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3,4-Dihydroxyphenylacetaldehyde synthase and cuticle formation in insects
Liao, Chenghong; Liang, Jing; Han, Qian; Li, Jianyong (2018-06-02)
Cuticle is the most important structure that protects mosquitoes and other insect species from adverse environmental conditions and infections of microorganism. The physiology and biochemistry of insect cuticle formation have been studied for many years and our understanding of cuticle formation and hardening has increased considerably. This is especially true for flexible cuticle. The recent discovery of a novel enzyme that catalyzes the production of 3,4-dihydroxyphenylacetaldehyde (DOPAL) in insects provides intriguing insights concerning the flexible cuticle formation in insects. For convenience, the enzyme that catalyzes the production DOPAL from L-dopa is named DOPAL synthase. In this mini-review, we summarize the biochemical pathways of cuticle formation and hardening in general and discuss DOPAL synthase-mediated protein crosslinking in insect flexible cuticle in particular.
Activation of PAD4 in NET formation
Rohrbach, Amanda S.; Slade, Daniel J.; Thompson, Paul R.; Mowen, Kerri A. (2012)
Peptidylarginine deiminases, or PADs, convert arginine residues to the non-ribosomally encoded amino acid citrulline in a variety of protein substrates. PAD4 is expressed in granulocytes and is essential for the formation of neutrophil extracellular traps (NETs) via PAD4-mediated histone citrullination. Citrullination of histones is thought to promote NET formation by inducing chromatin decondensation and facilitating the expulsion of chromosomal DNA that is coated with antimicrobial molecules. Numerous stimuli have been reported to lead to PAD4 activation and NET formation. However, how this signaling process proceeds and how PAD4 becomes activated in cells is largely unknown. Herein, we describe the various stimuli and signaling pathways that have been implicated in PAD4 activation and NET formation, including the role of reactive oxygen species generation. To provide a foundation for the above discussion, we first describe PAD4 structure and function, and how these studies led to the development of PAD-specific inhibitors. A comprehensive survey of the receptors and signaling pathways that regulate PAD4 activation will be important for our understanding of innate immunity, and the identification of signaling intermediates in PAD4 activation may also lead to the generation of pharmaceuticals to target NET-related pathogenesis.
Activation of SsoPK4, an Archaeal eIF2α Kinase Homolog, by Oxidized CoA
Ray, William K.; Potters, Mark B.; Haile, January D.; Kennelly, Peter J. (MDPI, 2015-05-15)
The eukaryotic protein kinase (ePK) paradigm provides integral components for signal transduction cascades throughout nature. However, while so-called typical ePKs permeate the Eucarya and Bacteria, atypical ePKs dominate the kinomes of the Archaea. Intriguingly, the catalytic domains of the handful of deduced typical ePKs from the archaeon Sulfolobus solfataricus P2 exhibit significant resemblance to the protein kinases that phosphorylate translation initiation factor 2α (eIF2α) in response to cellular stresses. We cloned and expressed one of these archaeal eIF2α protein kinases, SsoPK4. SsoPK4 exhibited protein-serine/threonine kinase activity toward several proteins, including the S. solfataricus homolog of eIF2α, aIF2α. The activity of SsoPK4 was inhibited in vitro by 3ʹ,5ʹ-cyclic AMP (K_i of ~23 µM) and was activated by oxidized Coenzyme A, an indicator of oxidative stress in the Archaea. Activation enhanced the apparent affinity for protein substrates, K_m, but had little effect on V_max. Autophosphorylation activated SsoPK4 and rendered it insensitive to oxidized Coenzyme A.
Analysis of T-DNA alleles of flavonoid biosynthesis genes in Arabidopsis ecotype Columbia
Bowerman, Peter A.; Ramirez, Melissa V.; Price, Michelle B.; Helm, Richard F.; Winkel, Brenda S. J. (2012-09-04)
BACKGROUND: The flavonoid pathway is a long-standing and important tool for plant genetics, biochemistry, and molecular biology. Numerous flavonoid mutants have been identified in Arabidopsis over the past several decades in a variety of ecotypes. Here we present an analysis of Arabidopsis lines of ecotype Columbia carrying T-DNA insertions in genes encoding enzymes of the central flavonoid pathway. We also provide a comprehensive summary of various mutant alleles for these structural genes that have been described in the literature to date in a wide variety of ecotypes. FINDINGS: The confirmed knockout lines present easily-scorable phenotypes due to altered pigmentation of the seed coat (or testa). Knockouts for seven alleles for six flavonoid biosynthetic genes were confirmed by PCR and characterized by UPLC for altered flavonol content. CONCLUSION: Seven mutant lines for six genes of the central flavonoid pathway were characterized in ecotype, Columbia. These lines represent a useful resource for integrating biochemical and physiological studies with genomic, transcriptomic, and proteomic data, much of which has been, and continues to be, generated in the Columbia background.
