Because of the overwhelming complexity of cell wall polymers in terms of their chemical compositions, linkages and structures, plant biomass formation and microbial degradation involve a surprisingly large num­ber of genes in plant and microbes, respectively. For example, presumably every different glycosidic bond in the polysaccharides will be formed using a different enzyme. It is estimated that ~ 10% of genes in Arabidopsis genome are involved in cell wall synthesis and modifi­cation (Yong et al., 2005), which account for ~2000 genes encoding enzymes for sugar and lignin precursor synthesis, polysaccharide and lignin synthesis and modification, lignin-polysaccharide cross-linking, tran­scription factors (TFs)and signaling proteins, etc.

The most important enzymes are clearly those involved in polysaccharide synthesis and lignin synthe­sis. To form polysaccharides, glycosyltransferases (GTs) take the activated sugar donors, nucleoside diphosphate sugars (NDP-sugars), as the substrates to build glyco — sidic bonds between two sugars. Except for celluloses, other cell wall polysaccharides are mostly synthesized in Golgi apparatus, where GTs, NDP-sugar biosynthetic enzymes and sugar transporters are located and work together. Glycoside hydrolases (GHs), on the other hand, are used to break glycosidic bonds through hydro­lysis reactions to release sugars from polysaccharides. In plants this is often used to modify existing polysaccha­rides, e. g. when plant cells are growing, while in mi­crobes GHs are the most critical enzymes degrading plant biomass. Clearly not all GH and GT enzymes are involved in cell wall polysaccharide metabolism, as many of them are involved in metabolism of storage polysaccharides, glycoproteins, glycolipids and other glycol-conjugates that are not relevant to plant cell walls.

All GT and GH enzymes are categorized by the CAZy (Carbohydrate Active enZyme) database (CAZyDB) (Cantarel et al., 2009), which provides a general classifi­cation scheme for all carbohydrate active enzymes (CAZymes) and is widely accepted by the carbohydrate research community. So far there are a limited number of enzymes biochemically or genetically characterized to be involved in plant cell wall synthesis or modification, many of which belong to some large GH and GT fam­ilies. For example, the GT2 family is known to include cellulose synthases and some hemicellulose backbone synthases (Lerouxel et al., 2006), such as mannan syn­thases (Dhugga et al., 2004; Liepman et al., 2005), puta­tive xyloglucan synthases (Cocuron et al., 2007), and mixed linkage glucan synthases (Burton et al., 2006). With respect to the synthesis of xylan, the most abun­dant hemicellulose, proteins of GT43, GT47 and GT8 are likely to be involved (Zhong et al., 2005; Brown et al., 2007; Lee et al., 2007; Pena et al., 2007; Persson et al., 2007; York and O’Neill, 2008; Brown et al., 2009; Wu et al., 2009).

Some of these known cell wall-related CAZyme fam­ilies are included in Purdue’s Cell Wall genomics data­base (Yong et al., 2005) and UC-Riverside’s (UCR) Cell Wall Navigator database (Girke et al., 2004), and more families are discussed in the literature or to be character­ized in terms of their roles in biomass-related polysac­charide formation and degradation. For example, a few recent papers (Scheller and Ulvskov, 2010; Driouich et al., 2012) and a book (Ulvskov, 2011) updated our knowledge about the GT family members involved in cell wall synthesis: GT2, 8, 31, 34, 37, 43, 47, 61, 64, 75, 77, while there must be more GT families not included and to be identified as cell wall related (CWR), e. g. GT92 (Liwanag et al., 2012).

Lignins are complex heterogeneous polymers with lots of aromatic rings. The monolignol synthesis pathway that starts from phenylalanine to synthesize G, S and H units has been relatively well known, with about 10 gene families characterized encoding most of the enzymes in the pathway (Humphreys and Chapple, 2002; Boerjan et al., 2003; Vanholme et al., 2008; Xu et al., 2009; Zhong and Ye, 2009; Li and Chapple, 2010; Weng and Chapple, 2010; Carpita, 2012). All these lignin synthesis-related enzymes have been extensively reviewed in the literature and are included in Purdue’s Cell Wall genomics database. Transporting the units to the outside of the cell and assembling them into lignin polymers are less understood but some candidate trans­porters and two major enzyme families, peroxidase and laccase, are suggested (McCaig et al., 2005; Liu et al., 2011; Zhang et al., 2011; Alejandro et al., 2012; Carpita, 2012; Handford et al., 2012; Sibout and Hofte, 2012).

