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https://www.readbyqxmd.com/read/29352746/the-common-bean-cok-4-and-the-arabidopsis-fer-kinase-domain-share-similar-function-in-plant-growth-and-defense
#1
Rafhael Felipin Azevedo, Maria Celeste Gonçalves Vidigal, Paula Rodrigues Oblessuc, Maeli Melotto
Receptor-like kinases are membrane proteins that can be shared by diverse signaling pathways. Among them, the Arabidopsis thaliana FERONIA (FER) plays a role in the balance between distinct signals to control growth and defense. We have found that COK-4, a putative kinase encoded in the common bean anthracnose resistance locus Co-4 that is transcriptionally regulated during immune response, is highly similar to the kinase domain of FER. To assess whether COK-4 is a functional ortholog of FER, we expressed COK-4 in the wild type Col-0 and the fer-5 mutant of Arabidopsis and evaluated FER-associated traits...
January 20, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29351733/glutamate-synthases-from-conifers-gene-structure-and-phylogenetic-studies
#2
Ángel García-Gutiérrez, Francisco M Cánovas, Concepción Ávila
BACKGROUND: Plants synthesize glutamate from ammonium by the combined activity of the enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT) through the glutamate synthase cycle. In plants, there are two forms of glutamate synthases that differ in their electron donors, NADH-GOGAT (EC 1.4.1.14) and Fd-GOGAT (EC 1.4.7.1), which have differential roles either in primary ammonia assimilation or in the reassimilation of ammonium from different catabolic processes. Glutamate synthases are complex iron-sulfur flavoproteins containing functional domains involved in the control and coordination of their catalytic activities in annual plants...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29349608/comparative-transcriptomics-uncovers-differences-in-photoautotrophic-versus-photoheterotrophic-modes-of-nutrition-in-relation-to-secondary-metabolites-biosynthesis-in-swertia-chirayita
#3
Tarun Pal, Jibesh Kumar Padhan, Pawan Kumar, Hemant Sood, Rajinder S Chauhan
Swertia chirayita is a high-value medicinal herb exhibiting antidiabetic, hepatoprotective, anticancer, antiediematogenic and antipyretic properties. Scarcity of its plant material has necessitated in vitro production of therapeutic metabolites; however, their yields were low compared to field grown plants. Possible reasons for this could be differences in physiological and biochemical processes between plants grown in photoautotrophic versus photoheterotrophic modes of nutrition. Comparative transcriptomes of S...
January 18, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29349599/evolution-of-eukaryal-and-archaeal-pseudouridine-synthase-pus10
#4
Elisabeth Fitzek, Archi Joardar, Ramesh Gupta, Matt Geisler
In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to m5U54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB. Although eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not clear for the two reasons...
January 18, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29348201/solution-structure-of-sperm-lysin-yields-novel-insights-into-molecular-dynamics-of-rapid-protein-evolution
#5
Damien B Wilburn, Lisa M Tuttle, Rachel E Klevit, Willie J Swanson
Protein evolution is driven by the sum of different physiochemical and genetic processes that usually results in strong purifying selection to maintain biochemical functions. However, proteins that are part of systems under arms race dynamics often evolve at unparalleled rates that can produce atypical biochemical properties. In the marine mollusk abalone, lysin and vitelline envelope receptor for lysin (VERL) are a pair of rapidly coevolving proteins that are essential for species-specific interactions between sperm and egg...
January 18, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29346364/mutations-in-caenorhabditis-elegans-neuroligin-like-glit-1-the-apoptosis-pathway-and-the-calcium-chaperone-crt-1-increase-dopaminergic-neurodegeneration-after-6-ohda-treatment
#6
Sarah-Lena Offenburger, Elisabeth Jongsma, Anton Gartner
The loss of dopaminergic neurons is a hallmark of Parkinson's disease, the aetiology of which is associated with increased levels of oxidative stress. We used C. elegans to screen for genes that protect dopaminergic neurons against oxidative stress and isolated glit-1 (gliotactin (Drosophila neuroligin-like) homologue). Loss of the C. elegans neuroligin-like glit-1 causes increased dopaminergic neurodegeneration after treatment with 6-hydroxydopamine (6-OHDA), an oxidative-stress inducing drug that is specifically taken up into dopaminergic neurons...