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation
Miller, Jason R.; Koren, Sergey; Dilley, Kari A.; Puri, Vinita; Brown, David M.; Harkins, Derel M.; Thibaud-Nissen, Françoise; Rosen, Benjamin D.; Xiao-Guang, Chen; Tu, Zhijian Jake; Sharakhov, Igor V.; Sharakhova, Maria V.; Sebra, R.; Stockwell, T. B.; Bergman, N. H.; Sutton, G. G.; Phillippi, A. M.; Pieemarini, P. M.; Shabman, R. S. (2018-03)
The 50-year old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome.
Antimalarial 5,6-Dihydro-alpha-pyrones from Cryptocarya rigidifolia: Related Bicyclic Tetrahydro-alpha-Pyrones Are Artifacts
Liu, Yixi; Rakotondraibe, L. Harinantenaina; Brodie, Peggy J.; Wiley, Jessica D.; Cassera, Maria B.; Miller, James S.; Ratovoson, F.; Rakotobe, Etienne; Rasamison, Vincent E.; Kingston, David G. I. (American Chemical Society, 2015-06-01)
Antiproliferative Compounds from Cleistanthus boivinianus from the Madagascar Dry Forest
Liu, Yixi; Young, Kelly; Rakotondraibe, L. Harinantenaina; Brodie, Peggy J.; Wiley, Jessica D.; Cassera, Maria B.; Callmander, Martin W.; Rakotondrajaona, R.; Rakotobe, Etienne; Rasamison, Vincent E.; TenDyke, Karen; Shen, Yongchun; Kingston, David G. I. (American Chemical Society, 2015-07-01)
Association of microRNAs with Argonaute proteins in the malaria mosquito Anopheles gambiae after blood ingestion
Fu, X.; Dimopoulos, G.; Zhu, J. (2017)
Attracting and Retaining Minorities in the Biomedical Sciences Including Genomics: a Community-based Approach
Smith, Edward J. (2014-08-21)
The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere
Compton, Austin; Liang, Jiangtao; Chen, Chujia; Lukyanchikova, Varvara; Qi, Yumin; Potters, Mark B.; Settlage, Robert; Miller, Dustin; Deschamps, Stephane; Mao, Chunhong; Llaca, Victor; Sharakhov, Igor V.; Tu, Zhijian Jake (Genetics Society of America, 2020-10-01)
Chromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved. Here we produce a de novo assembly of the New World malaria mosquito, Anopheles albimanus by integrating Oxford Nanopore sequencing, Illumina, Hi-C and optical mapping. This 172.6 Mbps female assembly, which we call AalbS3, is obtained by scaffolding polished large contigs (contig N50 = 13.7 Mbps) into three chromosomes. All chromosome arms end with telomeric repeats, which is the first in mosquito assemblies and represents a significant step toward the completion of a genome assembly. These telomeres consist of tandem repeats of a novel 30-32 bp Telomeric Repeat Unit (TRU) and are confirmed by analyzing the termini of long reads and through both chromosomal in situ hybridization and a Bal31 sensitivity assay. The AalbS3 assembly included previously uncharacterized centromeric and rDNA clusters and more than doubled the content of transposable elements and other repetitive sequences. This telomere-to-telomere assembly, although still containing gaps, represents a significant step toward resolving biologically important but previously hidden genomic components. The comparison of different scaffolding methods will also inform future efforts to obtain reference-quality genomes for other mosquito species.
