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https://www.readbyqxmd.com/read/29147015/structure-of-flgk-reveals-the-divergence-of-the-bacterial-hook-filament-junction-of-campylobacter
#1
Paula V Bulieris, Nausad H Shaikh, Peter L Freddolino, Fadel A Samatey
Evolution of a nano-machine consisting of multiple parts, each with a specific function, is a complex process. A change in one part should eventually result in changes in other parts, if the overall function is to be conserved. In bacterial flagella, the filament and the hook have distinct functions and their respective proteins, FliC and FlgE, have different three-dimensional structures. The filament functions as a helical propeller and the hook as a flexible universal joint. Two proteins, FlgK and FlgL, assure a smooth connectivity between the hook and the filament...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146598/structural-analyses-unravel-the-molecular-mechanism-of-cyclic-di-gmp-regulation-of-bacterial-chemotaxis-via-a-pilz-adaptor-protein
#2
Xin-Fu Yan, Lingyi Xin, Jackie Tan Yen, Yukai Zeng, Shengyang Jin, Qing Wei Cheang, Rachel Andrea Chea Yuen Fong, Keng-Hwee Chiam, Zhao-Xun Liang, Yong-Gui Gao
The bacterial second messenger cyclic di-GMP (c-di-GMP) has emerged as a prominent mediator of bacterial physiology, motility and pathogenicity. Cdi-GMP often regulates the function of its protein targets through a unique mechanism that involves a discrete PilZ adaptor protein. However, the molecular mechanism in c-di-GMP-mediated protein regulation is unclear. Here, we present the structure of the PilZ adaptor protein MapZ co-crystallized in complex with c-di-GMP and its protein target CheR1, a chemotaxis-regulating methyltransferase in Pseudomonas aeruginosa This co-crystal structure, together with the structure of free CheR1, revealed that the binding of c-di-GMP induces dramatic structural changes in MapZ that are crucial for CheR1 binding...
November 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29145811/genome-wide-analysis-of-the-auxin-indoleacetic-acid-aux-iaa-gene-family-in-allotetraploid-rapeseed-brassica-napus-l
#3
Haitao Li, Bo Wang, Qinghua Zhang, Jing Wang, Graham J King, Kede Liu
BACKGROUND: Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Although the Aux/IAA gene family has been identified in many plants, within allotetraploid Brassica napus little is known. RESULTS: In this study, a total of 119 Aux/IAA genes were found in the genome of B. napus. They were distributed non-randomly across all 19 chromosomes and other non-anchored random scaffolds, with a symmetric distribution in the A and C subgenomes...
November 16, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29145497/rare-genetic-variants-in-the-endocannabinoid-system-genes-cnr1-and-dagla-are-associated-with-neurological-phenotypes-in-humans
#4
Douglas R Smith, Christine M Stanley, Theodore Foss, Richard G Boles, Kevin McKernan
Rare genetic variants in the core endocannabinoid system genes CNR1, CNR2, DAGLA, MGLL and FAAH were identified in molecular testing data from 6,032 patients with a broad spectrum of neurological disorders. The variants were evaluated for association with phenotypes similar to those observed in the orthologous gene knockouts in mice. Heterozygous rare coding variants in CNR1, which encodes the type 1 cannabinoid receptor (CB1), were found to be significantly associated with pain sensitivity (especially migraine), sleep and memory disorders-alone or in combination with anxiety-compared to a set of controls without such CNR1 variants...
2017: PloS One
https://www.readbyqxmd.com/read/29141666/intron-retention-enhances-gene-regulatory-complexity-in-vertebrates
#5
Ulf Schmitz, Natalia Pinello, Fangzhi Jia, Sultan Alasmari, William Ritchie, Maria-Cristina Keightley, Shaniko Shini, Graham J Lieschke, Justin J-L Wong, John E J Rasko
BACKGROUND: While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of IR, we performed an exhaustive phylogenetic analysis in a highly purified and functionally defined cell type comprising neutrophilic granulocytes from five vertebrate species spanning 430 million years of evolution. RESULTS: Our RNA-sequencing-based analysis suggests that IR increases gene regulatory complexity, which is indicated by a strong anti-correlation between the number of genes affected by IR and the number of protein-coding genes in the genome of individual species...
