Transient kinetic analysis of L-serine interaction with Escherichia coli D-3-phosphoglycerate dehydrogenase containing amino acid mutations in the hinge regions

Comparative Transcriptome Analysis of Differentially Expressed Genes in the Testis and Ovary of Sea Urchin (Strongylocentrotus intermedius)

The quality of sea urchin gonad is important to consumers with high standards for nutrition and taste. However, few studies have been conductedon the molecular mechanisms that determine the quality of male and female sea urchins. In this study, our goal was to understand the differences and characteristics of gonad quality between sea urchin (Strongylocentrotus intermedius) males and females. The transcriptomes of males and females were obtained, with totals of 43,797,146 and 56,222,782 raw reads, respectively, comprising 128,979 transcripts and 85,745 unigenes. After comparative transcriptome analysis, a total of 6736 differentially expressed genes (DEGs) between the males and females were identified, of which 2950 genes were up-regulated and 3786 genes were down-regulated in males. We compared the expression of twelve DEGs with significant differences their expression levels and functional annotations to confirm the reliability of the RNA-Seq data. Five DEGs related to gonadal quality were found through enrichment analysis of KEGG pathways: 17β-HSD8, PGDH, FAXDC2, C4MO, and PNPLA7. Our study analyzes genes related to the taste and flavor of sea urchin gonads among the sexes and provides reference sequences and fundamental information concerning the nutrition and taste of S. intermedius gonads.

D-3-Phosphoglycerate Dehydrogenase

l-Serine is the immediate precursor of d-serine, a major agonist of the N-methyl-d-aspartate (NMDA) receptor. l-Serine is a pivotal amino acid since it serves as a precursor to a large number of essential metabolites besides d-serine. In all non-photosynthetic organisms, including mammals, a major source of l-serine is the phosphorylated pathway of l-serine biosynthesis. The pathway consists of three enzymes, d-3-phosphoglycerate dehydrogenase (PGDH), phosphoserine amino transferase (PSAT), and l-phosphoserine phosphatase (PSP). PGDH catalyzes the first step in the pathway by converting d-3-phosphoglycerate (PGA), an intermediate in glycolysis, to phosphohydroxypyruvate (PHP) concomitant with the reduction of NAD⁺. In some, but not all organisms, the catalytic activity of PGDH can be regulated by feedback inhibition by l-serine. Three types of PGDH can be distinguished based on their domain structure. Type III PGDHs contain only a nucleotide binding and substrate binding domain. Type II PGDHs contain an additional regulatory domain (ACT domain), and Type I PGDHs contain a fourth domain, termed the ASB domain. There is no consistent pattern of domain content that correlates with organism type, and even when additional domains are present, they are not always functional. PGDH deficiency results in metabolic defects of the nervous system whose systems range from microcephaly at birth, seizures, and psychomotor retardation. Although deficiency of any of the pathway enzymes have similar outcomes, PGDH deficiency is predominant. Dietary or intravenous supplementation with l-serine is effective in controlling seizures but has little effect on psychomotor development. An increase in PGDH levels, due to overexpression, is also associated with a wide array of cancers. In culture, PGDH is required for tumor cell proliferation, but extracellular l-serine is not able to support cell proliferation. This has led to the hypothesis that the pathway is performing some function related to tumor growth other than supplying l-serine. The most well-studied PGDHs are bacterial, primarily from Escherichia coli and Mycobacterium tuberculosis, perhaps because they have been of most interest mechanistically. However, the relatively recent association of PGDH with neuronal defects and human cancers has provoked renewed interest in human PGDH.

Contrasting catalytic and allosteric mechanisms for phosphoglycerate dehydrogenases

D-3-Phosphoglycerate dehydrogenases (PGDH) exist with at least three different structural motifs and the enzymes from different species display distinctly different mechanisms. In many species, particularly bacteria, the catalytic activity is regulated allosterically through binding of l-serine to a distinct structural domain, termed the ACT domain. Some species, such as Mycobacterium tuberculosis, contain an additional domain, called the "allosteric substrate binding" or ASB domain, that functions as a co-domain in the regulation of catalytic activity. That is, both substrate and effector function synergistically in the regulation of activity to give the enzyme some interesting properties that may have physiological relevance for the persistent state of tuberculosis. Both enzymes function through a V-type regulatory mechanism and, in the Escherichia coli enzyme, it has been demonstrated that this results from a dead-end complex that decreases the concentration of active species rather than a decrease in the velocity of the active species. This review compares and contrasts what we know about these enzymes and provides additional insight into their mechanism of allosteric regulation.