Biosynthesis and possible functions of inositol pyrophosphates in plants
Williams, Sarah P.; Gillaspy, Glenda E.; Perera, Imara Y. (Frontiers, 2015-02-12)
Inositol phosphates (InsPs) are intricately tied to lipid signaling, as at least one portion of the inositol phosphate signaling pool is derived from hydrolysis of the lipid precursor, phosphatidyl inositol (4,5) bisphosphate. The focus of this review is on the inositol pyrophosphates, which are a novel group of InsP signaling molecules containing diphosphate or triphosphate chains (i.e., PPx) attached to the inositol ring. These PPx-InsPs are emerging as critical players in the integration of cellular metabolism and stress signaling in non-plante ukaryotes. Most eukaryotes synthesize the precursor molecule, myo-inositol (1,2,3,4,5,6)-hexakisphosphate (InsP6), which can serve as a signaling molecule or as storage compound of inositol, phosphorus, and minerals( referred to as phytic acid). Even though plants produce huge amounts of precursor InsP6 in seeds, almost no attention has been paid to whether PPx-InsPs exist in plants, and if so, what roles these molecules play. Recent work has delineated that Arabidopsis has two genes capable of PP-InsP5 synthesis, and PPx-InsPs have been detected across the plant kingdom. This review will detail the known roles of PPx-InsPs in yeast and animal systems, and provide a description of recent data on the synthesis and accumulation of these novel molecules in plants, and potential roles in signaling.
Biosynthesis of Galactofuranose in Kinetoplastids: Novel Therapeutic Targets for Treating Leishmaniasis and Chagas' Disease
Oppenheimer, Michelle; Valenciano Murillo, Ana L.; Sobrado, Pablo (Hindawi, 2011-05-25)
Cell surface proteins of parasites play a role in pathogenesis by modulating mammalian cell recognition and cell adhesion during infection. β-Galactofuranose (Galf) is an important component of glycoproteins and glycolipids found on the cell surface of Leishmania spp. and Trypanosoma cruzi. β-Galf-containing glycans have been shown to be important in parasite-cell interaction and protection against oxidative stress. Here, we discuss the role of β-Galf in pathogenesis and recent studies on the Galf-biosynthetic enzymes: UDP-galactose 4′ epimerase (GalE), UDP-galactopyranose mutase (UGM), and UDP-galactofuranosyl transferase (GalfT). The central role in Galf formation, its unique chemical mechanism, and the absence of a homologous enzyme in humans identify UGM as the most attractive drug target in the β-Galf-biosynthetic pathway in protozoan parasites.
Borrelia burgdorferi SpoVG DNA- and RNA-Binding Protein Modulates the Physiology of the Lyme Disease Spirochete
Savage, Christina R.; Jutras, Brandon L.; Bestor, Aaron; Tilly, Kit; Rosa, Patricia A.; Tourand, Yvonne; Stewart, Philip E.; Brissette, Catherine A.; Stevenson, Brian (American Society for Microbiology, 2018-06-01)
Broccoli Fluorets: Split Aptamers as a User-Friendly Fluorescent Toolkit for Dynamic RNA Nanotechnology
Chandler, Morgan; Lyalina, Tatiana; Halman, Justin; Rackley, Lauren; Lee, Lauren; Dang, Dylan; Ke, Weina; Sajja, Sameer; Woods, Steven; Acharya, Shrija; Baumgarten, Elijah; Christopher, Jonathan; Elshalia, Emman; Hrebien, Gabriel; Kublank, Kinzey; Saleh, Saja; Stallings, Bailey; Tafere, Michael; Striplin, Caryn; Afonin, Kirill A. (MDPI, 2018-12-02)
RNA aptamers selected to bind fluorophores and activate their fluorescence offer a simple and modular way to visualize native RNAs in cells. Split aptamers which are inactive until the halves are brought within close proximity can become useful for visualizing the dynamic actions of RNA assemblies and their interactions in real time with low background noise and eliminated necessity for covalently attached dyes. Here, we design and test several sets of F30 Broccoli aptamer splits, that we call fluorets, to compare their relative fluorescence and physicochemical stabilities. We show that the splits can be simply assembled either through one-pot thermal annealing or co-transcriptionally, thus allowing for direct tracking of transcription reactions via the fluorescent response. We suggest a set of rules that enable for the construction of responsive biomaterials that readily change their fluorescent behavior when various stimuli such as the presence of divalent ions, exposure to various nucleases, or changes in temperature are applied. We also show that the strand displacement approach can be used to program the controllable fluorescent responses in isothermal conditions. Overall, this work lays a foundation for the future development of dynamic systems for molecular computing which can be used to monitor real-time processes in cells and construct biocompatible logic gates.
Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest
Sparks, Michael E.; Bansal, Raman; Benoit, Joshua B.; Blackburn, Michael B.; Chao, Hsu; Chen, Mengyao; Cheng, Sammy; Childers, Christopher; Dinh, Huyen; Doddapaneni, Harsha V.; Dugan, Shannon; Elpidina, Elena N.; Farrow, David W.; Friedrich, Markus; Gibbs, Richard A.; Hall, Brantley; Han, Yi; Hardy, Richard W.; Holmes, Christopher J.; Hughes, Daniel S. T.; Ioannidis, Panagiotis; Cheatle Jarvela, Alys M.; Johnston, J. Spencer; Jones, Jeffery W.; Kronmiller, Brent A.; Kung, Faith; Lee, Sandra L.; Martynov, Alexander G.; Masterson, Patrick; Maumus, Florian; Munoz-Torres, Monica; Murali, Shwetha C.; Murphy, Terence D.; Muzny, Donna M.; Nelson, David R.; Oppert, Brenda; Panfilio, Kristen A.; Paula, Débora P.; Pick, Leslie; Poelchau, Monica F.; Qu, Jiaxin; Reding, Katie; Rhoades, Joshua H.; Rhodes, Adelaide; Richards, Stephen; Richter, Rose; Robertson, Hugh M.; Rosendale, Andrew J.; Tu, Zhijian Jake; Velamuri, Arun S.; Waterhouse, Robert M.; Weirauch, Matthew T.; Wells, Jackson T.; Werren, John H.; Worley, Kim C.; Zdobnov, Evgeny M.; Gundersen-Rindal, Dawn E. (2020-03-14)
Background Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species’ feeding and habitat traits, defining potential targets for pest management strategies. Results Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys’ capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications. Conclusions Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.
Can Inositol Pyrophosphates Inform Strategies for Developing Low Phytate Crops?
Freed, Catherine P.; Adepoju, Olusegun; Gillaspy, Glenda E. (MDPI, 2020-01-17)
Inositol pyrophosphates (PP-InsPs) are an emerging class of “high-energy” intracellular signaling molecules, containing one or two diphosphate groups attached to an inositol ring, that are connected with phosphate sensing, jasmonate signaling, and inositol hexakisphosphate (InsP₆) storage in plants. While information regarding this new class of signaling molecules in plants is scarce, the enzymes responsible for their synthesis have recently been elucidated. This review focuses on InsP₆ synthesis and its conversion into PP-InsPs, containing seven and eight phosphate groups (InsP₇ and InsP₈). These steps involve two types of enzymes: the ITPKs that phosphorylate InsP₆ to InsP₇, and the PPIP5Ks that phosphorylate InsP₇ to InsP₈. This review also considers the potential roles of PP-InsPs in plant hormone and inorganic phosphate (Pi) signaling, along with an emerging role in bioenergetic homeostasis. PP-InsP synthesis and signaling are important for plant breeders to consider when developing strategies that reduce InsP₆ in plants, as this will likely also reduce PP-InsPs. Thus, this review is primarily intended to bridge the gap between the basic science aspects of PP-InsP synthesis/signaling and breeding/engineering strategies to fortify foods by reducing InsP₆.
The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View
Xavier, Joao B.; Young, Vincent B.; Skufca, Joseph; Ginty, Fiona; Testerman, Traci; Pearson, Alexander T.; Macklin, Paul; Mitchell, Amir; Shmulevich, Ilya; Xie, Lei; Caporaso, J. Gregory; Crandall, Keith A.; Simone, Nicole L.; Godoy-Vitorino, Filipa; Griffin, Timothy J.; Whiteson, Katrine L.; Gustafson, Heather H.; Slade, Daniel J.; Schmidt, Thomas M.; Walther-Antonio, Marina RS S.; Korem, Tal; Webb-Robertson, Bobbie-Jo M.; Styczynski, Mark P.; Johnson, W. Evan; Jobin, Christian; Ridlon, Jason M.; Koh, Andrew Y.; Yu, Michael; Kelly, Libusha; Wargo, Jennifer A. (Cell Press, 2020-03-01)
The collection of microbes that live in and on the human body – the human microbiome – can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions between microbes, diet, host factors, drugs, and cell–cell interactions within the cancer itself likely involve intricate feedbacks, and no single component can explain all the behavior of the system. Understanding the role of host-associated microbial communities in cancer systems will require a multidisciplinary approach combining microbial ecology, immunology, cancer cell biology, and computational biology – a systems biology approach.
