Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum
mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Heaphy, S. M., Mariotti, M., Gladyshev, V. N., Atkins, J. F., Baranov, P. V. Tags: Discoveries Source Type: research
Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life
Membrane proteins are crucial in transport, signaling, bioenergetics, catalysis, and as drug targets. Here, we show that membrane proteins have dramatically fewer detectable orthologs than water-soluble proteins, less than half in most species analyzed. This sparse distribution could reflect rapid divergence or gene loss. We find that both mechanisms operate. First, membrane proteins evolve faster than water-soluble proteins, particularly in their exterior-facing portions. Second, we demonstrate that predicted ancestral membrane proteins are preferentially lost compared with water-soluble proteins in closely related specie...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Sojo, V., Dessimoz, C., Pomiankowski, A., Lane, N. Tags: Discoveries Source Type: research
Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts
Large conjugative plasmids are important drivers of bacterial evolution and contribute significantly to the dissemination of antibiotic resistance. Although plasmid borne multidrug resistance is recognized as one of the main challenges in modern medicine, the adaptive forces shaping the evolution of these plasmids within pathogenic hosts are poorly understood. Here we study plasmid–host adaptations following transfer of a 73 kb conjugative multidrug resistance plasmid to naïve clinical isolates of Klebsiella pneumoniae and Escherichia coli. We use experimental evolution, mathematical modelling and population ...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Porse, A., Schonning, K., Munck, C., Sommer, M. O. A. Tags: Discoveries Source Type: research
Population Evolution of Helicobacter pylori through Diversification in DNA Methylation and Interstrain Sequence Homogenization
Decoding of closely related genomes is now revealing the process of population evolution. In bacteria, population divergence appears associated with a unique set of sequence-specific epigenetic DNA methylation systems, often within restriction–modification (RM) systems. They might define a unique gene expression pattern and limit genetic flux between lineages in population divergence. We addressed the contribution of methylation systems to population diversification in panmictic bacterial species, Helicobacter pylori, which shows an interconnected population structure through frequent mutual recombination. We analyze...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Kojima, K. K., Furuta, Y., Yahara, K., Fukuyo, M., Shiwa, Y., Nishiumi, S., Yoshida, M., Azuma, T., Yoshikawa, H., Kobayashi, I. Tags: Discoveries Source Type: research
Positive Selection Drives Evolution at the Host-Filovirus Interaction Surface
Filovirus infection is mediated by engagement of the surface-exposed glycoprotein (GP) by its cellular receptor, NPC1 (Niemann-Pick C1). Two loops in the C domain of NPC1 (NPC1-C) bind filovirus GP. Herein, we show that filovirus GP and NPC1-C evolve under mutual selective pressure. Analysis of a large mammalian phylogeny indicated that strong functional/structural constraints limit the NPC1 sequence space available for adaptive change and most sites at the contact interface with GP are under negative selection. These constraints notwithstanding, we detected positive selection at NPC1-C in all mammalian orders, from Primat...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Pontremoli, C., Forni, D., Cagliani, R., Filippi, G., De Gioia, L., Pozzoli, U., Clerici, M., Sironi, M. Tags: Discoveries Source Type: research
Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics
Biodiversity results from multiple evolutionary mechanisms, including genetic variation and natural selection. Whole-genome duplications (WGDs), or polyploidizations, provide opportunities for large-scale genetic modifications. Many evolutionarily successful lineages, including angiosperms and vertebrates, are ancient polyploids, suggesting that WGDs are a driving force in evolution. However, this hypothesis is challenged by the observed lower speciation and higher extinction rates of recently formed polyploids than diploids. Asteraceae includes about 10% of angiosperm species, is thus undoubtedly one of the most successfu...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Huang, C.-H., Zhang, C., Liu, M., Hu, Y., Gao, T., Qi, J., Ma, H. Tags: Discoveries Source Type: research
The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land
We report a stepwise increase in the number of transcription factor (TF) families and subfamilies in Archaeplastida before the colonization of the land. The subsequent increase in TF number on land was through duplication within existing TF families and subfamilies. Almost all subfamilies of the Homeodomain (HD) and basic Helix-Loop-Helix (bHLH) had evolved before the radiation of extant land plant lineages from a common ancestor. We demonstrate that the evolution of these TF families independently followed similar trends in both plants and metazoans; almost all extant HD and bHLH subfamilies were present in the first land...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., Dolan, L. Tags: Discoveries Source Type: research
Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole-Genome Sequences
As the largest European herbivore, the wisent (Bison bonasus) is emblematic of the continent wildlife but has unclear origins. Here, we infer its demographic and adaptive histories from two individual whole-genome sequences via a detailed comparative analysis with bovine genomes. We estimate that the wisent and bovine species diverged from 1.7 x 106 to 850,000 years before present (YBP) through a speciation process involving an extended period of limited gene flow. Our data further support the occurrence of more recent secondary contacts, posterior to the Bos taurus and Bos indicus divergence (~150,000 YBP), between the wi...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Gautier, M., Moazami-Goudarzi, K., Leveziel, H., Parinello, H., Grohs, C., Rialle, S., Kowalczyk, R., Flori, L. Tags: Discoveries Source Type: research
Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica
Allopolyploidization combines parental genomes and often confers broader species distribution. However, little is known about parentally transmitted gene expression underlying quantitative traits following allopolyploidization because of the complexity of polyploid genomes. The allopolyploid species Arabidopsis kamchatica is a natural hybrid of the zinc hyperaccumulator Arabidopsis halleri and of the nonaccumulator Arabidopsis lyrata. We found that A. kamchatica retained the ability to hyperaccumulate zinc from A. halleri and grows in soils with both low and high metal content. Hyperaccumulation of zinc by A. kamchatica wa...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Paape, T., Hatakeyama, M., Shimizu-Inatsugi, R., Cereghetti, T., Onda, Y., Kenta, T., Sese, J., Shimizu, K. K. Tags: Discoveries Source Type: research
Regulatory Divergence among Beta-Keratin Genes during Bird Evolution
Feathers, which are mainly composed of α- and β-keratins, are highly diversified, largely owing to duplication and diversification of β-keratin genes during bird evolution. However, little is known about the regulatory changes that contributed to the expressional diversification of β-keratin genes. To address this issue, we studied transcriptomes from five different parts of chicken contour and flight feathers. From these transcriptomes we inferred β-keratin enriched co-expression modules of genes and predicted transcription factors (TFs) of β-keratin genes. In total, we predicted 262 TF&ndas...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Bhattacharjee, M. J., Yu, C.-P., Lin, J.-J., Ng, C. S., Wang, T.-Y., Lin, H.-H., Li, W.-H. Tags: Fastrack Source Type: research
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Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
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Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
Study Pushes Back the Origin of HIV-Related Retroviruses to 60 Ma
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Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
