Figure 1. Xylose metabolism (A) and catabolite repression (B) of the xylose operon in Tetragenococcus halophilus. The xylose metabolic pathway consists of a transporter, an isomerase, and a kinase, encoded by xylE, xylA and xylB, respectively. The product of this pathway, xyulose phosphate, then feeds directly into the pentose phosphoketolase (PK) pathway. Expression of the xyl operon is mediated by positive (+) and negative (—) regulation. During active growth on glucose, the glycolytic metabolite fructose-1,6-bisphosphate (FBP) accumulates inside the cell. FBP then activates the enzyme HPr kinase, leading to the phosphorylation of the phosphotransferase protein HPr at a specific serine residue. HPr(Ser)-P then forms a complex with another protein called Catabolite-control protein A (CcpA). This complex, along with FDP, binds to a DNA sequence called catabolite repression element (CRE) located upstream of the promoter region of the xylose operon, preventing its transcription (indicated by the negative sign). In the absence of glucose (and its metabolites), CcpA repression is lifted. In addition, a xylose repressor that is expressed during growth on glucose binds to a putative operator region positioned near the xyl promoter, further repressing transcription. However, when xylose is present and glucose is absent, xylose can bind directly to the repressor, causing its release from the operator and allowing the operon to be transcribed (+). Adapted from Abe and Higuchi, 1998 and Takeda et al., 1998.

Box 12—2. Reducing the Dark Color in Soy Sauce (Continued)

catabolite repression mutants were subsequently isolated that fermented xylose concurrently with glucose. Biochemical analyses revealed that the mutant strain was defective in glucose transport. Specifically, the mannose phosphotransferase system (PTS), which is primarily responsible for glucose transport in this strain, was found to be non-functional. Thus, if a product or component of the mannose PTS is necessary for catabolite repression (as is the case for other Gram positive bacteria), then a non-functional PTS would result in the xylose-fermenting pheno-type these researchers observed.

Indeed, detailed analysis of the xylose operon revealed that catabolite repression of the xylose pathway was mediated, in part, by the phosphorylated form of the PTS protein HPr.Thus, repression required an intact PTS, which would explain why a PTS mutant would be de-repressed for xylose use. Furthermore, these researchers also identified an xylR gene, encoding a xylose repressor, whose expression (and effectiveness as a repressor) was activated by glucose-6-phosphate (Figure 1).


Abe, K., and K. Uchida. 1989. Correlation between depression of catabolite control of xylose metabolism and a defect in the phosphoenolpyruvate:mannose phosphotransferase system in Pediococcus halophilus.J. Bacteriol. 171:1793-1800. Kitamoto, N., S.Yoshino,M. Ito,T. Kimura, K. Ohmiya, and N.Tsukagoshi. 1998. Repression of the expression of genes encoding xylanolytic enzymes in Aspergillus oryzae by introduction of multiple copies of the xynFl promoter.Appl.Microbiol. Biotechnol. 50:558-563. Kitamoto, N., S.Yoshino, K. Ohmiya, and N.Tsukagoshi. 1999. Sequence analysis, overexpression, and antisense inhibition of a p-xylosidase gene, xylA, from Aspergillus oryzae KBN616.Appl. Environ. Micro-biol. 65:20-24.

Takeda,Y., K.Takase, I.Yamoto, and K.Abe. 1998. Sequencing and characterization of the xyl operon of a Gram-positive bacterium, Tetragenococcus halophila.Appl. Environ.Microbiol. 64:2513-2519.

ago, Japan is the leading producer and consumer, with per capita consumption at about 5 Kg per person per year or 14 g/day. Miso has a flavor similar to soy sauce, except instead of being a liquid, it is paste-like, with a texture like that of a thick peanut butter. It can be used like soy sauce as a seasoning or flavoring agent, but is more commonly used, at least in Japan, to make soups and broths. Similar products are produced in Korea (doenjang), China (jang), Indonesia (taoco), and the Philippines (taosi).

In Japan, there are three general types of miso Each is based mainly on composition, specifically the raw ingredients used to make the miso koji (Table 12-6). Rice miso is made using a rice koji, barley miso is made using a

Table 12.6. Types and properties of different types of miso1.


Moisture (%)

Protein (%)

Reducing sugar (%)

Fat (%)



Rice miso

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