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We also found an upregulation of pyridoxalphosphate biosynthesis which is consistent with an increased amino acid biosynthesis.
In RP-deficient zebrafish, we found activation of both nucleotide catabolism and biosynthesis, which is consistent with the need to break and replace the faulty ribosomal RNA.
Other ULs with high transcript frequencies in spores of G. clavigera encoded proteins involved in energy metabolism and protein biosynthesis, which is consistent with respiration and protein biosynthesis activated early in germination [ 30].
It was perhaps not surprising to find that two of the main pathways affected within the lipid metabolism category were LC-PUFA and steroid biosynthesis, which is consistent with previous studies (Leaver et al., 2008).
Most notably, we observed enrichment for animal-essential amino acid biosynthesis, which is consistent with its location in the gut and its host nematode's likely primary diet of phloem, which is generally depleted in amino acids.
F5H mutants had increased expression of MYB4, a negative regulator of chalcone synthase, thus reducing flavonoid biosynthesis which is consistent with the reduced levels of flavonoids detected in cultivated lettuce in the present investigation.
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This finding suggests a functional enrichment of BY-kinase regions in capsular biosynthesis proteins, which is consistent with the initial definition of BY-kinases as a component of the polysaccharide biosynthesis pathway.
TDC therefore could be considered as the rate-limiting reaction of the serotonin biosynthesis pathway which is consistent with several previous studies (Kang, Kim et al. 2009); (Ishihara, Hashimoto et al. 2008b); (Kanjanaphachoat, Wei et al. 2012).
The reduction in gene content is partly due to a drastic decrease in genes coding for cell wall-degrading enzymes (carbohydrate-active enzymes; CAZys) and secondary metabolite biosynthesis enzymes, which is consistent with their parasitic obligate biotrophic lifestyle.
In KRAP−/−-liver, the down-regulated genes were strongly associated with GO terms such as "cholesterol biosynthesis" and "lipid biosynthesis" (Table S4), which is consistent with the lower triglyceride contents in KRAP−/−-liver (Figure 1G).
Among the DBM-induced MYB transcription factors, only MYB34/ATR1 has previously been characterized as a positive regulator of indole glucosinolate biosynthesis [ 41], which is consistent with results that most of its target genes were up-regulated by DBM feeding.
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