Dataset Information

The mysterious orphans of Mycoplasmataceae.

ABSTRACT:

Background

The length of a protein sequence is largely determined by its function. In certain species, it may be also affected by additional factors, such as growth temperature or acidity. In 2002, it was shown that in the bacterium Escherichia coli and in the archaeon Archaeoglobus fulgidus, protein sequences with no homologs were, on average, shorter than those with homologs (BMC Evol Biol 2:20, 2002). It is now generally accepted that in bacterial and archaeal genomes the distributions of protein length are different between sequences with and without homologs. In this study, we examine this postulate by conducting a comprehensive analysis of all annotated prokaryotic genomes and by focusing on certain exceptions.

Results

We compared the distribution of lengths of "having homologs proteins" (HHPs) and "non-having homologs proteins" (orphans or ORFans) in all currently completely sequenced and COG-annotated 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 that the previous observation of 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, such as an adaptation to Mycoplasmataceae's ecological niche, specifically its "quiet" co-existence with host organisms, resulting in long ABC transporters.

SUBMITTER: Tatarinova TV

PROVIDER: S-EPMC4706650 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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Publications

The mysterious orphans of Mycoplasmataceae.

Tatarinova Tatiana V TV Lysnyansky Inna I Nikolsky Yuri V YV Bolshoy Alexander A

Biology direct 20160108 1

<h4>Background</h4>The length of a protein sequence is largely determined by its function. In certain species, it may be also affected by additional factors, such as growth temperature or acidity. In 2002, it was shown that in the bacterium Escherichia coli and in the archaeon Archaeoglobus fulgidus, protein sequences with no homologs were, on average, shorter than those with homologs (BMC Evol Biol 2:20, 2002). It is now generally accepted that in bacterial and archaeal genomes the distribution ...[more]

PMID: 26747447

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Project description:Binary silicon boride SiB3 has been reported to occur in two forms, as disordered and nonstoichiometric ?-SiB3-x , which relates to the ?-rhombohedral phase of boron, and as strictly ordered and stoichiometric ?-SiB3. Similar to other boron-rich icosahedral solids, these SiB3 phases represent potentially interesting refractory materials. However, their thermal stability, formation conditions, and thermodynamic relation are poorly understood. Here, we map the formation conditions of ?-SiB3-x and ?-SiB3 and analyze their relative thermodynamic stabilities. ?-SiB3-x is metastable (with respect to ?-SiB3 and Si), and its formation is kinetically driven. Pure polycrystalline bulk samples may be obtained within hours when heating stoichiometric mixtures of elemental silicon and boron at temperatures 1200-1300 °C. At the same time, ?-SiB3-x decomposes into SiB6 and Si, and optimum time-temperature synthesis conditions represent a trade-off between rates of formation and decomposition. The formation of stable ?-SiB3 was observed after prolonged treatment (days to weeks) of elemental mixtures with ratios Si/B = 1:1-1:4 at temperatures 1175-1200 °C. The application of high pressures greatly improves the kinetics of SiB3 formation and allows decoupling of SiB3 formation from decomposition. Quantitative formation of ?-SiB3 was seen at 1100 °C for samples pressurized to 5.5-8 GPa. ?-SiB3 decomposes peritectoidally at temperatures between 1250 and 1300 °C. The highly ordered nature of ?-SiB3 is reflected in its Raman spectrum, which features narrow and distinct lines. In contrast, the Raman spectrum of ?-SiB3-x is characterized by broad bands, which show a clear relation to the vibrational modes of isostructural, ordered B6P. The detailed composition and structural properties of disordered ?-SiB3-x were ascertained by a combination of single-crystal X-ray diffraction and 29Si magic angle spinning NMR experiments. Notably, the compositions of polycrystalline bulk samples (obtained at T ? 1200 °C) and single crystal samples (obtained from Si-rich molten Si-B mixtures at T > 1400 °C) are different, SiB2.93(7) and SiB2.64(2), respectively. The incorporation of Si in the polar position of B12 icosahedra results in highly strained cluster units. This disorder feature was accounted for in the refined crystal structure model by splitting the polar position into three sites. The electron-precise composition of ?-SiB3-x is SiB2.5 and corresponds to the incorporation of, on average, two Si atoms in each B12 icosahedron. Accordingly, ?-SiB3-x constitutes a mixture of B10Si2 and B11Si clusters. The structural and phase stability of ?-SiB3-x were explored using a first-principles cluster expansion. The most stable composition at 0 K is SiB2.5, which however is unstable with respect to the decomposition ?-SiB3 + Si. Modeling of the configurational and vibrational entropies suggests that ?-SiB3-x only becomes more stable than ?-SiB3 at temperatures above its decomposition into SiB6 and Si. Hence, we conclude that ?-SiB3-x is metastable at all temperatures. Density functional theory electronic structure calculations yield band gaps of similar size for electron-precise ?-SiB2.5 and ?-SiB3, whereas ?-SiB3 represents a p-type conductor.

Dataset Information

The mysterious orphans of Mycoplasmataceae.

Background

Results

Conclusions

Publications

The mysterious orphans of Mycoplasmataceae.

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