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moving toward the unknown
Worldwide, the growing demand for energy is driving increased fossil fuel consumption and contributing to rising levels of atmospheric carbon dioxide and associated effects on global climate (Asif and Muneer 2007; Quadrelli and Peterson 2007; Solomon et al. 2009). Combined, the situation has stimulated the search for alternative sustainable sources of energy and carbon-based materials. Plant cell wall-derived lignocellulosic biomass is a promising feedstock for cellulosic ethanol, a second generation biofuel (Rubin 2008; Wyman 2007), that does not compete with food production in contrast to starch-based biofuels (Cassman and Liska 2007; Karp and Shield 2008). In secondary tissues, the plant cell wall comprises primary and secondary wall layers. A thin, elastic primary cell wall is synthesized during initial cellular expansion, typically containing cellulose, xyloglucan and pectin (Cosgrove 1997). A thick secondary cell wall is deposited on the inside of the primary cell wall after cell expansion, and has higher amounts of cellulose, heteroxylan and is impregnated with lignin (Reiter 2002). Fast-growing Populus and Eucalyptus tree species are excellent sources of lignocellulosic biomass, as their secondary cell walls are rich in cellulose comprising 39 – 48% of biomass (Carroll and Somerville 2009).
While there are many advantages to employing woody species as biomass feedstock, the recalcitrance of plant cell walls to degradation confounds efficient extraction of polysaccharides (Himmel et al. 2007; Mansfield 2009). This is mainly due to the physical interactions between major biopolymer constituents of the cell wall namely; cellulose, hemicellulose and lignin (Chang and Holtzapple 2000; Cosgrove 2005; Gilbert 2010). The genetic contribution to recalcitrance is to a large extent the result of an underlying, highly coordinated biosynthetic program comprising biosynthetic, modifying and structural proteins which are regulated by a network of transcription factors, hormones and signaling proteins, ultimately resulting in the cell wall ultrastructure (Keegstra 2010; Plomion et al. 2001; Showalter 1993; Somerville et al. 2004). Functional characterization of genes contributing to the plant cell wall ultrastructure is a prerequisite to the design of strategies for engineering customized phenotypes (Galperin and Koonin 2010; Mansfield 2009). This has been demonstrated in planta, for example, transgenic Populus targeting known lignin biosynthetic-related genes caused a shift in biomass recalcitrance (Mansfield et al. 2012; Nookaraju et al. 2013; Pilate et al. 2002). Furthermore, appropriate growth conditions can promote extensive secondary growth in the model herbaceous plant Arabidopsis (Chaffey et al. 2002), facilitating functional testing of candidate genes implicated in cell wall biology.
Despite considerable research efforts focused on cell wall development and many genes empirically validated relating to lignin biosynthetic pathways (Boerjan et al. 2003; Vanholme et al. 2012a; Vanholme et al. 2008) and polysaccharide biosynthesis (Atmodjo et al. 2013; Doering et al. 2012; Taylor 2008), it is estimated that approximately 10-15% of ~27 000 protein coding genes in the Arabidopsis genome are involved in cell wall biology (Carpita et al. 2001; McCann and Carpita 2008; Yong et al. 2005). A study by Yang et al. (2011) found 121 experimentally validated cell wall-related genes via PubMed text mining. The discrepancy between the number of genes functionally validated and those implicated in cell wall biology highlights a clear gap between what is known and what remains to be discovered. Plant bioinformatics has been applied in meta-analyses of genome-wide expression data, resulting in the identification of genes putatively involved in cell wall biology. In many of these studies, a number of implicated genes lack any functional annotation (biochemical or cellular function) and are broadly characterized as proteins of unknown function (PUFs) (Horan et al. 2008). These genes, in the context of cell wall biology referred to as cell wall-related PUFs (CW-PUFs), show similar expression patterns to known cell wall-related genes such as those encoding cellulose synthase, enzymes essential for cellulose biosynthesis (Brown et al. 2005; Mutwil et al. 2009; Persson et al. 2005; Ruprecht et al. 2011). Although these CW-PUFs may not be directly involved in cell wall biosynthesis, many could be essential for normal cell wall developmental biology. In recent years CW-PUFs have been the focus of many functional studies and have been shown to be involved in various aspects of cell wall biology (Bischoff et al. 2010a; Brown et al. 2011; Gille et al. 2011; Jensen et al. 2011; Ruprecht et al. 2011; Urbanowicz et al. 2012). These studies highlight the importance of understanding the biological roles of other CW-PUFs, and suggest aspects of the biosynthetic pathway and/or alternative pathways of wall development not yet characterized.
CHAPTER 1 Cell Wall-related Proteins of Unknown Function: Missing Links in Plant Cell Wall Development
1.1. Abstract
1.2. Introduction: moving toward the unknown
1.3.1. CW-known unknown proteins
1.4. In search of a function for CW-PUFs
1.4.1. Prioritizing CW-PUFs with genomic analyses .
1.4.2. Functional inference of CW-PUFs through transcriptomics
1.4.3. Prioritizing CW-PUFs with proteomics
1.5. Concluding remarks .
1.6. Aim of the current study
1.7. References
1.8. Figures and Tables
CHAPTER 2 Genome-Wide Characterization of Plant-Specific Domain of Unknown Function 1218 (DUF1218) Family in Arabidopsis, Eucalyptus, Populus and Oryza
2.1. Abstract
2.2. Introduction
2.3. Results and Discussion
2.4. Conclusions
2.5. Materials and Methods
2.6. References
2.7. Figures and Tables
CHAPTER 3 The Arabidopsis Domain of Unknown Function 1218 (DUF-1218) Containing Proteins, MODIFYING WALL LIGNIN-1 and 2 (At1g31720/MWL-1 and At4g19370/MWL-2) Function Redundantly to Alter Secondary Cell Wall Lignin Content
3.1. Abstract
3.3. Results
3.4. Discussion
3.5. Materials and methods
3.6. References
3.7. Figures and Tables .
CHAPTER 4 The nuclear-localized Arabidopsis Protein of Obscure Features1 (AtPOF1, At1g47410) affects secondary cell wall glucose and lignin content
4.1. Abstract
4.2. Introduction
4.3. Results
4.4. Discussion
4.5. Materials and methods
4.6. References
4.7. Figures and Tables
CHAPTER 5 Concluding Remarks
5.1. The way forward
5.2. In conclusion
5.3. References
APPENDIXES
