Diversity of Aster Yellows Phytoplasmas in Lettuce
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Mobile Genetic Elements in Streptococci
Curr. Issues Mol. Biol. (2019) 32: 123-166. DOI: https://dx.doi.org/10.21775/cimb.032.123 Mobile Genetic Elements in Streptococci Miao Lu#, Tao Gong#, Anqi Zhang, Boyu Tang, Jiamin Chen, Zhong Zhang, Yuqing Li*, Xuedong Zhou* State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China. #Miao Lu and Tao Gong contributed equally to this work. *Address correspondence to: [email protected], [email protected] Abstract Streptococci are a group of Gram-positive bacteria belonging to the family Streptococcaceae, which are responsible of multiple diseases. Some of these species can cause invasive infection that may result in life-threatening illness. Moreover, antibiotic-resistant bacteria are considerably increasing, thus imposing a global consideration. One of the main causes of this resistance is the horizontal gene transfer (HGT), associated to gene transfer agents including transposons, integrons, plasmids and bacteriophages. These agents, which are called mobile genetic elements (MGEs), encode proteins able to mediate DNA movements. This review briefly describes MGEs in streptococci, focusing on their structure and properties related to HGT and antibiotic resistance. caister.com/cimb 123 Curr. Issues Mol. Biol. (2019) Vol. 32 Mobile Genetic Elements Lu et al Introduction Streptococci are a group of Gram-positive bacteria widely distributed across human and animals. Unlike the Staphylococcus species, streptococci are catalase negative and are subclassified into the three subspecies alpha, beta and gamma according to the partial, complete or absent hemolysis induced, respectively. The beta hemolytic streptococci species are further classified by the cell wall carbohydrate composition (Lancefield, 1933) and according to human diseases in Lancefield groups A, B, C and G. -
Bacterial Genetics
BACTERIAL GENETICS Genetics is the study of genes including the structure of genetic materials, what information is stored in the genes, how the genes are expressed and how the genetic information is transferred. Genetics is also the study of heredity and variation. The arrangement of genes within organisms is its genotype and the physical characteristics an organism based on its genotype and the interaction with its environment, make up its phenotype. The order of DNA bases constitutes the bacterium's genotype. A particular organism may possess alternate forms of some genes. Such alternate forms of genes are referred to as alleles. The cell's genome is stored in chromosomes, which are chains of double stranded DNA. Genes are sequences of nucleotides within DNA that code for functional proteins. The genetic material of bacteria and plasmids is DNA. The two essential functions of genetic material are replication and expression. Structure of DNA The DNA molecule is composed of two chains of nucleotides wound around each other in the form of “double helix”. Double-stranded DNA is helical, and the two strands in the helix are antiparallel. The backbone of each strand comprises of repeating units of deoxyribose and phosphate residue. Attached to the deoxyribose is purine (AG) or pyrimidine (CT) base. Nucleic acids are large polymers consisting of repeating nucleotide units. Each nucleotide contains one phosphate group, one deoxyribose sugar, and one purine or pyrimidine base. In DNA the sugar is deoxyribose; in RNA the sugar is ribose. The double helix is stabilized by hydrogen bonds between purine and pyrimidine bases on the opposite strands. -
Supporting Information
Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs. -
'Candidatus Phytoplasma Solani' (Quaglino Et Al., 2013)
‘Candidatus Phytoplasma solani’ (Quaglino et al., 2013) Synonyms Phytoplasma solani Common Name(s) Disease: Bois noir, blackwood disease of grapevine, maize redness, stolbur Phytoplasma: CaPsol, maize redness phytoplasma, potato stolbur phytoplasma, stolbur phytoplasma, tomato stolbur phytoplasma Figure 1: A ‘dornfelder’ grape cultivar Type of Pest infected with ‘Candidatus Phytoplasma Phytoplasma solani’. Courtesy of Dr. Michael Maixner, Julius Kühn-Institut (JKI). Taxonomic Position Class: Mollicutes, Order: Acholeplasmatales, Family: Acholeplasmataceae Genus: ‘Candidatus Phytoplasma’ Reason for Inclusion in Manual OPIS A pest list, CAPS community suggestion, known host range and distribution have both expanded; 2016 AHP listing. Background Information Phytoplasmas, formerly known as mycoplasma-like organisms (MLOs), are pleomorphic, cell wall-less bacteria with small genomes (530 to 1350 kbp) of low G + C content (23-29%). They belong to the class Mollicutes and are the putative causal agents of yellows diseases that affect at least 1,000 plant species worldwide (McCoy et al., 1989; Seemüller et al., 2002). These minute, endocellular prokaryotes colonize the phloem of their infected plant hosts as well as various tissues and organs of their respective insect vectors. Phytoplasmas are transmitted to plants during feeding activity by their vectors, primarily leafhoppers, planthoppers, and psyllids (IRPCM, 2004; Weintraub and Beanland, 2006). Although phytoplasmas cannot be routinely grown by laboratory culture in cell free media, they may be observed in infected plant or insect tissues by use of electron microscopy or detected by molecular assays incorporating antibodies or nucleic acids. Since biological and phenotypic properties in pure culture are unavailable as aids in their identification, analysis of 16S rRNA genes has been adopted instead as the major basis for phytoplasma taxonomy. -
Pl Path 502 Phytoplasma