January 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29344086/correlation-of-structure-function-and-protein-dynamics-in-gh7-cellobiohydrolases-from-trichoderma-atroviride-t-reesei-and-t-harzianum
#7
Anna S Borisova, Elena V Eneyskaya, Suvamay Jana, Silke F Badino, Jeppe Kari, Antonella Amore, Magnus Karlsson, Henrik Hansson, Mats Sandgren, Michael E Himmel, Peter Westh, Christina M Payne, Anna A Kulminskaya, Jerry Ståhlberg
Background: The ascomycete fungus Trichoderma reesei is the predominant source of enzymes for industrial conversion of lignocellulose. Its glycoside hydrolase family 7 cellobiohydrolase (GH7 CBH) TreCel7A constitutes nearly half of the enzyme cocktail by weight and is the major workhorse in the cellulose hydrolysis process. The orthologs from Trichoderma atroviride (TatCel7A) and Trichoderma harzianum (ThaCel7A) show high sequence identity with TreCel7A, ~ 80%, and represent naturally evolved combinations of cellulose-binding tunnel-enclosing loop motifs, which have been suggested to influence intrinsic cellobiohydrolase properties, such as endo-initiation, processivity, and off-rate...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29343515/discovery-of-genes-required-for-lipoteichoic-acid-glycosylation-predicts-two-distinct-mechanism-for-wall-teichoic-acid-glycosylation
#8
Jeanine Rismondo, Matthew G Percy, Angelika Gründling
The bacterial cell wall is an important and highly complex structure that is essential for bacterial growth because it protects bacteria from cell lysis and environmental insults. A typical Gram-positive bacterial cell wall is composed of peptidoglycan and the secondary cell wall polymers, wall teichoic acid (WTA) and lipoteichoic acid (LTA). In many Gram-positive bacteria, LTA is a polyglycerol-phosphate chain that is decorated with D-alanine and sugar residues. However, the function of and proteins responsible for the glycosylation of LTA are either unknown or not well-characterized...
January 17, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29343513/using-genetic-buffering-relationships-identified-in-fission-yeast-to-reveal-susceptibilities-in-cells-lacking-hamartin-or-tuberin-function
#9
Ashyad Rayhan, Adam Faller, Ryan Chevalier, Alannah Mattice, Jim Karagiannis
Tuberous sclerosis complex is an autosomal dominant disorder characterized by benign tumors arising from the abnormal activation of mTOR signaling in cells lacking TSC1 (hamartin) or TSC2 (tuberin) activity. To expand the genetic framework surrounding this group of growth regulators, we utilized the model eukaryote Schizosaccharomyces pombe to uncover and characterize genes that buffer the phenotypic effects of mutations in the orthologous tsc1 or tsc2 loci. Our study identified two genes: fft3 (encoding a DNA helicase) and ypa1 (encoding a peptidyle-prolyl cis/trans isomerase)...
January 17, 2018: Biology Open
https://www.readbyqxmd.com/read/29343494/uncovering-genomic-regions-associated-with-trypanosoma-infections-in-wild-populations-of-the-tsetse-fly-glossina-fuscipes
#10
Andrea Gloria-Soria, W Augustine Dunn, Xiaoqing Yu, Aurélien Vigneron, Kuang-Yao Lee, Mo Li, Brian L Weiss, Hongyu Zhao, Serap Aksoy, Adalgisa Caccone
Vector-borne diseases are responsible for more than one million deaths every year but genomic resources for most species responsible for their transmission are limited. This is true for neglected diseases such as sleeping sickness (Human African Trypanosomiasis), a disease caused by Trypanosoma parasites vectored by several species of tseste flies within the genus Glossina We describe an integrative approach that identifies statistical associations between trypanosome infection status of Glossina fuscipes fuscipes (Gff) flies from Uganda, for which functional studies are complicated because the species cannot be easily maintained in laboratory colonies, and ~73,000 polymorphic sites distributed across the genome...
