Transcriptome analysis of the Euglena gracilis plastid chromosome

Geimer, Simon; Belicová, Anna; Legen, Julia; Sláviková, Silvia; Herrmann, Reinhold G.; Krajčovič, Juraj

doi:10.1007/s00294-009-0256-8

Cited by 19 publications

(16 citation statements)

References 63 publications

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“…3). The E. gracilis plastid transcriptome exhibits significant quantitative changes under illumination [36]. The latter case might be detected because of the fewer copies of plastid DNA molecules in the dark in comparison to the light conditions.…”

Section: Discussionmentioning

confidence: 99%

A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis

et al. 2014

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Edited by Ulf-Ingo FlüggeKeywords: Plastid EST Euglenozoa Polyadenylation Quantitative PCR Trans-splicing a b s t r a c t Euglena gracilis possesses secondary plastids of green algal origin. In this study, E. gracilis expressed sequence tags (ESTs) derived from polyA-selected mRNA were searched and several ESTs corresponding to plastid genes were found. PCR experiments failed to detect SL sequence at the 5 0 -end of any of these transcripts, suggesting plastid origin of these polyadenylated molecules. Quantitative PCR experiments confirmed that polyadenylation of transcripts occurs in the Euglena plastids. Such transcripts have been previously observed in primary plastids of plants and algae as low-abundance intermediates of transcript degradation. Our results suggest that a similar mechanism exists in secondary plastids. Ó 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. IntroductionEuglena gracilis is a fresh-water photosynthetic flagellate belonging to the order Euglenida and to the protist phylum Euglenozoa [1,2]. This phylum includes also the orders Kinetoplastida, Diplonemida and Symbiontida [3,4], which comprise exclusively heterotrophic species. Most euglenid species are free-living heterotrophic flagellates, but some of them possess secondary plastids that arose via secondary endosymbiosis of a green alga [5]. Phylogenetic analysis of plastid genome sequences revealed that euglenid plastids are derived from a Pyramimonas-related prasinophyte alga [6].A common euglenozoan feature is the processing of primary nuclear transcripts by spliced leader (SL) RNA-mediated trans-splicing [7]. This process includes replacement of the 5 0 -end of premRNA by the 5 0 -end of SL-RNA, donating identical 5 0 -termini to the mRNA molecules. Similar to nuclear cis-splicing, trans-splicing process is also mediated by spliceosomes, but a Y-branch intron structure is formed instead of a lariat [8]. The only currently known nuclear mRNA lacking the SL sequence in E. gracilis is that of the fibrillarin gene [9]. Since SL-trans-splicing does not occur in organelles (mitochondria, plastids), the presence (or absence) of an SL sequence at the 5 0 -end of a euglenozoan mRNA is diagnostic for its synthesis in the nucleus (or organelles, respectively).E. gracilis cell possesses approximately eight secondary plastids bounded by three membranes [10,11]. The plastid genome of this species is circular and comprises 143.17 kb. It contains 96 protein and RNA gene loci [12], group II and III introns, and twintrons (i.e. introns within introns) [13].The evolutionary transition from an endosymbiont to the plastid organelle was accompanied by a loss of many genes and gene transfer from the endosymbiont genome(s) to the host genome [14]. Gene transfer from plastids and mitochondria is an ongoing process, as it has been demonstrated in animals, plants, fungi as well as protists [15,16].Nuclear copies of plastid DNA (NUPT) can be found in a variety of species [17]. However, some species, e.g. the ...

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Section: Discussionmentioning

confidence: 99%

A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis

et al. 2014

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“…While Chlamydomonas reinhardtii has only one nuclear gene encoding a sigma factor [26], land plants and the red algae, Cyanidioschyzon merolae and Cyanidium caldarium, possess several sigma factor genes ( [154,165,180], for reviews on higher plant sigma factors see [262,290,291]). It is not yet known whether the less complex organization of the transcriptional apparatus in algae (PEP alone and fewer sigma factors) is causally related to the lower degree of transcriptional regulation in algal chloroplasts versus those of higher plants [62,76]. PEP can be isolated from plastids as a soluble enzyme or an insoluble form, also known as transcriptionally active chromosome (TAC), which contains DNA, RNA, the PEP subunits, and a large number of other proteins [37,89,144,164,215,230].…”

