Plant Gene Expression, Regulation of

Abstract

Eukaryotic genomes are much more complex than prokaryotes and plant genomes present more complexities than other eukaryotes. The continuous process of development, absence of germ-line, flexible and reversible cellular differentiation, polyploidy, and so on, are characteristic features that distinguish plant genomes from other eukaryotes. The complexities observed in plant genomes can possibly be attributed to three major factors. Firstly, plants are nonmotile and hence exposed to various environmental conditions constantly. In the absence of any neuronal network or immunological system, plants have evolved various local and systemic mechanisms to adapt to the environment to cope with biotic and abiotic stresses. This is achieved mainly through various signaling systems of phytohormones and other metabolites and the scores of genes participating in it. Secondly, plants from various species and genera synthesize about 45 000 different natural products or secondary metabolites. The functions of many of these are unknown; however, a number of these are used in defense, as attractants and volatile signals. This involves complex metabolic pathways involving several genes that require specific regulatory mechanism for expression. Thirdly, and the most puzzling attribute that still remains to be answered satisfactorily, is the variability observed in its genome size. The genome size as such is quite variable throughout the biological world; however, plants show the greatest variation of any kingdom in the biological world. For example, angiospermic plants that do not differ much in their basic activities contain a genome varying from 7 × 104 kb/haploid (Arabidopsis) to 1 × 108 kb/haploid (Lilly). Majority of the DNA in plant genome is not transcribed and may account for up to 90% of the genome on the basis of the number of active genes. Further, DNA motifs ranging in length from single base to thousands of bases, repeated many hundreds or thousands of time, are characteristics of all eukaryotic genomes; however, plant genome may represent 50 to 90% or more of such DNA. The biological significance of this repetitive DNA is still not resolved properly. Of sequence motifs that are highly repeated, some are conserved from one species to another. Satellite DNA, minisatellite, variable-number tandem repeats (VNTR) are some of the major features of plant genome, which make them different from other eukaryotic genomes. The taxonomical usage of these sequences have added great knowledge in establishing phylogeny as well as biodiversity; however, whether they play any major role in plant gene expression and regulation is still not clear. It was in the early 1960s that the basic principles of gene regulation and its expression in prokaryotes were established. While in prokaryotes the gene regulatory elements were defined as promoters, operators, and positive control elements, unfortunately the mechanism of eukaryotic gene regulation had to wait till recombinant DNA technology was in practice in the early 1970s. High throughput sequencing of genome (genes) and development of various softwares for the analysis of these sequences made it possible to look into functional and regulatory aspects of plant genome. On the basis of the information obtained through Arabidopsis and rice genome sequencing and various ESTs (Expressed-sequence tags), plants may express 25 000 to 50 000 genes depending upon species and genera. Of these, about 30 to 35% may be expressed in all parts of the plant (constitutive), whereas others could be organ specific or event specific. The gene product may localize to a certain cell type, appear only at a specific developmental stage, or accumulate following distinct environmental stimuli. More than one inducer may turn on some genes or a single stimulus may have different effects on different genes. The existence of cross talk between different hormones, light, and environment during plant development further complicated the task of defining gene regulation of expression in plants. Fortunately, gene transfer technology and development of mutants and functional genomics have added tremendously to the knowledge of gene expression, regulation, and its function. Reverse genetics is being applied to investigate the function of candidate genes through approaches such as RNA interference (RNAi), TILLING (target induced local lesions in genome) and use of systematically generated T-DNA populations. Comparative genomic approaches, as well as functional assays using mini chromosomes, hold great promise for understanding both cis-DNA elements and the trans-protein components. In this article, we have tried to include some of the common and recent features of plant gene expression and its regulation. Though it is difficult to describe every gene regulation, the article will provide an overview of various classes of genes that are expressed in plants in general and the mechanism of their regulation. We will describe here topics like the basic mechanism of plant gene transcription and translation; hormonal and light regulation of genes; regulation of expression during biotic and abiotic stress; gene regulation during development; mitochondrial and chloroplast gene expression and regulation; and recent advances in plant gene expression and regulation. The emphasis has been given on the various DNA elements identified within and outside gene and transcription factors, which hold key to all gene expression and regulation. Keywords: Transcription; Transcript Processing; Translation; Cis-Elements and Trans-Acting Regulatory Factors; Photoreceptors; Nuclear Organelle Genome Interaction; Phytohormones; Proteasome; Abiotic and Biotic Stress Responses; MADS-Box Genes; Epigenetic Regulation of Transcription