Plant Genome Organization and Structure : Chloroplast Genome Organization
Introduction

Analysis of Genomes by Reassociation Experiments

Repeated Sequences

Organization of Single-copy Sequences

Evolution of Repeated Sequences in Cereals

Estimating the Number of Expressed Genes

Chloroplast Genome Organization

Mitochondrial Genome Organization

RNA Editing

Course Topics

Course Home Page

Chloroplast Genome Organization

All angiosperms and land plants have cpDNAs which range in size from 120-160 kb; three expceptions are:

Species Size (kb)
N. accuminati
171
Duckweed
180
Geranium
217

All cpDNA molecules are circular and spinach is used as the basis for all comparisons. Very few repeat elements are found other than short sequences of less than 100 bp. The notable exception is a large (10-76 kb) inverted repeat section, which when present, always contains the rRNA genes. (Legumes such as pea do not contain this repeat.) For the majority of species, this repeat region is 22-26 kb in size. Finally,the genetic order of the ribosomal unit is conserved in all species:

16S - tRNAile - tRNAala - 23S - 5S

Recent research has also described two other features of chloroplast DNA. First it was shown to that it can exist in in two orientations This implies that the molecule can undergo an isomerization event. Second is has been shown that spinach, corn, tomato and pea can all exist as multimers (PNAS 86:4156, June 1989).

Multimer Relative Abundance Percent
Monomer
1
67.5
Dimer
1/3
22.5
Trimer
1/9
7.5
Tetramer
1/27
2.5

Because photosysnthesis is the primary function of the chloroplast it is not surprising that the chlroplast genome contains genes which encode for proteins that are involved in that process.

Reaction Function
Dark Reactions rbcS (nuclear encoded)
rbcL (chloroplast encoded)
Light Reactions apoproteins for PSI andPSII
cytochrome b6
cytochrome f
6 of 9 ATPase subunits
cab, LHC proteins (nuclear encoded)
plastocyanin (nuclear encoded)
ferredoxin (nuclear encoded)
Other 19/60 ribosome binding proteins
translation factors
RNA polymerase subunits
tRNA and rRNA genes

Atrazine resistance is apparantley mediated through the psbA gene sequences of the 32 kd protein which is encoded by cpDNA. DNA sequence analysis revealed the following amino acid changes that are thought to be important.

Species AA# Susceptible Resistant
Blue green algae
264
Ser (TCG)
Ala (GCG)
Chlamydomonas
264
Ser (TCT)
Ala (GCT)
Solanum nigrum
264
Ser (AGT)
Gly (GGT)
Amaranthus
228
Ser (AGT)
Gly (GGT)

Evolutionary Changes of cpDNA

  1. The majority of changes are small insertions and deletions of 1-106bp; significantly, a few length mutations of 50-1200 bp are clusted in "hot spots".
  2. The largest deletion occured in pea where an entire rRNA cluster is lost.
  3. The most common evolutionary change is in gene order. Small changes in the gene order occur, especially in the algae, but inversions have generated large scale order changes:
    • legumes - about 50 kb inversion brought rbcL closer to psbA
    • wheat - about 25 kb inversion brought atpA closer to rbcL
Copyright © 1998. Phillip McClean