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https://www.readbyqxmd.com/read/28431018/disulfide-bonds-enable-accelerated-protein-evolution
#1
Felix Feyertag, David Alvarez-Ponce
The different proteins of any proteome evolve at enormously different rates. What factors contribute to this variability, and to what extent, is still a largely open question. We hypothesized that disulfide bonds, by increasing protein stability, should make proteins' structures relatively independent of their amino acid sequences, thus acting as buffers of deleterious mutations and enabling accelerated sequence evolution. In agreement with this hypothesis, we observed that membrane proteins with disulfide bonds evolved 88% faster than those without disulfide bonds, and that extracellular proteins with disulfide bonds evolved 49% faster than those without disulfide bonds...
April 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28430951/evidence-for-a-strong-correlation-between-transcription-factor-protein-disorder-and-organismic-complexity
#2
Inmaculada Yruela, Christopher J Oldfield, Karl J Niklas, A Keith Dunker
Studies of diverse phylogenetic lineages reveal that protein disorder increases in concert with organismic complexity but that differences nevertheless exist among lineages. To gain insight into this phenomenology, we analyzed all of the transcription factor (TF) families for which sequences are known for 17 species spanning bacteria, yeast, algae, land plants, and animals and for which the number of different cell types has been reported in the primary literature. Although the fraction of disordered residues in TF sequences is often moderately or poorly correlated with organismic complexity as gauged by cell type number (r2 < 0...
April 18, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28430886/intrinsic-protein-disorder-reduces-small-scale-gene-duplicability
#3
Sanghita Banerjee, Felix Feyertag, David Alvarez-Ponce
Whereas the rate of gene duplication is relatively high, only certain duplications survive the filter of natural selection and can contribute to genome evolution. However, the reasons why certain genes can be retained after duplication whereas others cannot remain largely unknown. Many proteins contain intrinsically disordered regions (IDRs), whose structures fluctuate between alternative conformational states. Due to their high flexibility, IDRs often enable protein-protein interactions and are the target of post-translational modifications...
April 19, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28430006/evolutionary-changes-in-lamin-expression-in-the-vertebrate-lineage
#4
Reimer Stick, Annette Peter
The nuclear lamina is involved in fundamental nuclear functions and provides mechanical stability to the nucleus. Lamin filaments form a meshwork closely apposed to the inner nuclear membrane and a small fraction of lamins exist in the nuclear interior. Mutations in lamin genes cause severe hereditary diseases, the laminopathies. During vertebrate evolution the lamin protein family has expanded. While most vertebrate genomes contain four lamin genes, encoding the lamins A, B1, B2, and LIII, the majority of non-vertebrate genomes harbor only a single lamin gene...
April 21, 2017: Nucleus
https://www.readbyqxmd.com/read/28429731/the-evolutionary-life-cycle-of-the-polysaccharide-biosynthetic-gene-cluster-based-on-the-sphingomonadaceae
#5
Mengmeng Wu, Haidong Huang, Guoqiang Li, Yi Ren, Zhong Shi, Xiaoyan Li, Xiaohui Dai, Ge Gao, Mengnan Ren, Ting Ma
Although clustering of genes from the same metabolic pathway is a widespread phenomenon, the evolution of the polysaccharide biosynthetic gene cluster remains poorly understood. To determine the evolution of this pathway, we identified a scattered production pathway of the polysaccharide sanxan by Sphingomonas sanxanigenens NX02, and compared the distribution of genes between sphingan-producing and other Sphingomonadaceae strains. This allowed us to determine how the scattered sanxan pathway developed, and how the polysaccharide gene cluster evolved...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429538/finding-a-partner-in-the-ocean-molecular-and-evolutionary-bases-of-the-response-to-sexual-cues-in-a-planktonic-diatom
#6
Swaraj Basu, Shrikant Patil, Daniel Mapleson, Monia Teresa Russo, Laura Vitale, Cristina Fevola, Florian Maumus, Raffaella Casotti, Thomas Mock, Mario Caccamo, Marina Montresor, Remo Sanges, Maria Immacolata Ferrante
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo-nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics. We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex-related genes...
April 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28429323/protein-targeting-to-the-plastid-of-euglena
#7
Dion G Durnford, Steven D Schwartzbach
The lateral transfer of photosynthesis between kingdoms through endosymbiosis is among the most spectacular examples of evolutionary innovation. Euglena, which acquired a chloroplast indirectly through an endosymbiosis with a green alga, represents such an example. As with other endosymbiont-derived plastids from eukaryotes, there are additional membranes that surround the organelle, of which Euglena has three. Thus, photosynthetic genes that were transferred from the endosymbiont to the host nucleus and whose proteins are required in the new plastid, are now faced with targeting and plastid import challenges...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28429303/natural-evolution-of-ige-responses-to-mite-allergens-and-relationship-to-progression-of-allergic-disease-a-review
#8
REVIEW
Daniela Posa, Stephanie Hofmaier, Stefania Arasi, Paolo Maria Matricardi
PURPOSE OF REVIEW: Allergenic molecules of the house dust mite (HDM) are crucially important indoor allergens, contributing to allergic rhinitis and asthma around the globe. In the past years, recombinant molecules for diagnostics opened new pathways to investigate individual sensitization profiles and new chances for the prevention and treatment of HDM allergy. This review summarizes the latest findings on the evolution of IgE responses towards mite allergens. RECENT FINDINGS: Several cross-sectional and longitudinal studies confirmed the role of Der p 1 and Der p 2 as major allergenic proteins of the HDM...
