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Bacterial genomics

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https://www.readbyqxmd.com/read/29786865/infection-with-phytopathogenic-bacterium-inhibits-melatonin-biosynthesis-decreases-longevity-of-its-vector-and-suppresses-the-free-radical-defense
#1
Yasser Nehela, Nabil Killiny
Vector-borne phytopathogenic bacteria may alter the reproductive fitness, survival, behavior, and metabolism of their vectors. Candidatus Liberibacter asiaticus (CLas) is associated with the Huanglongbing (HLB; also known as citrus greening disease), one of the most destructive citrus diseases worldwide, and transmitted by Asian citrus psyllid, Diaphorina citri (Insecta, Hemiptera, Liviidae). The genome sequencing of CLas revealed that it does not have the ability to synthesize tryptophan, the precursor of melatonin, and it must acquire it from its host plant or insect vector to achieve its biological processes, such as growth and multiplication...
May 22, 2018: Journal of Pineal Research
https://www.readbyqxmd.com/read/29786424/tuning-gene-activity-by-inducible-and-targeted-regulation-of-gene-expression-in-minimal-bacterial-cells
#2
Ana M Mariscal, Shigeyuki Kakizawa, Jonathan Y Hsu, Kazuki Tanaka, Luis González-González, Alicia Broto, Enrique Querol, Maria Lluch-Senar, Carlos Piñero-Lambea, Lijie Sun, Philip D Weyman, Kim S Wise, Chuck Merryman, Gavin Tse, Adam J Moore, Clyde A Hutchison, Hamilton O Smith, Masaru Tomita, J Craig Venter, John I Glass, Jaume Piñol, Yo Suzuki
Functional genomics studies in minimal mycoplasma cells enable unobstructed access to some of the most fundamental processes in biology. Conventional transposon bombardment and gene knockout approaches often fail to reveal functions of genes that are essential for viability, where lethality precludes phenotypic characterization. Conditional inactivation of genes is effective for characterizing functions central to cell growth and division, but tools are limited for this purpose in mycoplasmas. Here we demonstrate systems for inducible repression of gene expression based on clustered regularly interspaced short palindromic repeats-mediated interference (CRISPRi) in Mycoplasma pneumoniae and synthetic Mycoplasma mycoides, two organisms with reduced genomes actively used in systems biology studies...
May 22, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29786171/root-bacterial-endophytes-confer-drought-resistance-and-enhance-expression-and-activity-of-a-vacuolar-h-pumping-pyrophosphatase-in-pepper-plants
#3
Gianpiero Vigani, Eleonora Rolli, Ramona Marasco, Marta Dell'Orto, Grégoire Michoud, Asma Soussi, Noura Raddadi, Sara Borin, Claudia Sorlini, Graziano Zocchi, Daniele Daffonchio
It has been previously shown that the transgenic overexpression of the plant root vacuolar proton pumps H+ -ATPase (V-ATPase) and H+ -PPase (V-PPase) confer tolerance to drought. Since plant-root endophytic bacteria can also promote drought tolerance, we hypothesize that such promotion can be associated to the enhancement of the host vacuolar proton pumps expression and activity. To test this hypothesis, we selected two endophytic bacteria endowed with an array of in vitro plant growth promoting traits. Their genome sequences confirmed the presence of traits previously shown to confer drought resistance to plants, such as the synthesis of nitric oxide and of organic volatile organic compounds...
May 22, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29785904/identification-of-an-immune-modulation-locus-utilising-a-bovine-mammary-gland-infection-challenge-model
#4
Mathew D Littlejohn, Sally-Anne Turner, Caroline G Walker, Sarah D Berry, Kathryn Tiplady, Ric G Sherlock, Greg Sutherland, Simon Swift, Dorian Garrick, S Jane Lacy-Hulbert, Scott McDougall, Richard J Spelman, Russell G Snell, J Eric Hillerton
Inflammation of the mammary gland following bacterial infection, commonly known as mastitis, affects all mammalian species. Although the aetiology and epidemiology of mastitis in the dairy cow are well described, the genetic factors mediating resistance to mammary gland infection are not well known, due in part to the difficulty in obtaining robust phenotypic information from sufficiently large numbers of individuals. To address this problem, an experimental mammary gland infection experiment was undertaken, using a Friesian-Jersey cross breed F2 herd...
