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Difference in disorder between eukaryotes and prokaryotes is largely due to Serine in linker regions
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
(English)Manuscript (preprint) (Other academic)
Abstract [en]

In this study we ask what are the molecular properties that make eukaryotic proteins more disordered than prokaryotic ones. First, we show that on average eukaryotic proteins contain more amino acids that are promoting disorder. In particular the fraction of Serine residues is close to 8% of all residues in eukaryotes and less than 6% in prokaryotes. Second, we show that domains unique to eukaryotes and linker regions in eukaryotes are both more disordered and more abundant than corresponding regions in prokaryotic proteins. Serine is an important residue for post-translational modification and regulatory mechanisms. Therefore, we conclude that it is not unlikely that both the need for regulation in a complex eukaryotic cell and the increased amount of longer multi-domain proteins contribute to the higher intrinsic structural disorder in eukaryotic proteins.

National Category
Biological Sciences
Research subject
Biochemistry towards Bioinformatics
Identifiers
URN: urn:nbn:se:su:diva-149167OAI: oai:DiVA.org:su-149167DiVA, id: diva2:1158355
Available from: 2017-11-20 Created: 2017-11-20 Last updated: 2017-11-20Bibliographically approved
In thesis
1. Orphan Genes Bioinformatics: Identification and properties of de novo created genes
Open this publication in new window or tab >>Orphan Genes Bioinformatics: Identification and properties of de novo created genes
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Even today, many genes are without any known homolog. These "orphans" are found in all species, from Viruses to Prokaryotes and Eukaryotes. For a portion of these genes, we might simply not have enough data to find homologs yet. Some of them are imported from taxonomically distant organisms via lateral transfer; others have homologs, but mutated beyond the point of recognition.

However, a sizeable fraction of orphan genes is unambiguously created via "de novo" mechanisms. The study of such novel genes can contribute to our understanding of the emergence of functional novelty and the adaptation of species to new ecological niches.

In this work, we first survey the field of orphan studies, and illustrate some of the common issues. Next, we analyze some of the intrinsic properties of orphans proteins, including secondary structure elements and Intrinsic Structural Disorder; specifically, we observe that in young proteins the relationship between these properties and the G+C content of their coding sequence is stronger than in older proteins.

We then tackle some of the methodological problems often found in orphan studies. We find that using evolutionarily close species, and sensitive, state-of-the art homology recognition methods is instrumental to the identification of a set of orphans enriched in de novo created ones.

Finally, we compare how intrinsic disorder is distributed in bacteria versus eukaryota. Eukaryotic proteins are longer and more disordered; the difference is to be attributed primarily to eukaryotic-specific domains and linker regions. In these sections of the proteins, a higher frequency of the disorder-promoting amino acid Serine can be observed in Eukaryotes.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2017
Keywords
bioinformatics, de novo, orphans, evolutionary genetics
National Category
Biological Sciences
Research subject
Biochemistry towards Bioinformatics
Identifiers
urn:nbn:se:su:diva-149168 (URN)978-91-7797-085-9 (ISBN)978-91-7797-086-6 (ISBN)
Public defence
2018-01-12, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 4: Manuscript.

Available from: 2017-12-20 Created: 2017-11-20 Last updated: 2017-12-20Bibliographically approved

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