Expression of the chloroplast genome: Modern concepts and experimental approaches

  • M. G. Siniauskaya
  • N. G. Danilenko
  • N. V. Lukhanina
  • A. M. Shymkevich
  • O. G. Davydenko
Article
  • 29 Downloads

Abstract

A unique feature of plants is the presence of two extra-nuclear genomes of chloroplasts and mitochondria. The chloroplast (cp) genome is relatively small and contains only 100–120 genes, which encode less than 5% of all proteins required for plastid to function. Expression of the cpDNA retains certain prokaryotic features, such as gene cotranscription within the operon, bacteria-like RNA polymerases and promoters, and 70S ribosomes. However, eukaryotic features also appear in this process, such as the uncoupling of transcription and translation, the involvement of phage-type RNA polymerases, RNA editing, and splicing of the primary transcripts. The interaction between the nucleus (nuclear genome) and cytoplasm (plastid and mitochondrial genomes) during plant development is necessary for proper development and adaptation to the environment. The aim of this review is to disclose the peculiarities of plastid genome expression. The way how the genetic information in chloroplasts is used (transcription, editing, splicing, polyadenylation, and translation) is consequently described. Furthermore, the importance of all expression machinery components in plant life is discussed. Modern approaches for RNA pool studies are described, and the critical points of the nuclear-cytoplasmic interactions in the chloroplast function are revealed. Information about the most important factors of nuclear-cytoplasmic signaling in higher plants (sigma factors and PPR proteins encoded by the nucleus) are reviewed. Thus, the multilevelness and viability of regulating the plastid genome expression in plant cells and the interdependence of the processes in different compartments is proved. A summary of the latest studies of the expression of plastid genome using genetic chips (microarrays and macroarrays) is described. The original results are presented.

Keywords

сhloroplast plastids expression transcription RNA polymerases editing splicing translation microarray macroarray 

Abbreviations

cpDNA

chloroplast DNA

PEP

plastid—encoded plastid RNA polymerase

NEP

nuclear-encoded plastid RNA polymerase

PSI

photosystem I

PSII

photosystem II

dRNA-seq

differential RNA sequencing

σ-factor

sigma factor

SIG1-SIG6

sigma factors of arabidopsis

cpCK2

chloroplast casein kinase 2

UTR

untranslated region of the transcript

ncRNAs

non-coding RNA

PNPase

polynucleotide phosphorylase

RNase

ribonuclease

IR

inverted repeat

PPR proteins

proteins with pentatricopeptide repeats

TPR proteins

proteins with tetratrico peptide repeat

MORF

multiple sites organellar RNA editing factors

CRM protein

Chloroplast RNA splicing and ribosome maturation protein

SD

Shine-Dalgarno sequence

qRT-PCR

PCR in real time

RT-PCR

polymerase chain reaction after reverse transcription

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Copyright information

© Pleiades Publishing, Ltd. 2016

Authors and Affiliations

  • M. G. Siniauskaya
    • 1
  • N. G. Danilenko
    • 1
  • N. V. Lukhanina
    • 1
  • A. M. Shymkevich
    • 1
  • O. G. Davydenko
    • 1
  1. 1.Institute of Genetics and CytologyNational Academy of Sciences of Belarus (IGC NASB)MinskBelarus

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