May 2018: Journal of Dairy Research
https://www.readbyqxmd.com/read/29785479/ngspanpipe-a-pipeline-for-pan-genome-identification-in-microbial-strains-from-experimental-reads
#5
Umay Kulsum, Arti Kapil, Harpreet Singh, Punit Kaur
Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29784887/identification-of-the-thioredoxin-partner-of-vkor-in-mycobacterial-disulfide-bond-formation
#6
Na Ke, Cristina Landeta, Xiaoyun Wang, Dana Boyd, Markus Eser, Jon Beckwith
Disulfide bonds influence stability and activity of many proteins. In Escherichia coli the DsbA and DsbB enzymes promote disulfide bond formation. Other bacteria, including the Actinobacteria, use instead of DsbB the enzyme VKOR (Vitamin K Epoxide Reductase), which is found either fused to or encoded in the same operon as a dsbA -like protein. Mycobacterium tuberculosis and other gram-positive Actinobacteria secrete to the cell envelope many proteins with even numbers of cysteines. These organisms have predicted oxidoreductases and VKOR orthologs...
May 21, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29784861/genome-variation-and-molecular-epidemiology-of-salmonella-typhimurium-pathovariants
#7
Priscilla Branchu, Matt Bawn, Robert A Kingsley
Salmonella enterica serovar Typhimurium ( S Typhimurium) is one of approximately 2500 distinct serovars of the genus Salmonella , but is exceptional in its wide distribution in the environment, livestock, and wild animals. S Typhimurium causes a large proportion of non-typhoid Salmonella (NTS) infections, accounting for a quarter of infections, second only to S Enteritidis in incidence. S Typhimurium was once considered the archetypal broad host range Salmonella serovar due to its wide distribution in livestock and wild animals and much of what we know of the interaction of Salmonella with the host comes from research using a small number of laboratory strains of the serovar (LT2, SL1344, ATCC14028)...
May 21, 2018: Infection and Immunity
https://www.readbyqxmd.com/read/29784811/systematic-prediction-of-genes-functionally-linked-to-crispr-cas-systems-by-gene-neighborhood-analysis
#8
Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin
The CRISPR-Cas systems of bacterial and archaeal adaptive immunity consist of direct repeat arrays separated by unique spacers and multiple CRISPR-associated ( cas ) genes encoding proteins that mediate all stages of the CRISPR response. In addition to the relatively small set of core cas genes that are typically present in all CRISPR-Cas systems of a given (sub)type and are essential for the defense function, numerous genes occur in CRISPR- cas loci only sporadically. Some of these have been shown to perform various ancillary roles in CRISPR response, but the functional relevance of most remains unknown...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29784781/c-4-sterol-demethylation-enzymes-distinguish-bacterial-and-eukaryotic-sterol-synthesis
#9
Alysha K Lee, Amy B Banta, Jeremy H Wei, David J Kiemle, Ju Feng, José-Luis Giner, Paula V Welander
Sterols are essential eukaryotic lipids that are required for a variety of physiological roles. The diagenetic products of sterol lipids, sterane hydrocarbons, are preserved in ancient sedimentary rocks and are utilized as geological biomarkers, indicating the presence of both eukaryotes and oxic environments throughout Earth's history. However, a few bacterial species are also known to produce sterols, bringing into question the significance of bacterial sterol synthesis for our interpretation of sterane biomarkers...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29784711/quantitative-proteome-and-phosphoproteome-analyses-of-streptomyces-coelicolor-reveal-proteins-and-phosphoproteins-modulating-differentiation-and-secondary-metabolism
#10
Beatriz Rioseras, Pavel V Sliaha, Vladimir Gorshkov, Paula Yagüe, Maria T López-García, Nathaly González-Quiñónez, Sergey Kovalchuk, Adelina Rogowska-Wrzesinska, Ole N Jensen, Angel Manteca
Streptomycetes are multicellular bacteria with complex developmental cycles. They are of biotechnological importance as they produce most bioactive compounds used in biomedicine, e.g. antibiotic, antitumoral and immunosupressor compounds. Streptomyces genomes encode a large number of Ser/Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor...
