Identification and characterization of the TCA cycle genes in maize

Abstract

BackgroundThe tricarboxylic acid (TCA) cycle is crucial for cellular energy metabolism and carbon skeleton supply. However, the detailed functions of the maize TCA cycle genes remain unclear.ResultsIn this study, 91 TCA genes were identified in maize by a homology search, and they were distributed on 10 chromosomes and 1 contig. Phylogenetic results showed that almost all maize TCA genes could be classified into eight major clades according to their enzyme families. Sequence alignment revealed that several genes in the same subunit shared high protein sequence similarity. The results of cis-acting element analysis suggested that several TCA genes might be involved in signal transduction and plant growth. Expression profile analysis showed that many maize TCA cycle genes were expressed in specific tissues, and replicate genes always shared similar expression patterns. Moreover, qPCR analysis revealed that some TCA genes were highly expressed in the anthers at the microspore meiosis phase. In addition, we predicted the potential interaction networks among the maize TCA genes. Next, we cloned five TCA genes located on different TCA enzyme complexes, Zm00001d008244 (isocitrate dehydrogenase, IDH), Zm00001d017258 (succinyl-CoA synthetase, SCoAL), Zm00001d025258 (α-ketoglutarate dehydrogenase, αKGDH), Zm00001d027558 (aconitase, ACO) and Zm00001d044042 (malate dehydrogenase, MDH). Confocal observation showed that their protein products were mainly localized to the mitochondria; however, Zm00001d025258 and Zm00001d027558 were also distributed in the nucleus, and Zm00001d017258 and Zm00001d044042 were also located in other unknown positions in the cytoplasm. Through the bimolecular fluorescent complimentary (BiFC) method, it was determined that Zm00001d027558 and Zm00001d044042 could form homologous dimers, and both homologous dimers were mainly distributed in the mitochondria. However, no heterodimers were detected between these five genes. Finally, Arabidopsis lines overexpressing the above five genes were constructed, and those transgenic lines exhibited altered primary root length, salt tolerance, and fertility.ConclusionSequence compositions, duplication patterns, phylogenetic relationships, cis-elements, expression patterns, and interaction networks were investigated for all maize TCA cycle genes. Five maize TCA genes were overexpressed in Arabidopsis, and they could alter primary root length, salt tolerance, and fertility. In conclusion, our findings may help to reveal the molecular function of the TCA genes in maize.

Genome-Wide Investigation and Expression Profiling Under Abiotic Stresses of a Soybean Unknown Function (DUF21) and Cystathionine-β-Synthase (CBS) Domain-Containing Protein Family

“…Multiple elements were identified, and the stress and hormone signaling-related sites are shown in Table 2 . The table describes information pertaining to functions, such as elements in response to hormones, including abscisic acid (ABRE, CE1, and MRE) (Narusaka et al 2003 ), salicylic acid (TCA element) (Liu et al 2020 ), ethylene (ERE) (Song et al 2019 ), gibberellin acid (GARE-motif, P-box and TATC-box) (Zhang et al 2017 ), auxin (TGA-element) (Xin et al 2016 ), MeJA (CGTCA-motif and TGACG-motif) (Yu et al 2018 ), temperature-responsive elements (HSE and LTR) (Wu et al . 2019 ), drought-inducible elements (MBS) (Xu et al 2019 ), wound-responsive element (WUN-motif), defense and stress element (TC-rich repeats) (Li et al 2019 ), salt-inducible element (GT1-motif), anaerobic induction element (ARE), and light- and nitrogen-inducible element (GATA-motif) (Brenna and Talora 2019 ).…”

Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake

“…Studies suggests that histones are subject to numerous covalent modifications and these modifications control many aspects of chromatin function including histone mediated gene expression [ 40 , 41 ]. Increase in abundance of ribosomal proteins has been reported in maize seminal roots during drought [ 42 ] and the TCA cycle generate cellular energy metabolism and carbon skeleton supply for root development [ 43 ], likely contributed to the enhanced water uptake observed in MR.…”

“…These ribosomal proteins are associated with cell cycle regulation, replication recombination, and repair but were significantly down-regulated in LR. Taken together, the increase in abundance of histones and ribosomal proteins in MR supported the enhanced water uptake in MR possibly by modifying proteins abundance that promotes cell wall reorganization and increased root wall permeability, to allowed for more water acquisition [ 41 – 43 ].…”

Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum

“…In a previous study, we preliminarily identified the members of tomato TCA cycle [ 17 ]. The individual genes of each enzyme complex of the TCA cycle in tomato have been functionally analyzed.…”