Novel Gene Clusters

The proliferation of complete genome sequences in public databases provides an additional means to track the evolution of cellulose in bacteria. Conservation of operons and/or gene clusters (synteny) can be used to trace not only the history of cellulose synthase, but also its associated proteins. The existence of a few these gene clusters has been well documented. In the sections below, I would like to give a brief review of the known gene organizations and introduce two novel ones which may be linked to the eukaryotic acquisition of cellulose biosynthesis. 

Although all proteins encoded by Group I and II gene clusters are necessary for wild-type cellulose biosynthesis, only cellulose synthases have a known function.  

The cellulose synthase sequences of Arthrobacter sp. FB24 and Corynebac-terium efficiens YS-314 are divided into two open reading frames the first containing domain A (U1 and U2) and the second containing domain B (U3 and U4). There is no report of cellulose biosynthesis in these bacteria and therefore, it is unknown whether this split enzyme is functional. However, if the products of these two ORFs can combine to create a functional cellulose synthase, they would be useful tools for experiments to determine substrate binding properties and catalytic function of the conserved domains. 

Current data suggest that cellulose biosynthesis is a bacterial invention and that eukaryotes acquired the process via multiple lateral gene transfers. Bacteria and eukaryota have independently evolved regulatory mechanisms and molecular structures to utilize the p-1,4-homopolymer synthesized by the catalytic activity of homologous cellulose synthase enzymes. The differences in accessory enzymes probably reflect not only convergent evolution to produce a cellulose I crystalline allomorph, but also inventions of alternative products such as cellulose II, noncrystalline cellulose, or nematic ordered cellulose. 

Aloni Y, Delmer D.P., and Benziman M. 1982. Achievement of high rates of in vitro synthesis of 1, 4-beta-D-glucan activation by cooperative interaction of the Acetobacter xylinum enzyme system with GTP, polyethylene glycol, and a protein factor. Proc Natl Acad Sci USA 79(21) 6448-6452. Amikam D. and Benziman M. 1989. Cyclic diguanylic acid and cellulose synthesis in Agrobacterium tumefaciens. J Bacterid 171(12) 6649-6655. 

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Kwak, M.K., Wakahayashi, N., Itoh, K., Motohashi, H., Yamamoto, M., and Kensler, T.W. 2003. Modulation of gene expression hy cancer chemopreventive dithiolethiones through the Keapl-Nrf2 pathway. Identihcation of novel gene clusters for ceU survival.. 1. Biol. Chem. 278, 8135-8145. 

Azad AK, Sirakova TD, Fernandes ND, Kolattuku-dy PE (1997) Gene knockout reveals a novel gene cluster for the synthesis of a class of cell wall lipids unique to pathogenic mycobacteria. J Biol Chem... 

Koike-Takeshita, A., Koyama, T, and Ogura, K., Identification of a novel gene cluster participating in menaquinone (vitamin Kj) biosynthesis. Cloning and sequence determination of the 2-hepta-prenyl-l,4-naphthoquinone methyltransferase gene of Bacillus stearothermophilus, J. Biol Ghem., 272, 12,380, 1997. 

Recently, a novel class of type 1-like human IFNs, named 1FN-A,1 or lL-29,1FN-A.2 (1F-28A) and 1FN-X3 (1F-28B), was identified (Dumoutier et al. 2003 Sheppard et al. 2003). The three IFN-A, genes cluster on human chromosome 19 and comprise 5 exons for 1FN-A,1 and 6 for 1FN-A.2 and 1FN-A.3, and several introns (Table 1). They encode 20- to 22-kDa secreted monomeric proteins of 196 to 200 amino acids. Type 111 IFNs have also been identified in other species such as mice, birds, and fish. 

Tao, L. et al., A carotenoid synthesis gene cluster from Algoriphagus sp. KK10202C with a novel fusion-type lycopene beta-cyclase gene. Mol. Genet. Genomics 379, 101, 2006. 

Kitagawa W, N Kimura, Y Kamagata (2004) A novel p-nitrophenol degradation gene cluster from a Grampositive hact c mm Rhodococcus opacus SAOIOI. J Bacteriol 186 4894-4902. 

Particularly important to the pathways of modular synthases is the incorporation of novel precursors, including nonproteinogenic amino acids in NRP systems [17] and unique CoA thioesters in PK and fatty acid synthases [18]. These building blocks expand the primary metabolism and offer practically unlimited variability applied to natural products. Noteworthy within this context is the contiguous placement of biosynthetic genes for novel precursors within the biosynthetic gene cluster in prokaryotes. Such placement has allowed relatively facile elucidation of biosynthetic pathways and rapid discovery of novel enzyme mechanisms to create such unique building blocks. These new pathways offer a continued expansion of the enzymatic toolbox available for chemical catalysis. 

Doughty, S., Sloan, J., Bennett-Wood, V., Robertson, M., Robins-Brown, R. M., and Hartland, E. L. (2002). Identification of a novel fibrial gene cluster related to long polar fimbriae in locus of enterocyte effacement-negative strains of enterohemorrhagic Escherichia coli. Infect. Immun. 70, 6761-6769. 

H. Dodd M. Gasson M. Mayer A. Narbad, Identitying Lantibiotic Gene Clusters and Novel Lantibiotic Genes. WO 2006/111743 A2, October 26, 2006. 

N. Menendez, M. Nur-e-Alam, A. F. Brana, J. Rohr, J. A. Salas, and C. Mendez, Biosynthesis of the antitumor chromomycin A3 in Streptomyces griseus Analysis of the gene cluster and rational design of novel chromomycin analogs, Chem. Biol., 11 (2004) 21-32. 

S. L. Ward, Z. Hu, A. Schirmer, R. Reid, W. P. Revill, C. D. Reeves, O. V. Petrakovsky, S. D. Dong, and L. Katz, Chalcomycin biosynthesis gene cluster from Streptomyces bikiniensis Novel features of an unusual ketolide produced through expression of the chm polyketide synthase in Streptomyces fradiae, Antimicrob. Agents Chemother., 48 (2004) 4703-4712 and references therein. 

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