As with all other metabolic pathways, biomass forma­tion and degradation are also under strict regulation. However, compared to enzymatic activities, regulatory mechanism is even more difficult to elucidate. In plants, only a handful of TFs are known to regulate cell wall synthesis. The most studied process is the regulation of lignin biosynthesis (Zhong and Ye, 2009; Zhong et al., 2010; Zhao and Dixon, 2011; Wang and Dixon,

2012) . TF families NAC, WRKY, and MYB among a few others have been shown to directly or indirectly con­trol the monolignol synthesis. Some of the TF family members are global regulators that regulate the entire secondary cell wall synthesis, including the synthesis of celluloses and xylans, suggesting that the different biopolymers in biomass are not synthesized indepen­dently but in a coordinated way. On the other hand, genetically modifying the regulation of cell wall biosyn­thesis represents a very promising way to improve the desired traits of bioenergy crops. For example, Wang et al. showed that a mutation found in a WRKY TF could rewire the regulatory network of secondary cell wall synthesis and improve 50% of the biomass production in Arabidopsis (Wang et al., 2010). Similarly, micro ribo­nucleic acids (miRNAs) are also excellent targets for controlling the regulation of cell wall synthesis (Fu et al., 2012), which is less discussed in the literature. Clearly looking for novel transcription regulators, either TFs and miRNAs, and further building the regulatory network of cell wall synthesis is the ultimate goal for the elucidation of the mechanism of biomass formation.

Recently a few plant journals published special issues on plant cell wall researches: Plant Physiology (McCann and Rose, 2010), Current Opinion in Plant Biology (Pauly and Keegstra, 2008b), Frontiers in Plant Science (Debolt and Estevez, 2012) and Molecular Plant (has a cell wall biology category). Particularly, a number of review articles published in these special issues and a few book chapters (Table 6.1) gave overviews of latest progress in a specific area of cell wall research and are very useful for pointing to the original research papers reporting the characterization of specific CWR genes.

In terms of degradation, cell wall polysaccharides are degraded by microbial GHs and other CAZymes that are defined and categorized in CAZyDB. Lignins are mostly degraded by microbes too particularly by certain fungi (Dashtban et al., 2009). Enzymes involved in the degradation include fungal laccases and peroxidases, which are categorized in the FOLy (fungal oxidative enzymes) database (Levasseur et al., 2008). Note that these two families are not restricted to fungi. Instead they both belong to large protein families having many homologs in various organisms such as plants, animals and bacteria, bearing slightly different biochemical activities (Welinder, 1992). As mentioned above, these enzyme families are also used for lignin polymerization

in plants. There is also increasing evidence to show that such enzymes are also used for lignin degradation in bacteria (Claus, 2003; Li et al., 2009; Bugg et al., 2011a, 2011b).

Notably many cell wall biosynthesis-related gene families are also rooted in bacteria (Royo et al., 2000; Nobles and Brown, 2004; Emiliani et al., 2009; Yin et al., 2009; Weng and Chapple, 2010; Yin et al., 2010, 2011; Popper et al., 2011). In other words, although car­bohydrate and lignin-rich plant cell walls are almost unique to plants, the biosynthetic machinery has evolved from ancient gene families that were already present in early prokaryotes. On the degradation side, microbes are responsible for breaking down biomass, while plants also contain homologs of many microbial degrading enzymes such GHs and peroxidases. Obvi­ously plants also inherited these enzymes for different purposes: modify existing polysaccharide or complete the lignification process.

Similarly, less is known about the regulation of enzymes for the polysaccharide and lignin degradation in microbes than the enzymes themselves. As opposed to plants, microbes involved in biomass degradation are more taxonomically distributed spanning from eukaryotic fungi (e. g. Neurospora crassa) to prokaryotic bacteria (Clostridium thermocellum). As a result, the regu­lation systems in these divergent organisms are often not very conserved, e. g. many of the TFs found in fungi are not present in bacteria and vice versa. Furthermore, there are numerous model microbes used for bioenergy research and the transcription regulators regulating cellulases, hemicellulases or ligninases are highly dispersed in the literature, e. g. (Aro et al., 2005; Portnoy et al., 2011; Coradetti et al., 2012; Sun et al., 2012). All these make the curation and annotation of the regulators and targeting cis elements to be very difficult. Recently, global gene expression data (e. g. microarray) and other omics data have been generated to help study the regu­lation of biomass degradation (Nataf et al., 2010; Raman et al., 2011; Riederer et al., 2011; Yang et al., 2012), which represents the future trend of understanding biofuel production at the systems biology level. Similar to regu­lators for cell wall synthesis, there is a lack of web-based bioinformatics databases to include the regulatory genes for bioenergy-related degradation enzymes.