Certain Malvaceae Plants Have a Unique Accumulation of myo-Inositol 1,2,4,5,6-Pentakisphosphate
Phillippy, Brian Q.; Perera, Imara Y.; Donahue, Janet L.; Gillaspy, Glenda E. (MDPI, 2015-05-29)
Methods used to quantify inositol phosphates in seeds lack the sensitivity and specificity necessary to accurately detect the lower concentrations of these compounds contained in the leaves of many plants. In order to measure inositol hexakisphosphate (InsP₆) and inositol pentakisphosphate (InsP₅) levels in leaves of different plants, a method was developed to concentrate and pre-purify these compounds prior to analysis. Inositol phosphates were extracted from leaves with diluted HCl and concentrated on small anion exchange columns. Reversed-phase solid phase extraction cartridges were used to remove compounds that give peaks that sometimes interfere during HPLC. The method permitted the determination of InsP₆ and InsP₅ concentrations in leaves as low as 10 µM and 2 µM, respectively. Most plants analyzed contained a high ratio of InsP₆ to InsP₅. In contrast, certain members of the Malvaceae family, such as cotton (Gossypium) and some hibiscus (Hibiscus) species, had a preponderance of InsP₅. Radiolabeling of cotton seedlings also showed increased amounts of InsP₅ relative to InsP₆. Why some Malvaceae species exhibit a reversal of the typical ratios of these inositol phosphates is an intriguing question for future research.
Characterization of ESBL (SHV-12) producing clinical isolate of Enterobacter aerogenes from a tertiary care hospital in Nigeria
Kasap, Murat; Fashae, Kayode; Torol, Sinem; Kolayli, Fetiye; Budak, Fatma; Vahaboglu, Haluk (2010-01-12)
Background We studied the beta-lactamases of an E. aerogenes isolate recovered from the blood of a two-year-old patient. The isolate demonstrated a disk-diffusion phenotype typical for an AmpC-ESBL co-producer. Methods Microbiology studies were performed according to standard protocols. The resistance gene was identified by transconjugation and cloning experiments. Results By transconjugation only a narrow spectrum beta-lactamase (TEM-1) encoded on a small plasmid was transmitted. The ESBL was cloned and expressed in an E. coli host. Sequence analysis of the recombinant plasmid revealed blaSHV-12 associated to the insertion sequence, IS26. Conclusion This is the first study demonstrated the occurrence of SHV-12 in Nigeria.
Characterization of the inositol monophosphatase gene family in Arabidopsis
Nourbakhsh, Aida; Collakova, Eva; Gillaspy, Glenda E. (Frontiers, 2015-01-09)
Synthes is of myo-inositol is crucial in multicellular eukaryote for production of phosphatidylinositol and inositol phosphate signaling molecules. The myo-inositol monophosphatase (IMP) enzyme is required for the synthesis of myo-inositol, breakdown of inositol (1,4,5)-trisphosphate, a second messenger involved in Ca2+ signaling, and synthesis of L-galactose, a precursor of ascorbic acid. Two myo-inositol monophosphatase-like (IMPL) genes in Arabidopsis encode chloroplast proteins with homology to the prokaryotic IMPs and one of these, IMPL2, can complement a bacterial histidinol 1-phosphate phosphatase mutant defective in histidine synthesis, indicating an important role for IMPL2 in amino acid synthesis. To delineate how this small gene family functions in inositol synthesis and metabolism, we sought to compare recombinant enzyme activities, expression patterns, and impact of genetic loss-of-function mutations for each. Our data show that purified IMPL2 protein is an active histidinol-phosphate phosphatase enzyme in contrast to the IMPL1 enzyme, which has the ability to hydrolyze D-galactose 1-phosphate, and D-myo-inositol 1-phosphate, a breakdown product of D-inositol (1,4,5) trisphosphate. Expression studies indicated that all three genes are expressed in multiple tissues, however, IMPL1 expression is restricted to above-ground tissues only. Identification and characterization of impl1 and impl2 mutants revealed no viable mutants for IMPL1, while two different impl2 mutants were identified and shown to be severely compromised in growth, which can be rescued by histidine. Analyses of metabolite levels in impl2 and complemented mutants reveals impl2 mutant grow this impacted by alterations in the histidine biosynthesis pathway, but does not impact myo-inositol synthesis. Together, these data indicate that IMPL2 functions in the histidine biosynthetic pathway, while IMP and IMPL1 catalyze the hydrolysis of inositol- and galactose-phosphates in the plant cell.

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