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The mysterious orphans of Mycoplasmataceae

Tatiana V. Tatarinova, Inna Lysnyansky, Yuri V. Nikolsky, Alexander Bolshoy
doi: https://doi.org/10.1101/025700
Tatiana V. Tatarinova
1Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, 90027, California, USA
2Spatial Science Institute, University of Southern California, Los Angeles, 90089, California, USA
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Inna Lysnyansky
3Mycoplasma Unit, Division of Avian and Aquatic Diseases, Kimron Veterinary Institute, POB 12, Beit Dagan, 50250, Israel
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Yuri V. Nikolsky
4School of Systems Biology, George Mason University, 10900 University Blvd, MSN 5B3, Manassas, VA 20110, USA
5Biomedical Cluster, Skolkovo Foundation, 4 Lugovaya str., Skolkovo Innovation Centre, Mozhajskij region, Moscow, 143026, Russian Federation
6Vavilov Institute of General Genetics, Moscow, Russian Federation
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Alexander Bolshoy
7Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Israel
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Abstract

Background The length of a protein sequence is largely determined by its function, i.e. each functional group is associated with an optimal size. However, comparative genomics revealed that proteins’ length may be affected by additional factors. In 2002 it was shown that in bacterium Escherichia coli and the archaeon Archaeoglobus fulgidus, protein sequences with no homologs are, on average, shorter than those with homologs [1]. Most experts now agree that the length distributions are distinctly different between protein sequences with and without homologs in bacterial and archaeal genomes. In this study, we examine this postulate by a comprehensive analysis of all annotated prokaryotic genomes and focusing on certain exceptions.

Results We compared lengths’ distributions of “having homologs proteins” (HHPs) and “non-having homologs proteins” (orphans or ORFans) in all currently annotated completely sequenced prokaryotic genomes. As expected, the HHPs and ORFans have strikingly different length distributions in almost all genomes. As previously established, the HHPs, indeed, are, on average, longer than the ORFans, and the length distributions for the ORFans have a relatively narrow peak, in contrast to the HHPs, whose lengths spread over a wider range of values. However, about thirty genomes do not obey these rules. Practically all genomes of Mycoplasma and Ureaplasma have atypical ORFans distributions, with the mean lengths of ORFan larger than the mean lengths of HHPs. These genera constitute over 80% of atypical genomes.

Conclusions We confirmed on a ubiquitous set of genomes the previous observation that HHPs and ORFans have different gene length distributions. We also showed that Mycoplasmataceae genomes have very distinctive distributions of ORFans lengths. We offer several possible biological explanations of this phenomenon.

  • List of abbreviations

    COG -
    a cluster of orthologous groups of genes; each COG consists of groups of proteins found to be orthologous across at least three lineages
    HHP -
    having homologs protein; here COG-annotated protein
    ORF –
    an open reading frame
    ORFan –
    non-HHP; here a protein-encoding gene that is not linked to any COG
    CG content -
    relative frequency of guanine and cytosine
    CG3 content -
    relative frequency of guanine and cytosine in the 3rd position of a codon
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Posted August 29, 2015.
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    The mysterious orphans of Mycoplasmataceae
    Tatiana V. Tatarinova, Inna Lysnyansky, Yuri V. Nikolsky, Alexander Bolshoy
    bioRxiv 025700; doi: https://doi.org/10.1101/025700
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    The mysterious orphans of Mycoplasmataceae
    Tatiana V. Tatarinova, Inna Lysnyansky, Yuri V. Nikolsky, Alexander Bolshoy
    bioRxiv 025700; doi: https://doi.org/10.1101/025700

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