Mewalal Ritesh, Mizrachi Eshchar, Mansfield Shawn D, Myburg Alexander A
Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa.
Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
Plant Cell Physiol. 2014 Jun;55(6):1031-43. doi: 10.1093/pcp/pcu050. Epub 2014 Mar 28.
Lignocellulosic biomass is an important feedstock for the pulp and paper industry as well as emerging biofuel and biomaterial industries. However, the recalcitrance of the secondary cell wall to chemical or enzymatic degradation remains a major hurdle for efficient extraction of economically important biopolymers such as cellulose. It has been estimated that approximately 10-15% of about 27,000 protein-coding genes in the Arabidopsis genome are dedicated to cell wall development; however, only about 130 Arabidopsis genes thus far have experimental evidence validating cell wall function. While many genes have been implicated through co-expression analysis with known genes, a large number are broadly classified as proteins of unknown function (PUFs). Recently the functionality of some of these unknown proteins in cell wall development has been revealed using reverse genetic approaches. Given the large number of cell wall-related PUFs, how do we approach and subsequently prioritize the investigation of such unknown genes that may be essential to or influence plant cell wall development and structure? Here, we address the aforementioned question in two parts; we first identify the different kinds of PUFs based on known and predicted features such as protein domains. Knowledge of inherent features of PUFs may allow for functional inference and a concomitant link to biological context. Secondly, we discuss omics-based technologies and approaches that are helping identify and prioritize cell wall-related PUFs by functional association. In this way, hypothesis-driven experiments can be designed for functional elucidation of many proteins that remain missing links in our understanding of plant cell wall biosynthesis.
木质纤维素生物质是纸浆和造纸工业以及新兴生物燃料和生物材料工业的重要原料。然而，次生细胞壁对化学或酶促降解的抗性仍然是高效提取经济上重要的生物聚合物（如纤维素）的主要障碍。据估计，拟南芥基因组中约27000个蛋白质编码基因中，约10 - 15%致力于细胞壁发育；然而，迄今为止，只有约130个拟南芥基因有实验证据证实细胞壁功能。虽然许多基因通过与已知基因的共表达分析被牵连其中，但大量基因被广泛归类为功能未知蛋白（PUFs）。最近，利用反向遗传学方法揭示了其中一些未知蛋白在细胞壁发育中的功能。鉴于大量与细胞壁相关的PUFs，我们如何着手并随后对可能对植物细胞壁发育和结构至关重要或有影响的此类未知基因进行优先研究呢？在这里，我们分两部分解决上述问题；我们首先根据已知和预测的特征（如蛋白质结构域）识别不同类型的PUFs。了解PUFs的固有特征可能有助于进行功能推断，并与生物学背景建立相应联系。其次，我们讨论基于组学的技术和方法，这些技术和方法通过功能关联帮助识别与细胞壁相关的PUFs并对其进行优先排序。通过这种方式，可以设计假设驱动的实验来阐明许多在我们对植物细胞壁生物合成的理解中仍缺失环节的蛋白质的功能。
