Plastid, the chloroplast and photosynthesis

1 Introduction

1.1 Plastid, the chloroplast and photosynthesis

On earth, plant and algae are photoautotrophic organisms that have the ability to fix light energy and convert it into chemical energy. This process called photosynthesis, is a fundamental basis of energy’s flow through life, food chains and energy pyramids. Photosynthesis occurs entirely within the chloroplast. As the most noticeable organelle in plants and green algae cells, it serves as an ‘energy factory’

for supporting the activities of most living organisms on earth.

Plant chloroplasts originated from a cyanobacterial ancestor, through an endosymbiotic process (Raven and Allen, 2003; Yagi and Shiina, 2014). Chloroplasts belong to a family of plant organelles called the plastid, which represents a variety of inter-convertible forms depending on the differentiation of the respective cell type (Figure 1-1). Most of the distinct plastids are derived from undifferentiated proplastids which are found in meristematic and undifferentiated cells. Each meristematic cell contains around 10 to 20 of such proplastids (Pyke and Leech, 1992). Proplastids are colorless and vary in size between 0.2 and 1 μm. When seedlings are grown without any light, proplastids differentiate into etioplasts, containing an undeveloped internal membrane system with semicrystalline structures called the prolamellar body. Upon illumination, the etioplast can develop into a functional chloroplast carrying stacks of membranes – the thylakoids, where most of the photosynthetic protein complexes are situated. In comparison to chloroplasts, all other plastids are non-photosynthetic while still representing important sites for the biosynthesis of metabolites like starch, fatty acids and amino acids in a broad range of plant tissues (Neuhaus and Emes, 2000). One such kind of plastid, the amyloplasts, can be found in root cells where it serves as a storage compartment of starch granules. Besides roots, cells of the storage tissues such as endosperm, tubers and cotyledons also contain amyloplasts.

In addition to amyloplasts, elaioplasts represent another form of colorless plastids and are specialized in storing lipids as observed in the cells of oilseeds. Moreover, organs, such as flowers and fruits, possess chromoplasts with relatively high levels of carotenoids thus give rise to the red, orange, and yellow colors. Among all types of plastids, chloroplasts are the only photosynthetically active plastids and thus are a

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prerequisite for plant growth and development. In all subsequent sections the focus will be on the chloroplast.

Figure 1-1: Diversity of plastid types. Plastids can differentiate into several forms, depending on their function in the cell. The functions of respective plastids were indicated as bulleted items or lists.

All types of plastids derive from the undifferentiated proplastids present in meristematic cells.

Etioplasts, the predecessors of chloroplasts, are formed when grown in the dark. The figure was adopted and modified from Lopez-Juez and Pyke (2005).

1.1.1 Structure and function of the chloroplast

Chloroplasts make the most prominent components of the mesophyll cells in leaf tissue of higher plants. Depending on the species, their number varies from dozens to over hundred per mesophyll cell. Each chloroplast comprises three different membranes, the double membraned envelope and the inner-most thylakoid membrane, which enclose three distinct soluble compartments (intermembrane space, stroma and thylakoid lumen). The outer and inner membrane of the envelope form the boundary to delimit the territory of a chloroplast. It builds the supporting frame for the translocon components, the TRANSLOCON AT THE OUTER

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ENVELOPE MEMBRANE OF CHLOROPLASTS (TOC) and TRANSLOCON AT THE INNER ENVELOPE MEMBRANE OF CHLOROPLASTS (TIC) proteins, which establish pores or channels in the membrane to allow the passage of essential nucleus-encoded proteins (Li and Chiu, 2010). The internal membrane thylakoids are organized in two patterns, either forming grana which are stacks of thylakoid discs in a cylinder shape or appearing as individual lamellae in the stroma as a connector between the thylakoids. Thylakoids are sites of the light-dependent reactions of photosynthesis. The core photosynthesis related proteins or protein complexes are located at distinct locations of the thylakoids, which termed as ‘lateral heterogeneity’

(Jensen and Leister, 2014). PHOTOSYSTEM II (PS II) and LIGHT-HARVESTING COMPLEX II (LHC II) are limited to the grana membranes. On the contrary, PHOTOSYSTEM I (PS I) and its LIGHT-HARVESTING COMPLEX I (LHC I) as well as the ATP SYNTHASE are exclusively concentrated in the stroma lamellae. The CYTOCHROME B6F complex is present in both types of the thylakoids. The space between thylakoids is occupied by the stroma, where carbon fixation takes place.

