Catabolic genes

Iwagami S, K Yang, J Davies (2000) Characterization of the protocatechuate acid catabolic gene cluster from Streptomyces sp. strain 2065. Appl Environ Microbiol 66 1499-1508. 

Jahnke M, E Lehmann, A Schoebel, G Auling (1993) Transposition of the TOL catabolic genes Tn46521 into the degradative plasmid pSAH of Alcaligenes sp. 0-1 ensures simultaneous mineralization of sulpho-and methyl-substituted aromatics. J Gen Microbiol 139 1959-1966. 

Stuart-Keil KG, AM Hohnstock, KP Drees, JB Herrick, EL Madsen (1998) Plasmids responsible for horizontal transfer of naphthalene catabolism genes between bacteria at a coal tar-contaminated site are homologous to pDTGl from Pseudomonas putida NCIB 9816-4. Appl Environ Microbiol 64 3633-3640. 

Pinyakong O, H Habe, T Omori (2003) The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons. J Gen Appl Microbiol 49 1-19. 

Inoue K, H Habe, H Yamane, H Nojiri (2006) Characterization of novel carbazole catabolism genes from Gram-positive carbazole degrader Nocardioides aromaticivorans IC177. Appl Environ Microbiol 72 3321-3329. 

Armengaud J, B Happe, KN Timmis (1998) Genetic analysis of dioxin dioxygenase of Sphingomonas sp. strain RWl catabolic genes dispersed on the genome. J Bacterial 180 3954-3966. 

Widada, J. Nojiri, H. Omori,T. Recent developments in molecular techniques for identification and monitoring of xenobiotic-degrading bacteria and their catabolic genes in bioremediation. Appl. Microbiol. Biotechnol. 2002,60,45-59. 

Wilson and Madsen [152] used the metabolic pathway for bacterial naphthalene oxidation as a guide for selecting l,2-dihydroxy-l,2-dihydronaphthalene as a unique transient intermediary metabolite whose presence in samples from a contaminated field site would indicate active in situ naphthalene biodegradation (Fig. 26). Naphthalene is a component of a variety of pollutant mixtures. It is the major constituent of coal tar [345], the pure compound was commonly used as a moth repellant and insecticide [345], and it is a predominant constituent of the fraction of crude oil used to produce diesel and jet fuels [346]. Prior studies at a coal tar-contaminated field site have focused upon contaminant transport [10,347], the presence of naphthalene catabolic genes [348, 349], and non-metabolite-based in situ contaminant biodegradation [343]. 

Figure 4. Comparative detection of 4-chlorobiphenyl catabolic gene abundance by blot hybridization of pSSSO plasmid DNA probe to target DNA extracted from sediments. A B spatially separated sediments C control self hybridizations. (Units A B, ug total DNA C ng of probe DNA.)...

The naphthalene catabolic genes are located in most cases on plasmids. In this group the best-studied plasmid is NAH7 of P. putida PpG7. It carries two operons, one of which enables the utilization of naphthalene and the other salicylate. Both operons are turned on by the product of another NAH7 gene, nahR, in the presence... 

As previously discussed for the NAH plasmids, the TOL plasmids also constitute a family of related plasmids, with differences that Can be attributed to DNA rearrangements. One such rearrangement is a duplication of catabolic genes that occurs in many TOL plasmids (Osborne et al., 1993)- In P. putida R5-3 it has been shown that plasmid DNA content was altered in specific ways depending on... 

Non-catabolic genes for catabolic pathway constructions Bacterial hemoglobin... 

McClure, N. C., Weightman, A.J. Fry,J.C. (1989). Survival of Pseudomonas putida UWC1 containing cloned catabolic genes in a model activated-sludge unit. Applied and Environmental Microbiology, 55, 2627-34. 

Eaton, R.W. and J.S. Kams (1991a). Cloning and analysis of s-triazine catabolic genes from Pseudomonas spp. strain NRRLB-12227. J. Bacteriol., 173 1215-1222. 

Sajjaphan, K., N. Shapir, L.P. Wackett, M. Palmer, B. Blackmon, J. Tomkins, and MJ. Sadowsky (2004). Arthrobacter aurescens TCI atrazine catabolism genes trzN, atzB, and atzC are linked on a 160-kilobase region and are functional in Escherichia coli. Appl. Environ. Microbiol., 70(7) 4402 4407. 

All the DNA-binding proteins discussed thus far function by inhibiting transcription until some environmental condition, such as the presence of lactose, is met. There are also DNA-binding proteins that stimulate transcription. One particularly well studied example is the catabolite activator protein (CAP), which is also known as the cAMP response protein (CRP). When bound to cAMP, CAP, which also is a sequence-specific DNA-binding protein, stimulates the transcription of lactose- and arabinose-catabolizing genes. Within the lac operon, CAP binds to an inverted repeat that is centered near position -61 relative to the start site for transcription (Figure 31.10). CAP functions as a dimer of identical subunits. 

Beller H. R., Kane S. R., Legler T. C., and Alvarez P. J. J. (2002) A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene. Environ. Sci. Technol. 36(18), 3977-3984. 

When bound to cAM P, CAP stimulates the transcription of lactose- and arabinose-catabolizing genes. CAP is a sequence-specific DNA-binding protein. Within the lac operon, CAP binds to an inverted repeat that is cen tered near position —61 relative to the start site for transcription (Figure 31.15). CAP functions as a dimer of identical subunits. 

It has also been shown (Duetz et al. 1994) that cultures of P. putida grown with growth-limiting concentrations of succinate express TOL catabolic genes in both the upper and lower pathways in... 

Catabolic Gene-Activator Protein (CAP) Positively Regulates the lac Operon... 

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