May 2017: Current Allergy and Asthma Reports
https://www.readbyqxmd.com/read/28428061/identification-and-characterization-of-an-interleukin-16-like-gene-from-pacific-white-shrimp-litopenaeus-vannamei
#9
Qianhui Liang, Jiefu Zheng, Hongliang Zuo, Chaozheng Li, Shengwen Niu, Linwei Yang, Muting Yan, Shao-Ping Weng, Jianguo He, Xiaopeng Xu
Interleukins are a group of cytokines that play essential roles in immune regulation. Almost all interleukin genes are only found in vertebrates. In this study, an interleukin-16-like gene (LvIL-16L) was identified from Pacific white shrimp, Litopenaeus vannamei. LvIL-16L was predicted to encode a precursor (pro-LvIL-16L) with 1378 amino acids, sharing similarities with predicted pro-IL-16-like proteins from insects. The C-terminus of pro-LvIL-16L protein contained two PDZ domains homologous to the mature IL-16 cytokine of vertebrates...
April 17, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28427348/comparative-genomics-and-evolution-of-the-amylase-binding-proteins-of-oral-streptococci
#10
Elaine M Haase, Yurong Kou, Amarpreet Sabharwal, Yu-Chieh Liao, Tianying Lan, Charlotte Lindqvist, Frank A Scannapieco
BACKGROUND: Successful commensal bacteria have evolved to maintain colonization in challenging environments. The oral viridans streptococci are pioneer colonizers of dental plaque biofilm. Some of these bacteria have adapted to life in the oral cavity by binding salivary α-amylase, which hydrolyzes dietary starch, thus providing a source of nutrition. Oral streptococcal species bind α-amylase by expressing a variety of amylase-binding proteins (ABPs). Here we determine the genotypic basis of amylase binding where proteins of diverse size and function share a common phenotype...
April 20, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28427100/dystrophinopathies-and-limb-girdle-muscular-dystrophies
#11
Joana Domingos, Anna Sarkozy, Mariacristina Scoto, Francesco Muntoni
Muscular dystrophies are a heterogeneous group of inherited diseases. The natural history of these disorders along with their management have changed mainly due to a better understanding of their pathophysiology, the evolution of standards of care, and new treatment options. Dystrophinopathies include both Duchenne's and Becker's muscular dystrophies, but in reality they are a spectrum of muscle diseases caused by mutations in the gene that encodes the protein dystrophin. Duchenne's muscular dystrophy is the most common form of inherited muscle disease of childhood...
April 20, 2017: Neuropediatrics
https://www.readbyqxmd.com/read/28426805/evidence-of-horizontal-gene-transfer-by-transposase-gene-analyses-in-fervidobacterium-species
#12
Alba Cuecas, Wirojne Kanoksilapatham, Juan M Gonzalez
Horizontal Gene Transfer (HGT) plays an important role in the physiology and evolution of microorganisms above all thermophilic prokaryotes. Some members of the Phylum Thermotogae (i.e., Thermotoga spp.) have been reported to present genomes constituted by a mosaic of genes from a variety of origins. This study presents a novel approach to search on the potential plasticity of Fervidobacterium genomes using putative transposase-encoding genes as the target of analysis. Transposases are key proteins involved in genomic DNA rearrangements...
2017: PloS One
https://www.readbyqxmd.com/read/28426191/genome-wide-abolishment-of-mobile-genetic-elements-using-genome-shuffling-and-crispr-cas-assisted-mage-allows-the-efficient-stabilization-of-a-bacterial-chassis
#13
Kinga Umenhoffer, Gábor Draskovits, Ákos Nyerges, Ildikó Karcagi, Balázs Bogos, Edit Tímár, Bálint Csörgő, Róbert Herczeg, István Nagy, Tamás Fehér, Csaba Pal, Gyorgy Posfai
The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, non-essential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization...