November 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/29140250/gdf3-is-required-for-robust-nodal-signaling-during-germ-layer-formation-and-left-right-patterning
#6
Jose L Pelliccia, Granton A Jindal, Rebecca D Burdine
Vertebrate embryonic patterning depends on signaling from Nodal, a TGFβ superfamily member. There are three Nodal orthologs in zebrafish; southpaw directs left-right asymmetries, while squint and cyclops function earlier to pattern mesendoderm. TGFβ member Vg1 is implicated in mesoderm formation but the role of the zebrafish ortholog, Growth differentiation factor 3 (Gdf3), has not been fully explored. We show that zygotic expression of gdf3 is dispensable for embryonic development, while maternally deposited gdf3 is required for mesendoderm formation and dorsal-ventral patterning...
November 15, 2017: ELife
https://www.readbyqxmd.com/read/29138237/natural-variation-in-ser1-and-ena6-underlie-condition-specific-growth-defects-in-saccharomyces%C3%A2-cerevisiae
#7
Amy Sirr, Adrian C Scott, Gareth A Cromie, Catherine L Ludlow, Vida Ahyong, Trey S Morgan, Teresa Gilbert, Aimée M Dudley
Despite their ubiquitous use in laboratory strains, naturally occurring loss-of-function mutations in genes encoding core metabolic enzymes are relatively rare in wild isolates of Saccharomyces cerevisiae Here, we identify a naturally occurring serine auxotrophy in a sake brewing strain from Japan. Through a cross with a honey wine (white tecc) brewing strain from Ethiopia, we map the minimal medium growth defect to SER1, which encodes 3-phosphoserine aminotransferase and is orthologous to the human disease gene, PSAT1 To investigate the impact of this polymorphism under conditions of abundant external nutrients, we examine growth in rich medium alone or with additional stresses, including the drugs caffeine and rapamycin and relatively high concentrations of copper, salt, and ethanol...
November 14, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29136137/copy-number-variation-and-expression-analysis-reveals-a-non-orthologous-pinta-gene-family-member-involved-in-butterfly-vision
#8
Aide Macias-Muñoz, Kyle J McCulloch, Adriana D Briscoe
Vertebrate (CRALBP) and Drosophila (PINTA) proteins with a CRAL-TRIO domain transport retinal-based chromophores that bind to opsin proteins and are necessary for phototransduction. The CRAL-TRIO domain gene family is composed of genes that encode proteins with a common N-terminal structural domain. While there is an expansion of this gene family in Lepidoptera, there is no lepidopteran ortholog of pinta. Further, the function of these genes in lepidopterans has not yet been established. Here we explored the molecular evolution and expression of CRAL-TRIO domain genes in the butterfly Heliconius melpomene in order to identify a member of this gene family as a candidate chromophore transporter...
November 9, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29133276/de-novo-assembly-and-annotation-of-the-whole-genomic-analysis-of-vibrio-campbellii-rt-1-strain-from-infected-shrimp-litopenaeus-vannamei
#9
R Thirugnanasambandam, D Inbakandan, L Stanley Abraham, C Kumar, S M Sundaram, B Subashni, R Vasantharaja, A Arul Anantha Kumar, R Kirubagaran, S Ajmal Khan, T Balasubramanian
OBJECTIVES: This study aimed to sequence the whole genome of Vibrio campbellii RT-1 strain. METHODS: V. campbellii strain was isolated from an infected shrimp, Litopenaeus vannamei collected from aquaculture ponds, India (12.1899° N, 79.9249° E). The whole genome sequencing (WGS) was performed using the Illumina Hiseq 2500 platform and assembled de novo using SPAdes and Velvet optimiser. Furthermore, the gene prediction and annotation were performed by a rapid prokaryotic genome tool-Prokka...
November 10, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29132315/comprehensive-genomic-analysis-of-the-cngc-gene-family-in-brassica-oleracea-novel-insights-into-synteny-structures-and-transcript-profiles
#10
Kaleem U Kakar, Zarqa Nawaz, Khadija Kakar, Essa Ali, Abdulwareth A Almoneafy, Raqeeb Ullah, Xue-Liang Ren, Qing-Yao Shu
BACKGROUND: The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism. RESULTS: In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29131830/transcriptome-profiling-and-digital-gene-expression-analysis-of-sweet-potato-for-the-identification-of-putative-genes-involved-in-the-defense-response-against-fusarium-oxysporum-f-sp-batatas
#11
Yuli Lin, Weikun Zou, Shiqiang Lin, Dennis Onofua, Zhijian Yang, Haizhou Chen, Songliang Wang, Xuanyang Chen
Sweet potato production is constrained by Fusarium wilt, which is caused by Fusarium oxysporum f. sp. batatas (Fob). The identification of genes related to disease resistance and the underlying mechanisms will contribute to improving disease resistance via sweet potato breeding programs. In the present study, we performed de novo transcriptome assembly and digital gene expression (DGE) profiling of sweet potato challenged with Fob using Illumina HiSeq technology. In total, 89,944,188 clean reads were generated from 12 samples and assembled into 101,988 unigenes with an average length of 666 bp; of these unigenes, 62,605 (61...
