22/12/2017 · What Is a Biosynthesis Pathway
FIGURE 158 Biosynthesis of histidine in bacteria and plants. Atomsderived from PRPP and ATP are shaded red and blue, respectively. Two of thehistidine nitrogens are derived from glutamine and glutamate (green). Note thatthe derivative of ATP remaining after step 5 (AICAR) is an intermediate inpurine biosynthesis, so ATP is rapidly regenerated.
Candida albicans lysine biosynthesis - Pathway Tools …
The amino acid sequences of candidate LBPGs for maize and other species were obtained from the lysine biosynthesis pathway annotation of KEGG PATHWAY (). The LBPGs were selected based on the functional annotations and Enzyme Commission (EC) annotations in Phytozome 9.0 () or when the KEGG amino acid sequence had 100% identity to the sequence in Phytozome. LBPG gene IDs were obtained by using the BLASTP algorithm to search Phytozome 9.0 with the corresponding genomes of each species. For each lysine biosynthesis enzyme, the phylogenetic trees were constructed with the full-length protein sequences of Zea may (v5b), Sorghum bicolor (v2.0), Setaria italica (v2.0), Oryza sativa (v7.0), Brachypodium distachyon (v2.0), Arabidopsis thaliana (TAIR10), Medicago truncatula (Mt4.0v1), Populus trichocarpa (v3.0), Solanum lycopersicum (v2.3), Selaginella moellendorffii (v1.0), Physcomitrella patens (v3.0) and Chlamydomonas reinhardtii (v5.0) using MEGA5  by the neighbor-joining method with 500 bootstrap replicates.
The actions of Akt in the cell are numerous and diverse, but all result in anti-apoptosis, or pro-cell proliferation effects. These physiological roles of Akt include involvement in metabolism, protein synthesis, apoptosis pathways, transcription factor regulation and the cell cycle. Akt exerts its effects in the cell by phosphorylating a variety of downstream substrates. The downstream targets of Akt include BAD (BCL2 Antagonist of Cell Death), Caspase9, FKHR (Forkhead Transcriptional Factor), GLUTs (Glucose Transporters), eNOS (Nitric Oxide Synthase), PFK2 (6-Phosphofructo-2-Kinase), PFK1(6-Phosphofructo-Kinase), mTOR (Mammalian Target of Rapamycin), IKK (I-KappaB Kinase), NF-KappaB (Nuclear Factor-KappaB), GSK3 (Glycogen Synthase Kinase-3), WNK1(WNK Lysine deficient Protein Kinase-1), PRAS40 (Proline-Rich Akt Substrate 40 kDa), p47Phox, YAP (Yes-Associated Protein-1), Htt (Huntingtin), Ataxin, AR (Androgen Receptor), ASK1 (Apoptosis Signal-Regulating Kinase-1), MDM2 (Mouse Double Minute-2), CREB (cAMP Response Element-Binding Protein), p21CIP1 (Cyclin Dependent Kinase Inhibitor-p21), p27KIP1 (Cyclin Dependent Kinase Inhibitor-p27) , Chk1 (Cell Cycle Checkpoint Kinase-1), XIAP (X-Linked Inhibitor of Apoptosis Protein), Raf1 (v-Raf1 Murine Leukemia Viral Oncogene Homolog-1), PDE3B (Phosphodiesterase 3B cGMP-Inhibited), TSC (Tuberous Sclerosis Gene) and GABA(A)R (Gamma-Aminobutyric Acid Receptor-A) (Ref.4).
LYSINE: Uses, Side Effects, Interactions and Warnings - …
To identify LBPGs in maize, the annotation of the maize lysine biosynthesis pathway on KEGG pathways was used, and a BLASTP algorithm-based search was performed in Phytozome 9.0 using the maize genome [,]. Using the Phytozome functional annotations, we identified 15 LBPGs: three genes encode AK (EC: 22.214.171.124), one gene encodes an aspartate-semialdehyde dehydrogenase (ASD, EC: 126.96.36.199), two genes encode DHDPS (EC: 188.8.131.52), two genes encode DapB (EC: 184.108.40.206), three genes encode LL-DAP-AT (EC: 220.127.116.11), two genes encode DapF (EC: 18.104.22.168), and two genes encode LysA (EC: 22.214.171.124) (). These enzymes are all found in the diaminopimelate variant pathway identified in Arabidopsis . The homolog genes of DapD, DapC, DapE and Ddh which participate in other diaminopimelate variant pathways were not found, indicating that the pathway of Lysine biosynthesis is conserved between Zea mays and Arabidopsis.
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In this study, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Phytozome databases, we identified LBPGs and analyzed whether a diaminopimelate pathway variant exists in maize. We also explored the LBPGs phylogenetic relationships. Additionally, to reveal the lysine biosynthesis network during maize seed development, we constructed a coexpression network of LBPGs using publicly available RNA-Seq data from 21 developmental stages of B73 maize seed. We also analyzed differences between two DHDPS encoding genes, DHDPS1 and DHDPS2, and their coexpressed genes, and found that DHDPS1 and DHDPS2 play different roles in lysine biosynthesis in maize seed. Furthermore, eQTL mapping was used to identify genetic variants that regulated LBPG expression. Our results should increase our knowledge of the lysine biosynthesis network in maize seed.
Amino Acid Synthesis and Metabolism
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.