May 21, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29783718/functional-genomics-approaches-to-studying-symbioses-between-legumes-and-nitrogen-fixing-rhizobia
#11
REVIEW
Martina Lardi, Gabriella Pessi
Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used...
May 18, 2018: High-throughput
https://www.readbyqxmd.com/read/29782536/fungal-type-carbohydrate-binding-modules-from-the-coccolithophore-emiliania-huxleyi-show-binding-affinity-to-cellulose-and-chitin
#12
Bart J M Rooijakkers, Martina S Ikonen, Markus B Linder
Six fungal-type cellulose binding domains were found in the genome of the coccolithophore Emiliania huxleyi and cloned and expressed in Escherichia coli. Sequence comparison indicate high similarity to fungal cellulose binding domains, raising the question of why these domains exist in coccolithophores. The proteins were tested for binding with cellulose and chitin as ligands, which resulted in the identification of two functional carbohydrate binding modules: EHUX2 and EHUX4. Compared to benchmark fungal cellulose binding domain Cel7A-CBM1 from Trichoderma reesei, these proteins showed slightly lower binding to birch and bacterial cellulose, but were more efficient chitin binders...
2018: PloS One
https://www.readbyqxmd.com/read/29782468/potential-role-of-gut-microbiota-in-als-pathogenesis-and-possible-novel-therapeutic-strategies
#13
Letizia Mazzini, Luca Mogna, Fabiola De Marchi, Angela Amoruso, Marco Pane, Irene Aloisio, Nicole Bozzi Cionci, Francesca Gaggìa, Ausiliatrice Lucenti, Enrica Bersano, Roberto Cantello, Diana Di Gioia, Giovanni Mogna
BACKGROUND: Recent preclinical studies suggest that dysfunction of gastrointestinal tract may play a role in amyotrophic lateral sclerosis (ALS) pathogenesis through a modification of the gut microbiota brain axis. Our study is the first focused on microbiota analysis in ALS patients. AIM: Our aim was to study the main human gut microbial groups and the overall microbial diversity in ALS and healthy subjects. Moreover we have examined the influence of a treatment with a specific bacteriotherapy composed of Lactobacillus strains (Lactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus plantarum, Lactobacillus salivarius) acting on the gastrointestinal barrier...
May 18, 2018: Journal of Clinical Gastroenterology
https://www.readbyqxmd.com/read/29781800/linkage-of-the-nit1c-gene-cluster-to-bacterial-cyanide-assimilation-as-a-nitrogen-source
#14
Lauren B Jones, Pallab Ghosh, Jung-Hyun Lee, Chia-Ni Chou, Daniel A Kunz
A genetic linkage between a conserved gene cluster (Nit1C) and the ability of bacteria to utilize cyanide as the sole nitrogen source was demonstrated for nine different bacterial species. These included three strains whose cyanide nutritional ability has formerly been documented (Pseudomonas fluorescens Pf11764, Pseudomonas putida BCN3 and Klebsiella pneumoniae BCN33), and six not previously known to have this ability [Burkholderia (Paraburkholderia) xenovorans LB400, Paraburkholderia phymatum STM815, Paraburkholderia phytofirmans PsJN, Cupriavidus (Ralstonia) eutropha H16, Gluconoacetobacter diazotrophicus PA1 5 and Methylobacterium extorquens AM1]...
May 21, 2018: Microbiology
https://www.readbyqxmd.com/read/29781799/an-outbreak-of-a-rare-shiga-toxin-producing-escherichia-coli-serotype-o117-h7-among-men-who-have-sex-with-men
#15
Kate S Baker, Timothy J Dallman, Nicholas R Thomson, Claire Jenkins
Sexually transmissible enteric infections (STEIs) are commonly associated with transmission among men who have sex with men (MSM). In the past decade, the UK has experienced multiple parallel STEI emergences in MSM caused by a range of bacterial species of the genus Shigella, and an outbreak of an uncommon serotype (O117 : H7) of Shiga-toxin-producing Escherichia coli (STEC). Here, we used microbial genomics on 6 outbreak and 30 sporadic STEC O117 : H7 isolates to explore the origins and pathogenic drivers of the STEC O117 : H7 emergence in MSM...
