What makes a plant different from other organisms?
To answer this question it is important to understand both what is similar between plants and other organisms and also what are the differences.
Although many studies are based upon sequence similarities between genes in different species, suprisingly few studies have been reported that focus on the genome-wide differences between plants and organisms that belong to other phylogenetic lineages.
In an effort to shed light into this important question in plant biology, we have classified Arabidopsis protein-coding genes based on their pattern
of sequence similarity to protein sequences of organisms that belong to the three domains of life (Eukaryota, Bacteria and Archea). This classification allowed the identification of 3848 Arabidopsis genes that encode putative plant-specific proteins,
as similar protein sequences were only found in other plant species. Plant-specific proteins are
likely to play important roles in processes that are unique and of significance to plants.
Hence the study of their functions should greatly contribute to plant biology and to the understanding
of how plants differ from other organisms. However, we found that many plant-specific proteins
have unknown functions.
To facilitate the functional characterization of plant-specific proteins, we have compiled
and integrated information from multiple public databases (e.g. TIGR, MIPS, TAIR, SIGNAL), as well as provide results obtained with predictive algorithms (e.g. TargetP, TMHMM, BLASTCLUST). We also
provide flexible search capabilities that should allow the analysis of single as well as lists
of proteins of interest to individual researchers.
- A previous version of this work is available from:
In addition to plant-specific proteins, we have also identified 5132 other Arabidopsis proteins
that exhibit specific patterns of conservation across the three domains of life. We have classified
these proteins in nine groups (below) according to the organisms in which we found similar protein sequences.
- For a description of the database and its functionality see Gutierrez et al., 2004. Plant Physiol. 135, 1888-1892
- The complete analysis of the plant specific proteins is described in Gutierrez et al., 2004. Genome Biol.. 5(8), R53
- Follow this link for an introduction to this work and brief explanation of how it was done.
- Follow this link for the main conclusions obtained in in this work.
- Follow this link for a list of common questions about our work.
Use the links below to explore the list of plant-specific and other classifications of Arabidopsis proteins:
Click here to see a list of 3848 Arabidopsis proteins classified as plant-specific.