January 17, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29340253/rbiomirgs-an-all-in-one-mirna-gene-set-analysis-solution-featuring-target-mrna-mapping-and-expression-profile-integration
#11
Jing Zhang, Kenneth B Storey
Background: With the continuous discovery of microRNA's (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Profound advancement in bioinformatics has been made to enable in depth investigation of miRNA's role in regulating cellular and molecular events, resulting in a huge quantity of software packages covering different aspects of miRNA functional analysis...
2018: PeerJ
https://www.readbyqxmd.com/read/29339519/evidence-for-convergent-evolution-of-sine-directed-staufen-mediated-mrna-decay
#12
Bronwyn A Lucas, Eitan Lavi, Lily Shiue, Hana Cho, Sol Katzman, Keita Miyoshi, Mikiko C Siomi, Liran Carmel, Manuel Ares, Lynne E Maquat
Primate-specific Alu short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3'-untranslated regions (3'-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339407/genomic-identification-and-functional-characterization-of-essential-genes-in-caenorhabditis-elegans
#13
Zhaozhao Qin, Robert Johnsen, Shicheng Yu, Jeffrey Shih-Chieh Chu, David Baillie, Nansheng Chen
Using combined genetic mapping, Illumina sequencing, bioinformatics analyses, and experimental validation, we identified 60 essential genes from 104 lethal mutations in two genomic regions of C. elegans totalling approximately 14 Mb on chromosome III(mid) and chromosome V(left). Five of the 60 genes had not previously been shown to have lethal phenotypes by RNA interference depletion. By analyzing the regions around the lethal missense mutations, we identified four putative new protein functional domains. Furthermore, functional characterization of the identified essential genes shows that most are enzymes, including helicases, tRNA synthetases, and kinases in addition to ribosomal proteins...
January 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29338542/the-novel-microtubule-associated-cap-glycine-protein-cgp1-governs-growth-differentiation-and-virulence-of-cryptococcus-neoformans
#14
Li Li Wang, Kyung-Tae Lee, Kwang-Woo Jung, Dong-Gi Lee, Yong-Sun Bahn
Microtubules are involved in mechanical support, cytoplasmic organization, and several cellular processes by interacting with diverse microtubule-associated proteins such as plus-end tracking proteins, motor proteins, and tubulin-folding cofactors. A number of the cytoskeleton-associated proteins (CAPs) contain the CAP-glycine-rich (CAP-Gly) domain, which is evolutionarily conserved and generally considered to bind to α-tubulin to regulate the function of microtubules. However, there has been a dearth of research on CAP-Gly proteins in fungal pathogens, including Cryptococcus neoformans, which is a global cause of fatal meningoencephalitis in immunocompromised patients...
January 17, 2018: Virulence
https://www.readbyqxmd.com/read/29338035/genome-wide-identification-of-wheat-and-brachypodium-type-one-protein-phosphatases-and-functional-characterization-of-durum-wheat-tdpp1a
#15
Mariem Bradai, Habib Mahjoubi, Andrea Chini, Marie-Edith Chabouté, Moez Hanin, Chantal Ebel
Reversible phosphorylation is an essential mechanism regulating signal transduction during development and environmental stress responses. An important number of dephosphorylation events in the cell are catalyzed by type one protein phosphatases (PP1), which catalytic activity is driven by the binding of regulatory proteins that control their substrate specificity or subcellular localization. Plants harbor several PP1 isoforms accounting for large functional redundancies. While animal PP1s were reported to play relevant roles in controlling multiple cellular processes, plant orthologs remain poorly studied...