Section: The Plastid-encoded Plastid Rna Polymerase (Pep) Is a Bactermentioning

confidence: 99%

Chloroplast Gene Expression—RNA Synthesis and Processing

Börner¹,

Zhelyazkova²,

Legen³

et al. 2014

Plastid Biology

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Both transcription and transcript processing are more complex in chloroplasts than in bacteria. Plastid genes are transcribed by a plastid-encoded RNA polymerase (PEP) and one (monocots) or two (dicots) nuclear-encoded RNA polymerase(s) (NEP). PEP is a bacterial-type multisubunit enzyme composed of core subunits (coded for by the plastid rpoA, B, C1 and C2 genes) and additional protein factors encoded in the nuclear genome. The nuclear genome of Arabidopsis contains six genes for sigma factors required by PEP for promoter recognition. NEP activity is represented by phage-type RNA polymerases. Factors supporting NEP activity have not been identified yet. NEP and PEP use different promoters. Both types of RNA polymerase are active in proplastids and all stages of chloroplast development. PEP is the dominating transcriptase in chloroplasts.Chloroplast RNA processing consists of hundreds of mostly independent events. In recent years, much progress has been made in identifying factors behind RNA splicing and RNA editing. Namely, pentatricopeptide repeat (PPR) proteins have come into focus as RNA binding proteins conferring specificity to individual processing events. Also, studies on chloroplast RNases have helped considerably to understand chloroplast RNA turnover. Such mechanistic insights are set in contrast to how little we know about the regulatory role of RNA processing in chloroplasts.Keywords Chloroplast transcription · Chloroplast RNA polymerase · Chloroplast promoter · Chloroplast RNA processing · Chloroplast RNA-binding proteins · PPR proteins · Chloroplast splicing · Chloroplast editing · Chloroplast RNA degradation · Chloroplast nucleases Abbreviations CRS2 Chloroplast RNA splicing 2 protein IR Inverted repeat NEP Nuclear-encoded plastid RNA polymerase

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“…Proplastids in dark grown cells have low levels of chloroplast rRNA (Chelm et al 1977b(Chelm et al , 1978(Chelm et al , 1979Cohen and Schiff 1976;Geimer et al 2009;Rawson et al 1981) and tRNA (Goins et al 1973;Reger et al 1970;Schwartzbach et al 1976a). The cellular content of chloroplast rRNA and chloroplast tRNA increases from approximately 5-25% of the cellular rRNA and tRNA content after 72 h of light exposure (Chelm et al 1977b(Chelm et al , 1978(Chelm et al , 1979Cohen and Schiff 1976;Rawson et al 1981;Schwartzbach et al 1976a).…”

Section: Photocontrol Of Chloroplast Developmentmentioning

confidence: 98%

Photo and Nutritional Regulation of Euglena Organelle Development

Schwartzbach

2017

Advances in Experimental Medicine and Biology

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Euglena can use light and CO, photosynthesis, as well as a large variety of organic molecules as the sole source of carbon and energy for growth. Light induces the enzymes, in this case an entire organelle, the chloroplast, that is required to use CO as the sole source of carbon and energy for growth. Ethanol, but not malate, inhibits the photoinduction of chloroplast enzymes and induces the synthesis of the glyoxylate cycle enzymes that comprise the unique metabolic pathway leading to two carbon, ethanol and acetate, assimilation. In resting, carbon starved cells, light mobilizes the degradation of the storage carbohydrate paramylum and transiently induces the mitochondrial proteins required for the aerobic metabolism of paramylum to provide the carbon and energy required for chloroplast development. Other mitochondrial proteins are degraded upon light exposure providing the amino acids required for the synthesis of light induced proteins. Changes in protein levels are due to increased and decreased rates of synthesis rather than changes in degradation rates. Changes in protein synthesis rates occur in the absence of a concomitant increase in the levels of mRNAs encoding these proteins indicative of photo and metabolic control at the translational rather than the transcriptional level. The fraction of mRNA encoding a light induced protein such as the light harvesting chlorophyll a/b binding protein of photosystem II, (LHCPII) associated with polysomes in the dark is similar to the fraction associated with polysomes in the light indicative of photoregulation at the level of translational elongation. Ethanol, a carbon source whose assimilation requires carbon source specific enzymes, the glyoxylate cycle enzymes, represses the synthesis of chloroplast enzymes uniquely required to use light and CO as the sole source of carbon and energy for growth. The catabolite sensitivity of chloroplast development provides a mechanism to prioritize carbon source utilization. Euglena uses all of its resources to develop the metabolic capacity to utilize carbon sources such as ethanol which are rarely in the environment and delays until the rare carbon source is no longer available forming the chloroplast which is required to utilize the ubiquitous carbon source, light and CO.

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Transcriptome analysis of the Euglena gracilis plastid chromosome

Cited by 19 publications

References 63 publications

A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis

A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis

Chloroplast Gene Expression—RNA Synthesis and Processing

Photo and Nutritional Regulation of Euglena Organelle Development

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