Skip to main content

Genes encoding the photosystem II proteins are under purifying selection: an insight into the early evolution of oxygenic photosynthesis


The molecular evolution concerns coding sequences (CDSs) of genes and may affect the structure and function of proteins. Non-uniform use of synonymous codons during translation, known as codon usage bias (CUB), depends on the balance between mutations bias and natural selection. We estimated different CUB indices, i.e. the effective number of codons (ENC), G + C content in the 3rd codon positions (GC3), and codon adaptation index for CDSs of intrinsic proteins of photosystem II (PSII), such as psbA (D1), psbD (D2), psbB (CP47), psbC (CP43), and CDSs of the extrinsic protein psbO (PsbO). These genes occur in all organisms that perform oxygenic photosynthesis (OP) on Earth: cyanobacteria, algae and plants. Comparatively, a similar analysis of codon bias for CDSs of L and M subunits that constitute the core proteins of the type II reaction centre (RCII) in anoxygenic bacteria was performed. Analysis of CUB indices and determination of the number of synonymous (dS) and nonsynonymous substitutions (dN) in all analysed CDSs indicated that the crucial PSII and RCII proteins were under strong purifying (negative) selection in course of evolution. Purifying selection was also estimated for CDSs of atpA, the α subunit of ATP synthase, an enzyme that was most likely already present in the last universal common ancestor (LUCA). The data obtained point to an ancient origin of OP, even in the earliest stages of the evolution of life on Earth.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6


Download references


We also thank the anonymous reviewers for several suggestions that helped to improve the quality of the article.


This research was supported by The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences in Kraków, Poland.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Ireneusz Ślesak.

Ethics declarations

Conflict of interest

The author declares that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 958 kb)

Supplementary file2 (XLSX 12 kb)

Supplementary file3 (XLSX 42 kb)

Supplementary file4 (XLSX 41 kb)

Supplementary file5 (XLSX 12 kb)

Supplementary file6 (XLSX 40 kb)

Supplementary file7 (XLSX 43 kb)

Supplementary file8 (XLSX 12 kb)

Supplementary file9 (XLSX 36 kb)

Supplementary file10 (XLSX 39 kb)

Supplementary file11 (XLSX 13 kb)

Supplementary file12 (XLSX 35 kb)

Supplementary file13 (XLSX 36 kb)

Supplementary file14 (XLSX 12 kb)

Supplementary file15 (XLSX 39 kb)

Supplementary file16 (XLSX 40 kb)

Supplementary file17 (XLSX 12 kb)

Supplementary file18 (XLSX 14 kb)

Supplementary file19 (XLSX 14 kb)

Supplementary file20 (XLSX 12 kb)

Supplementary file21 (XLSX 14 kb)

Supplementary file22 (XLSX 14 kb)

Supplementary file23 (XLSX 12 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ślesak, I., Mazur, Z. & Ślesak, H. Genes encoding the photosystem II proteins are under purifying selection: an insight into the early evolution of oxygenic photosynthesis. Photosynth Res (2022).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI:


  • Arabidopsis
  • Chloroflexi
  • Evolution
  • Natural selection
  • Proteobacteria