The regression method was used to assess coregulatory networks of genes for cellulose biosynthesis in Arabidopsis. The notion that three CESA subunits are required to assemble into a functional CESA complex implies coexpression of the corresponding genes. Analysis of the levels of mRNA for the known CESA genes in barley was consistent with this idea (). Indeed, the genes for the three CESA subunits involved in primary and secondary cell wall cellulose biosynthesis were highly coexpressed over the 408 microarray data sets analyzed here. Additionally, genes such as COBRA and CTL1, which have previously been implicated in cellulose synthesis by genetic analysis, were highly coexpressed with CESA1, 3, and 6. Similarly, the COBRA homolog COBL4, which has been implicated in cellulose synthesis in rice (), was highly coregulated with CESA4, 7, and 8. A CTL1 homolog (At3g16920) was found here to be highly coexpressed with CESA4, 7, and 8, and disruption of the gene caused an FTIR phenotype indicative of alterations in the cell wall composition. Several other pairs of homologous genes are also present in Tables and (i.e., several ADP-glucose pyrophosphorylases and glycosyltransferases). Thus, it appears that the two types of CESA complexes have specialized homologs of other proteins that are involved in synthesis and assembly of the cell wall.
Depending on the purpose, engineering strategies can be subdivided into different categories. One goal of EPS production engineering is an increased volumetric productivity to cost-effectively produce the various EPS. These studies were mostly aiming at increasing the pool of sugar nucleotides (i.e., EPS precursors) to enhance the carbon flux toward the final polymer. In particular genes of precursor biosynthesis were overexpressed. This strategy was demonstrated to be successful for some EPS producers, but failed in some cases (; ; ; ; ). Additionally, in some cases the overexpression of genes involved in the EPS assembly (e.g., GTs, Wzx, Wzy) resulted in enhanced yields and precursor conversion rates while in other cases it had a negative effect presumably due to distorting the multidomain protein complex involved in polymerization and secretion (). These approaches included overexpression of single genes as well as whole gene clusters (; ; ). Additionally the targeted engineering of regulatory proteins could increase productivity by increasing transcription of the operons, which encode the EPS biosynthesis proteins. Furthermore, the disruption of pathways competing for precursors used for EPS formation did also increase the productivity (; ). Single gene knock-outs were also described to enhance yield as well as to alter the chemical structure of the EPS (; ). Unfortunately, the titer of bacterial polysaccharides is limited in the production because the highly viscous polysaccharides have a massive negative influence on mass transfer (). However, the strategy to enhance productivity based on genetic engineering might be interesting for EPS with reduced viscosifying properties, for example due to lower molecular weight. The optimization of manufacturing process parameters might be more promising than engineering EPS biosynthesis for many established industrial EPS producers. The highest titers of highly viscous EPS such as xanthan are around 30–50 g/L (; ) and represent the current maximum amount, which is manageable by existing bioprocess units.
Pathways and genes involved in cellulose biosynthesis
For WcaB and WcaF a high similarity with the family of acetyltransferases is observed, but no precise role of WcaB or WcaF in acetylation process or explanation for presence of two acetyltrasnferases is given up to now (Figure ). The Wzx protein was identified within the CA gene cluster by its typical transmembrane segments and the large periplasmic loop. WcaD is predicted to span the inner membrane with nine transmembrane segments, and to polymerize the repeat units of CA (), therefore representing the Wzy polymerase. The OPX protein involved in the secretion process in concert with the PCP proteins is encoded by wza and can be categorized as OPX group A protein, which can functionally replace its homolog in K30 biosynthesis pathway (; ). Wzc forms the typical contiguous molecular scaffold that spans the cell envelope together with Wza and belongs to the PCP-2a family. The Wzb protein represents the protein tyrosine phosphatase, which controls the phosphorylation state of Wzc, the corresponding tyrosine kinase. The detailed regulatory interactions between Wzb and Wzc were recently characterized for the first time (). Several characterization and mutation experiments were performed for the K30 analog of Wza and Wzc, giving further insights into mechanism and structure (; ; ; ).
De novo transcriptome sequence and identification of …
The 40 most highly ranked genes for CESA4, 7, and 8 are listed in . CESA4, 7, and 8 were among the top ranked candidates, confirming tight coregulation of the three CESA subunits. Interestingly, both the COBRA homolog, COBL4, and a CTL1 homolog (At3g216920) are ranked among the 10 most highly coexpressed genes for CESA 4, 7, and 8 (). The presence of a number of lignin-related genes in (i.e., laccases and phenylalanine ammonia lyase) is consistent with the fact that lignin synthesis is associated with the final stages of secondary wall synthesis in vascular tissues. Overall, 16 of the top 40 proteins in are known to be involved in, or are good candidates for, cell wall synthesis or modification (i.e., glycosyltransferases, arabinogalactan proteins, epimerases, polygalacturonases, laccases, and glycoside hydrolases), and 10 have no functional annotation. Of the remaining proteins on the list, none can be excluded as having a role in cellulose synthesis.
Pathways associated with lignin biosynthesis in ..
Several pathways differed significantly in coregulation for the CESA complexes (e.g., brassinosteroid, dTDP-rhamnose, and lignin biosynthesis pathways). A connection between brassinosteroids and the cell wall matrix was previously suggested by a reduction of transcription of KORRIGAN observed in det2, a mutant deficient in brassinosteroid synthesis (). In addition, brassinosteroids modulate the transcript levels of cell wall-related genes involved in cell elongation and morphogenesis (). Because secondary wall synthesis takes place when cell expansion has ceased, it makes sense that expression of the CESA4, 7, and 8 genes are not linked to brassinosteroid synthesis. Lignin deposition, however, is largely associated with secondary wall formation (). Genes encoding lignin monomer-polymerizing laccases and lignin monomer synthesis are among the 50 most closely coexpressed genes for CESA 4, 7, and 8 (). In addition, genes linked to the lignin-related pathway for suberin synthesis are highly coexpressed with CESA4, 7, and 8 (Tables 5 and 6).