2017: PloS One
https://www.readbyqxmd.com/read/29128673/bi-allelic-irf8-mutation-a-complex-immunodeficiency-syndrome-with-dendritic-cell-deficiency-monocytopenia-and-immune-dysregulation
#12
Venetia Bigley, Sheetal Maisuria, Urszula Cytlak, Laura Jardine, Matthew A Care, Kile Green, Merry Gunawan, Paul Milne, Rachel Dickinson, Sarah Wiscombe, David Parry, Rainer Doffinger, Arian Laurence, Claudia Fonseca Lic, Oda Stoevesandt, Andrew Gennery, Andrew Cant, Reuben Tooze, A John Simpson, Sophie Hambleton, Sinisa Savic, Gina Doody, Matthew Collin
BACKGROUND: Homozygous K108E mutation of interferon regulatory factor 8 (IRF8) is reported to cause dendritic cell and monocyte deficiency. However, more widespread immune dysfunction is predicted from the multiple roles ascribed to IRF8 in immune cell development and function. OBJECTIVE: We sought to describe the effect on hematopoiesis and immunity of compound heterozygous R83C/ R291Q mutation of IRF8, present in a patient with recurrent viral infection, granulo-proliferation and intracerebral calcification...
November 8, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29127313/current-source-density-mapping-of-antennal-sensory-selectivity-reveals-conserved-olfactory-systems-between-tephritids-and-drosophila
#13
Vincent Jacob, Francesca Scolari, Hélène Delatte, Giuliano Gasperi, Emmanuelle Jacquin-Joly, Anna R Malacrida, Pierre-François Duyck
Ecological specialization of insects involves the functional and morphological reshaping of olfactory systems. Little is known about the degree to which insect sensitivity to odorant compounds is conserved between genera, tribes, or families. Here we compared the olfactory systems of six tephritid fruit fly species spanning two tribes and the distantly related Drosophila melanogaster at molecular, functional, and morphological levels. Olfaction in these flies is mediated by a set of olfactory receptors (ORs) expressed in different functional classes of neurons located in distinct antennal regions...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29127261/shortroot-mediated-increase-in-stomatal-density-has-no-impact-on-photosynthetic-efficiency
#14
Mara L Schuler, Olga V Sedelnikova, Berkley J Walker, Peter Westhoff, Jane A Langdale
The co-ordinated positioning of veins, mesophyll cells and stomata across a leaf is crucial for efficient gas exchange and transpiration, and therefore for overall function. In monocot leaves, stomatal cell files are positioned at the flanks of underlying longitudinal leaf veins, rather than directly above or below. This pattern suggests either that stomatal formation is inhibited in epidermal cells directly in contact with the vein, or that specification is induced in cells files beyond the vein. The SHORTROOT pathway specifies distinct cell-types around the vasculature in sub-epidermal layers of both root and shoots, with cell-type identity determined by distance from the vein...
November 10, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29127144/disruption-of-thrombocyte-and-t-lymphocyte-development-by-a-mutation-in-arpc1b
#15
Raz Somech, Atar Lev, Yu Nee Lee, Amos J Simon, Ortal Barel, Ginette Schiby, Camila Avivi, Iris Barshack, Michele Rhodes, Jiejing Yin, Minshi Wang, Yibin Yang, Jennifer Rhodes, Nufar Marcus, Ben-Zion Garty, Jerry Stein, Ninette Amariglio, Gideon Rechavi, David L Wiest, Yong Zhang
Regulation of the actin cytoskeleton is crucial for normal development and function of the immune system, as evidenced by the severe immune abnormalities exhibited by patients bearing inactivating mutations in the Wiskott-Aldrich syndrome protein (WASP), a key regulator of actin dynamics. WASP exerts its effects on actin dynamics through a multisubunit complex termed Arp2/3. Despite the critical role played by Arp2/3 as an effector of WASP-mediated control over actin polymerization, mutations in protein components of the Arp2/3 complex had not previously been identified as a cause of immunodeficiency...