2018: PloS One
https://www.readbyqxmd.com/read/29335584/genome-wide-identification-and-characterization-of-spl-transcription-factor-family-and-their-evolution-and-expression-profiling-analysis-in-cotton
#16
Caiping Cai, Wangzhen Guo, Baohong Zhang
Plant specific transcription factors, SQUAMOSA promoter-binding protein-like (SPL), are involved in many biological processes. However, no systematical study has been reported in cotton. In this study, a total of 177 SPL genes were identified, including 29, 30, 59 and 59 SPLs in Gossypium arboreum, G. raimondii, G. barbadense, and G. hirsutum, respectively. These SPL genes were classified into eight phylogenetical groups. The gene structure, conserved motif, and clustering were highly conserved within each orthologs...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329292/transcriptome-profiling-with-focus-on-potential-key-genes-for-wing-development-and-evolution-in-megaloprepus-caerulatus-the-damselfly-species-with-the-world-s-largest-wings
#17
Wiebke Feindt, Sara J Oppenheim, Robert DeSalle, Paul Z Goldstein, Heike Hadrys
The evolution, development and coloration of insect wings remains a puzzling subject in evolutionary research. In basal flying insects such as Odonata, genomic research regarding bauplan evolution is still rare. Here we focus on the world's largest odonate species-the "forest giant" Megaloprepus caerulatus, to explore its potential for looking deeper into the development and evolution of wings. A recently discovered cryptic species complex in this genus previously considered monotypic is characterized by morphological differences in wing shape and color patterns...
2018: PloS One
https://www.readbyqxmd.com/read/29321589/comparative-analysis-of-low-complexity-regions-in-plasmodia
#18
S R Chaudhry, N Lwin, D Phelan, A A Escalante, F U Battistuzzi
Low complexity regions (LCRs) are a common feature shared by many genomes, but their evolutionary and functional significance remains mostly unknown. At the core of the uncertainty is a poor understanding of the mechanisms that regulate their retention in genomes, whether driven by natural selection or neutral evolution. Applying a comparative approach of LCRs to multiple strains and species is a powerful approach to identify patterns of conservation in these regions. Using this method, we investigate the evolutionary history of LCRs in the genus Plasmodium based on orthologous protein coding genes shared by 11 species and strains from primate and rodent-infecting pathogens...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321304/determinants-in-the-igv-domain-of-human-havcr1-tim-1-are-required-to-enhance-hepatitis-c-virus-entry
#19
Alla Kachko, Maria Isabel Costafreda, Iryna Zubkova, Jerome Jacques, Kazuyo Takeda, Frances Wells, Gerardo Kaplan, Marian E Major
Hepatitis C virus (HCV) is the leading cause of chronic hepatitis in humans. Several host molecules participate in HCV cell entry but this process remains unclear. The complete unraveling of the HCV entry process is important to further understand viral pathogenesis and develop therapeutics. The human hepatitis A virus (HAV) cellular receptor 1 (HAVCR1), CD365, also known as TIM-1, functions as a phospholipid receptor involved in cell entry of several enveloped viruses. Here, we studied the role of HAVCR1 in HCV infection...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29319812/deuterostome-genomics-lineage-specific-protein-expansions-that-enabled-chordate-muscle-evolution
#20
Jun Inoue, Noriyuki Satoh
Fish-like larvae were foundational to the chordate body plan, given the basal placement of free-living lancelets. That body plan probably made it possible for chordate ancestors to swim by beating a tail formed of notochord and bilateral paraxial muscles. In order to investigate the molecular genetic basis of the origin and evolution of paraxial muscle, we deduced the evolutionary histories of 16 contractile protein genes from paraxial muscle, based on genomic data from all five deuterostome lineages, using a newly developed orthology identification pipeline and a species tree...
January 8, 2018: Molecular Biology and Evolution
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