Genome size variation in deep-sea amphipods

Funding: This work was supported by the HADEEP projects, funded by the Nippon Foundation, Japan (2009765188); the Natural Environment Research Council (NERC), UK (NE/E007171/1); Total Foundation, France; National Institute of Water and Atmospheric Research (NIWA), New Zealand (CO1_0906); Schmidt Ocean Institute, USA (FK141109) (A.J.J. and S.B.P); Marine Alliance for Science and Technology for Scotland (MASTS) (HR09011 and DSSG15) (H.R., A.J.J., S.B.P); and the Leverhulme Trust (S.B.P.). Acknowledgements: We thank the chief scientists, crew and company of the New Zealand RV Kaharoa (KAH1301 and KAH1310) and the United States RV Falkor (Cruise FK141109). From NIWA, we thank Malcolm Clark, Ashley Rowden, Kareen Schnabel, and Sadie Mills for logistical support at the NIWA Invertebrate Collection. We thank NOAA Marine National Monuments, Richard Hall and Eric Breuer for their support and collaboration. We also thank Attila Bebes and the Iain Fraser Cytometry Centre (IFCC) for technical assistance. Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare.c.3868216.Peer reviewedPublisher PD

Complete genome sequences of escherichia coli phages vB_EcoM-EP75 and vB_EcoP-EP335

Phages vB_EcoM-EP75 (EP75) and vB_EcoP-EP335 (EP335) specifically infect Shiga toxin (Stx)-producing Escherichia coli (STEC) O157 strains. EP75 has a genome size of 158,143 bp and belongs to the genus Vi1virus The genome size of EP335 is 76,622 bp, and it belongs to the genus Phieco32virus

Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

Number of natively unfolded proteins scales with genome size

Natively unfolded proteins exist as an ensemble of flexible conformations lacking a well defined tertiary structure along a large portion of their polypeptide chain. Despite the absence of a stable configuration, they are involved in important cellular processes. In this work we used from three indicators of folding status, derived from the analysis of mean packing and mean contact energy of a protein sequence as well as from VSL2, a disorder predictor, and we combined them into a consensus score to identify natively unfolded proteins in several genomes from Archaea, Bacteria and Eukarya. We found a high correlation among the number of predicted natively unfolded proteins and the number of proteins in the genomes. More specifically, the number of natively unfolded proteins scaled with the number of proteins in the genomes, with exponent 1.81 +- 0.10. This scaling law may be important to understand the relation between the number of natively unfolded proteins and their roles in cellular processes.Comment: Submitted to Biophysics and Bioengineering Letters http://padis2.uniroma1.it:81/ojs/index.php/CISB-BB