Apart from these structural features, chloroplasts possess their own heritable information, called plastome, which is organized into complex structures, the nucleoids. On average, each nucleoid consists of 10 to 20 copies of the chloroplast genome and further RNA and various proteins (Sakai et al., 2004; Krupinska et al., 2013).

Besides photosynthesis, chloroplasts fulfill a major role in metabolism. This includes among others starch synthesis, nitrogen assimilation and fatty acid biosynthesis (Neuhaus and Emes, 2000). Moreover, it serves as a source of retrograde signaling, which is referring to the process of signaling from organelles (chloroplast and mitochondria) to modulate nuclear gene expression.

1.1.2 The chloroplast genome

Since it was demonstrated during the 1960s that chloroplasts contain their own DNA (Chun et al., 1963; Sager and Ishida, 1963), extensive studies with respect to the chloroplast genome, the plastome, established the area of ‘chloroplast molecular biology’. The first physical map of chloroplast DNA was constructed for maize in 1976 (Bedbrook and Bogorad, 1976), Later on, complete chloroplast genomes were sequenced for tobacco (Shinozaki et al., 1986), liverwort (Ohyama et al., 1986), and

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subsequently for rice (Hiratsuka et al., 1989) and other species (http://chloroplast.cbio.psu.edu/). To date, the sequence of the full chloroplast genome of a total of 746 eukaryotic photosynthetic organisms have been determined according to the NCBI Organelle Genome Resources Database (As of April 16, 2015.

http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=2759&opt=plastid).

The genome size of almost all chloroplast DNAs is within the range of 120 Kbp and 160 Kbp (Palmer, 1985; Sugiura, 1992). Normally, the chloroplast genome of higher plants, organized in a circular molecule, harbors a large single-copy (LSC) and a small single-copy region (SSC) that are separated by a large inverted repeat (IR) with a size of between 6 and 76 Kbp (Palmer, 1985; Chumley et al., 2006; Guisinger et al., 2011). Exceptions can be found in species such as pea, broad bean, alfalfa and pine, whose chloroplast DNAs do not possess the IR structure (Sugiura, 1992). It was suggested that one segment of the IR, present in the common ancestor of land plants, was lost in some legumes and conifers during evolution (Sugiura, 1992).

Chloroplast genomes, on average, contain 120 genes. These genes can be further classified into two main functional groups: one clade for the maintenance and expression of the organelle’s own genes, including ribosomal RNA (rRNA) genes, transfer-RNA (tRNA) genes, ribosomal protein genes, translation factors and RNA polymerase subunits genes. The other clade contains photosynthesis associated genes, which consist of ribulose-1,5-bisphosphate carboxylase (RuBisCO) subunit gene(s), PS II genes, PS I genes, cytochrome b6f complex genes, ATP synthase gene and nicotinamide dehydrogenase (ndh) genes (Sugiura, 1992). The majority of these genes are arranged in operons and transcribed as polycistronic precursor molecules that are subjected to splicing and nucleolytic cleavage in order to produce mature and translatable mRNAs (Stern et al., 2010; Wicke et al., 2011). For instance, the chloroplast genome of barley cv. Morex (NC_008951) contains 113 unique genes, among which, 78 are encoding proteins and 37 encode tRNAs or rRNAs (Saski et al., 2007). Taken advantage of differential RNA sequencing (dRNA-seq) (Sharma et al., 2010), transcriptome analysis of the barley chloroplast in green and white leaves of the barley mutant ‘albostrians’ revealed that among the 113 chloroplast genes, eighty-nine were arranged in 20 polycistronic operons, while the remaining 24 genes were transcribed monocistronically (Zhelyazkova et al., 2012).

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