November 10, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29126087/label-free-based-quantitative-proteomic-analysis-identifies-proteins-involved-in-the-testis-maturation-of-bactrocera-dorsalis-hendel
#16
Dong Wei, Meng-Yi Zhang, Pei-Ming Gu, Guy Smagghe, Jin-Jun Wang
Complex structural and biochemical processes take place in insect testis maturation, but the mechanisms by which functional proteins induce and regulate male fertility are unknown. Proteomics has been widely used to identify functional proteins involved in such complex physiological processes. In this study, we performed a label-free based quantitative proteomic analysis of developing testis of Bactrocera dorsalis with the aim of shedding light on spermatogenesis, sperm formation and also tissue development...
October 18, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29123525/identification-of-new-features-from-known-bacterial-protective-vaccine-antigens-enhances-rational-vaccine-design
#17
Edison Ong, Mei U Wong, Yongqun He
With many protective vaccine antigens reported in the literature and verified experimentally, how to use the knowledge mined from these antigens to support rational vaccine design and study underlying design mechanism remains unclear. In order to address the problem, a systematic bioinformatics analysis was performed on 291 Gram-positive and Gram-negative bacterial protective antigens with experimental evidence manually curated in the Protegen database. The bioinformatics analyses evaluated included subcellular localization, adhesin probability, peptide signaling, transmembrane α-helix and β-barrel, conserved domain, Clusters of Orthologous Groups, and Gene Ontology functional annotations...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29123030/the-nonproton-ligand-of-acid-sensing-ion-channel-3-activates-mollusk-specific-fanac-channels-via-a-mechanism-independent-of-native-fmrfamide-peptide
#18
Xiao-Na Yang, You-Ya Niu, Yan Liu, Yang Yang, Wang Jin, Xiao-Yang Cheng, Hong Liang, Heng-Shan Wang, You-Min Hu, Xiang-Yang Lu, Michael X Zhu, Tian-Le Xu, Yun Tian, Ye Yu
The degenerin/epithelial sodium channel (DEG/ENaC) superfamily of ion channels contains subfamilies with diverse functions that are fundamental to many physiological and pathological processes, ranging from synaptic transmission to epileptogenesis. The absence in mammals of some DEG/ENaCs subfamily orthologs such as FMRFamide peptide-activated sodium channels (FaNaCs), which have been identified only in mollusks, indicates that the various subfamilies diverged early in evolution. We recently reported that the nonproton agonist 2-guanidine-4-methylquinazoline (GMQ) activates acid-sensing ion channels (ASICs), a DEG/ENaC subfamily mainly in mammals, in the absence of acidosis...
November 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29121518/genome-wide-identification-phylogenetic-analysis-and-expression-profiles-of-atp-binding-cassette-transporter-genes-in-the-oriental-fruit-fly-bactrocera-dorsalis-hendel-diptera-tephritidae
#19
Lin-Fan Xiao, Wei Zhang, Tian-Xing Jing, Meng-Yi Zhang, Ze-Qing Miao, Dan-Dan Wei, Guo-Rui Yuan, Jin-Jun Wang
The ATP-binding cassette (ABC) is the largest transporter gene family and the genes play key roles in xenobiotic resistance, metabolism, and development of all phyla. However, the specific functions of ABC gene families in insects is unclear. We report a genome-wide identification, phylogenetic, and transcriptional analysis of the ABC genes in the oriental fruit fly, Bactrocera dorsalis (Hendel). We identified a total of 47 ABC genes (BdABCs) from the transcriptomic and genomic databases of B. dorsalis and classified these genes into eight subfamilies (A-H), including 7 ABCAs, 7 ABCBs, 9 ABCCs, 2 ABCDs, 1 ABCE, 3 ABCFs, 15 ABCGs, and 3 ABCHs...
October 10, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29119346/structure-target-specificity-and-expression-of-pn_lnc_n13-a-long-non-coding-rna-differentially-expressed-in-apomictic-and-sexual-paspalum-notatum
#20
Ana Ochogavía, Giulio Galla, José Guillermo Seijo, Ana María González, Michele Bellucci, Fulvio Pupilli, Gianni Barcaccia, Emidio Albertini, Silvina Pessino
KEY MESSAGE: ncRNA PN_LNC_N13 shows contrasting expression in reproductive organs of sexual and apomictic Paspalum notatum genotypes. Apomictic plants set genetically maternal seeds whose embryos derive by parthenogenesis from unreduced egg cells, giving rise to clonal offspring. Several Paspalum notatum apomixis related genes were identified in prior work by comparative transcriptome analyses. Here, one of these candidates (namely N13) was characterized. N13 belongs to a Paspalum gene family including 30-60 members, of which at least eight are expressed at moderate levels in florets...
November 8, 2017: Plant Molecular Biology
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