May 21, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29781797/from-plants-to-nematodes-serratia-grimesii-bxf1-genome-reveals-an-adaptation-to-the-modulation-of-multi-species-interactions
#16
Francisco Nascimento, Cláudia Vicente, Peter Cock, Maria Tavares, Márcio Rossi, Koichi Hasegawa, Manuel Mota
Serratia grimesii BXF1 is a bacterium with the ability to modulate the development of several eukaryotic hosts. Strain BXF1 was isolated from the pinewood nematode, Bursaphelenchus xylophilus, the causative agent of pine wilt disease affecting pine forests worldwide. This bacterium potentiates Bursaphelenchus xylophilus reproduction, acts as a beneficial pine endophyte, and possesses fungal and bacterial antagonistic activities, further indicating a complex role in a wide range of trophic relationships. In this work, we describe and analyse the genome sequence of strain BXF1, and discuss several important aspects of its ecological role...
May 21, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29778228/the-highly-heterogeneous-methylated-genomes-and-diverse-restriction-modification-systems-of-bloom-forming-microcystis
#17
Liang Zhao, Yulong Song, Lin Li, Nanqin Gan, Jerry J Brand, Lirong Song
The occurrence of harmful Microcystis blooms is increasing in frequency in a myriad of freshwater ecosystems. Despite considerable research pertaining to the cause and nature of these blooms, the molecular mechanisms behind the cosmopolitan distribution and phenotypic diversity in Microcystis are still unclear. We compared the patterns and extent of DNA methylation in three strains of Microcystis, PCC 7806SL, NIES-2549 and FACHB-1757, using Single Molecule Real-Time (SMRT) sequencing technology. Intact restriction-modification (R-M) systems were identified from the genomes of these strains, and from two previously sequenced strains of Microcystis, NIES-843 and TAIHU98...
May 2018: Harmful Algae
https://www.readbyqxmd.com/read/29777624/characterisation-of-a-putative-glutamate-5-kinase-from-leishmania-donovani
#18
Natasha Sienkiewicz, Han B Ong, Alan H Fairlamb
Previous metabolic studies have demonstrated that leishmania parasites are able to synthesise proline from glutamic acid and threonine from aspartic acid. The first committed step in both biosynthetic pathways involves an amino acid kinase, either a glutamate 5-kinase (EC 2.7.2.11) or an aspartokinase (EC 2.7.2.4). Bioinformatic analysis of multiple leishmania genomes identifies a single amino-acid-kinase gene (LdBPK 262740.1) variously annotated as either a putative glutamate or aspartate kinase. To establish the catalytic function of this Leishmania donovani gene product, we have determined the physical and kinetic properties of the recombinant enzyme purified from Escherichia coli...
May 19, 2018: FEBS Journal
https://www.readbyqxmd.com/read/29775460/genus-wide-comparison-of-pseudovibrio-bacterial-genomes-reveal-diverse-adaptations-to-different-marine-invertebrate-hosts
#19
Anoop Alex, Agostinho Antunes
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater...
2018: PloS One
https://www.readbyqxmd.com/read/29774830/frequent-implication-of-multistress-tolerant-campylobacter-jejuni-in-human-infections
#20
Euna Oh, Linda Chui, Junghee Bae, Vincent Li, Angela Ma, Steven K Mutschall, Eduardo N Taboada, Lynn M McMullen, Byeonghwa Jeon
Campylobacter jejuni, a major cause of bacterial foodborne illnesses, is considered highly susceptible to environmental stresses. In this study, we extensively investigated the stress tolerance of 121 clinical strains of C. jejuni against 5 stress conditions (aerobic stress, disinfectant exposure, freeze-thaw, heat treatment, and osmotic stress) that this pathogenic bacterium might encounter during foodborne transmission to humans. In contrast to our current perception about high stress sensitivity of C. jejuni, a number of clinical strains of C...
June 2018: Emerging Infectious Diseases
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