April 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28424711/genomic-molecular-evolution-and-expression-analysis-of-genes-encoding-putative-classical-agps-lysine-rich-agps-and-ag-peptides-in-brassica-rapa
#14
Tianyu Han, Heng Dong, Jie Cui, Ming Li, Sue Lin, Jiashu Cao, Li Huang
Arabinogalactan proteins (AGPs) belong to a class of Pro/Hyp-rich glycoproteins and are some of the most complex types of macromolecules found in plants. In the economically important plant species, Brassica rapa, only chimeric AGPs have been identified to date. This has significantly limited our understanding of the functional roles of AGPs in this plant. In this study, 64 AGPs were identified in the genome of B. rapa, including 33 classical AGPs, 28 AG peptides and three lys-rich AGPs. Syntenic gene analysis between B...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28424693/human-melanoma-derived-extracellular-vesicles-regulate-dendritic-cell-maturation
#15
Rachel L G Maus, James W Jakub, Wendy K Nevala, Trace A Christensen, Klara Noble-Orcutt, Zohar Sachs, Tina J Hieken, Svetomir N Markovic
Evolution of melanoma from a primary tumor to widespread metastasis is crucially dependent on lymphatic spread. The mechanisms regulating the initial step in metastatic dissemination via regional lymph nodes remain largely unknown; however, evidence supporting the establishment of a pre-metastatic niche is evolving. We have previously described a dysfunctional immune profile including reduced expression of dendritic cell (DC) maturation markers in the first node draining from the primary tumor, the sentinel lymph node (SLN)...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28424662/untangling-genomes-of-novel-planctomycetal-and-verrucomicrobial-species-from-monterey-bay-kelp-forest-metagenomes-by-refined-binning
#16
John Vollmers, Martinique Frentrup, Patrick Rast, Christian Jogler, Anne-Kristin Kaster
The kelp forest of the Pacific temperate rocky marine coastline of Monterey Bay in California is a dominant habitat for large brown macro-algae in the order of Laminariales. It is probably one of the most species-rich, structurally complex and productive ecosystems in temperate waters and well-studied in terms of trophic ecology. However, still little is known about the microorganisms thriving in this habitat. A growing body of evidence suggests that bacteria associated with macro-algae represent a huge and largely untapped resource of natural products with chemical structures that have been optimized by evolution for biological and ecological purposes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28423210/intrinsic-incompatibilities-evolving-as-a-by-product-of-divergent-ecological-selection-considering-them-in-empirical-studies-on-divergence-with-gene-flow
#17
J Kulmuni, A M Westram
The possibility of intrinsic barriers to gene flow is often neglected in empirical research on local adaptation and speciation with gene flow, e.g. when interpreting patterns observed in genome scans. However, we draw attention to the fact that, even with gene flow, divergent ecological selection may generate intrinsic barriers involving both ecologically selected and other interacting loci. Mechanistically, the link between the two types of barriers may be generated by genes that have multiple functions (i...
April 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28423184/the-differentiated-and-conserved-roles-of-swi5-sfr1-in-homologous-recombination
#18
REVIEW
Bilge Argunhan, Yasuto Murayama, Hiroshi Iwasaki
Homologous recombination (HR) is the process whereby two DNA molecules that share high sequence similarity are able to recombine to generate hybrid DNA molecules. Throughout evolution, the ability of HR to identify highly similar DNA sequences has been adopted for numerous biological phenomena including DNA repair, meiosis, telomere maintenance, ribosomal DNA amplification, and immunological diversity. Although Rad51 and Dmc1 are the key proteins that promote HR in mitotic and meiotic cells, respectively, accessory proteins that allow Rad51 and Dmc1 to effectively fulfil their functions have been identified in all examined model systems...
April 19, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28423051/biochemical-and-molecular-characterization-of-the-isocitrate-dehydrogenase-with-dual-coenzyme-specificity-from-the-obligate-methylotroph-methylobacillus-flagellatus
#19
Anastasia Y Romkina, Michael Y Kiriukhin
The isocitrate dehydrogenase (MfIDH) with unique double coenzyme specificity from Methylobacillus flagellatus was purified and characterized, and its gene was cloned and overexpressed in E. coli as a fused protein. This enzyme is homodimeric,-with a subunit molecular mass of 45 kDa and a specific activity of 182 U mg -1 with NAD+ and 63 U mg -1 with NADP+. The MfIDH activity was dependent on divalent cations and Mn2+ enhanced the activity the most effectively. MfIDH exhibited a cofactor-dependent pH-activity profile...
2017: PloS One
https://www.readbyqxmd.com/read/28422318/computational-analysis-of-breast-cancer-gwas-loci-identifies-the-putative-deleterious-effect-of-stxbp4-and-znf404-gene-variants
#20
Tariq Ahmad Masoodi, Babajan Banaganapalli, Venkatesh Vaidyanathan, Venkateswar Rao Talluri, Noor Ahmad Shaik
The genome-wide association studies (GWAS) have enabled us in identifying different breast cancer susceptibility loci. However, majority of these are non-coding variants with no annotated biological function. We investigated such 78 noncoding genome wide associated SNPs of breast cancer and further expanded the list to 2162 variants with strong linkage-disequilibrium (LD, r2 ≥0.8). Using multiple publically available algorithms such as CADD, GWAVA and FATHAMM, we classified all these variants in to deleterious, damaging or benign categories...
April 19, 2017: Journal of Cellular Biochemistry
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