in different tissues, developmental stages under cold and drought stresses (A) K⁺ transport in anatomical tissues, (B) K⁺ transport in developmental stages, (C) K⁺ transport gene expressions under cold and drought stresses. Sb, Sorghum bicolor; HAK, high affinity potassium; KEA, K⁺ efflux antiporter; VDPC, voltage-dependent potassium channel; TPC, two-pore channels.

FIGURE 10

Relative expression analysis of sorghum K⁺ transporter gene homologs. Sorghum transporter expressions during salt, drought, heat, and cold stresses. Relative expression of transporters is shown during different stress conditions compared to its corresponding controls. Values represent the expression levels obtained after normalizing against control tissues. All samples were analyzed in triplicate, in two independent experiments. Names on the vertical axis indicate the tissues and the horizontal axis represents various genes. R, root; S, stem; L, leaf; S, salt; D. drought; H, heat; C, cold. Each color represents the relative expression levels of the transcripts. Sb, Sorghum bicolor; HAK, high affinity potassium; KEA, K⁺ efflux antiporter; VDPC, voltage-dependent potassium channel; TPC, two-pore channels.