Abstract
Lysine is one of the most limiting essential amino acids for humans and livestock. The nutritional value of maize (Zea mays L.) is reduced by its poor lysine content. To better understand the lysine biosynthesis pathway in maize seed, we conducted a genome-wide analysis of the genes involved in lysine biosynthesis. We identified lysine biosynthesis pathway genes (LBPGs) and investigated whether a diaminopimelate pathway variant exists in maize. We analyzed two genes encoding the key enzyme dihydrodipicolinate synthase, and determined that they contribute differently to lysine synthesis during maize seed development. A coexpression network of LBPGs was constructed using RNA-sequencing data from 21 developmental stages of B73 maize seed. We found a large set of genes encoding ribosomal proteins, elongation factors and zein proteins that were coexpressed with LBPGs. The coexpressed genes were enriched in cellular metabolism terms and protein related terms. A phylogenetic analysis of the LBPGs from different plant species revealed different relationships. Additionally, six transcription factor (TF) families containing 13 TFs were identified as the Hub TFs of the LBPGs modules. Several expression quantitative trait loci of LBPGs were also identified. Our results should help to elucidate the lysine biosynthesis pathway network in maize seed.
Highlights
Lysine cannot be synthesized in the body and must be obtained from food, and it is one of the most limiting essential amino acids for human and livestock
To identify lysine biosynthesis pathway genes (LBPGs) in maize, the annotation of the maize lysine biosynthesis pathway on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways was used, and a BLASTP algorithm-based search was performed in Phytozome 9.0 using the maize genome [17,50]
Using the Phytozome functional annotations, we identified 15 LBPGs: three genes encode aspartate kinase (AK) (EC: 2.7.2.4), one gene encodes an aspartate-semialdehyde dehydrogenase (ASD, Enzyme Commission (EC): 1.2.1.11), two genes encode Dihydrodipicolinate synthase (DHDPS) (EC: 4.3.3.7), two genes encode DapB (EC: 1.17.1.8), three genes encode LL-days after pollination (DAP)-AT (EC: 2.6.1.83), two genes encode DapF (EC: 5.1.1.7), and two genes encode LysA (EC: 4.1.1.20) (Table 1)
Summary
Lysine cannot be synthesized in the body and must be obtained from food, and it is one of the most limiting essential amino acids for human and livestock. Lysine is highly limited in cereal grains [1].The poor lysine content of maize (Zea mays L.), one of the most important cereal crops, greatly reduces its nutritional value to monogastric animals [2]. Two different lysine biosynthesis pathways occur in nature. One is via α-aminoadipate which exists in fungi and Euglena [3]. The other is the diaminopimelate pathway which exists in bacteria, plants, and archaea [4]. Diaminopimelate pathway belongs to the aspartate family pathway in which aspartate kinase (AK) is the first enzyme that catalyzes aspartate phosphorylation to form aspartate-β-semialdehydea [5].
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