Phytoplasmas Pl. Path. 502 Dr. PN SHARMA Department of Plant Pathology CSK HP Agricultural University Palampur-176 062 (HP State) INDIA What are Phytoplasmas ? Phytoplasmas have diverged from gram-positive eubacteria, and belong to the Genus Phytoplasma within the Class Mollicutes. Mycoplasmas dramatically differ phenotypically from other bacteria by their minute size (0.3 - 0.5 and lack of cell wall. The lack of cell wall was used to separate mycoplasmas from other bacteria in a class named Mollicutes. Due to degenerative or reductive evolution, accompanied by significant losses of genomic sequences, the genomes of mollicutes have shrunk and are relatively small compared to other bacteria, ranging from 580 kb. to 2,200 kb. Phytoplasma •Phytoplasma are wall-less prokaryotic organisms •Seen with electron microscope in the phloem of infected plant •Unable to grow on culture media •Pleomorphic shaped and spiral Phytoplasma •Most phytoplasma transmitted from plant to plant by • leafhoppers, • but some are transmitted by Psyllids and planthoppers •Caused Yellowing, Big bud, Stuntting, Witchbroom •Sensitive to antibiotics, especially Tetracycline group Mycoplasma (Phytoplsma): Doi et al. (1970) are submicroscopic, measuring 150- 300 nm in diameter having ribosomes and DNA strands enclosed by a bilayer membrane but not the cell wall, replicate by binary fission, can be cultured artificially in vitro on specific medium and are sensitive to certain antibiotics (tetracycline not to penicillin). E.g. Little leaf of brinjal, Peach yellow Spiroplasm citri (Fudt Allh et al. 1571) Citrus stubbesh. Classification Class : Mollicutes Order: Mycoplasmatales. Three families, each with one genus: Mycoplasmataceae, genus Mycoplasma, Acholeplasmataceae, . genus Acholeplasma, Spiroplasmataceae . genus Spiroplasma. -
An Integrated Study on Microbial Community in Anaerobic Digestion Systems
An Integrated Study on Microbial Community in Anaerobic Digestion Systems DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Yueh-Fen Li Graduate Program in Environmental Science The Ohio State University 2013 Dissertation Committee: Dr. Zhongtang Yu, Advisor Dr. Brian Ahmer Dr. Richard Dick Dr. Olli Tuovinen Copyrighted by Yueh-Fen Li 2013 Abstract Anaerobic digestion (AD) is an attractive microbiological technology for both waste treatment and energy production. Microorganisms are the driving force for the whole transformation process in anaerobic digesters. However, the microbial community underpinning the AD process remains poorly understood, especially with respect to community composition and dynamics in response to variations in feedstocks and operations. The overall objective was to better understand the microbiology driving anaerobic digestion processes by systematically investigating the diversity, composition and succession of microbial communities, both bacterial and archaeal, in anaerobic digesters of different designs, fed different feedstocks, and operated under different conditions. The first two studies focused on propionate-degrading bacteria with an emphasis on syntrophic propionate-oxidizing bacteria. Propionate is one of the most important intermediates and has great influence on AD stability in AD systems because it is inhibitory to methanogens and it can only be metabolized through syntrophic propionate- oxidizing acetogenesis under methanogenic conditions. In the first study (chapter 3), primers specific to the propionate-CoA transferase gene (pct) were designed and used to construct clone libraries, which were sequenced and analyzed to investigate the diversity and distribution of propionate-utilizing bacteria present in the granular and the liquid portions of samples collected from four digesters of different designs, fed different ii feedstocks, and operated at different temperatures. -
A New Phytoplasma Taxon Associated with Japanese Hydrangea Phyllody
international Journal of Systematic Bacteriology (1 999), 49, 1275-1 285 Printed in Great Britain 'Candidatus Phytoplasma japonicum', a new phytoplasma taxon associated with Japanese Hydrangea phyllody Toshimi Sawayanagi,' Norio Horikoshi12Tsutomu Kanehira12 Masayuki Shinohara,2 Assunta Berta~cini,~M.-T. C~usin,~Chuji Hiruki5 and Shigetou Nambal Author for correspondence: Shigetou Namba. Tel: +81 424 69 3125. Fax: + 81 424 69 8786. e-mail : snamba(3ims.u-tokyo.ac.jp Laboratory of Bioresource A phytoplasma was discovered in diseased specimens of f ield-grown hortensia Technology, The University (Hydrangea spp.) exhibiting typical phyllody symptoms. PCR amplification of of Tokyo, 1-1-1 Yayoi, Bunkyo-ku 113-8657, DNA using phytoplasma specific primers detected phytoplasma DNA in all of Japan the diseased plants examined. No phytoplasma DNA was found in healthy College of Bioresource hortensia seedlings. RFLP patterns of amplified 165 rDNA differed from the Sciences, Nihon University, patterns previously described for other phytoplasmas including six isolates of Fujisawa, Kanagawa 252- foreign hortensia phytoplasmas. Based on the RFLP, the Japanese Hydrangea 0813, Japan phyllody (JHP) phytoplasma was classified as a representative of a new sub- 3 lstituto di Patologia group in the phytoplasma 165 rRNA group I (aster yellows, onion yellows, all vegetale, U niversita degli Studi, Bologna 40126, Italy of the previously reported hortensia phytoplasmas, and related phytoplasmas). A phylogenetic analysis of 16s rRNA gene sequences from this 4 Unite de Pathologie Vegetale, Centre de and other group Iphytoplasmas identified the JHP phytoplasma as a member Versa iI les, Inst it ut Nat iona I of a distinct sub-group (sub-group Id) in the phytoplasma clade of the class de la Recherche Mollicutes. -
Ability of Euscelidius Variegatus to Transmit Flavescence Dorée Phytoplasma with a Short Latency Period
insects Article Ability of Euscelidius variegatus to Transmit Flavescence Dorée Phytoplasma with a Short Latency Period Luca Picciau 1, Bianca Orrù 1, Mauro Mandrioli 2 , Elena Gonella 1,* and Alberto Alma 1,* 1 Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), University of Torino, I-10095 Grugliasco (TO), Italy; [email protected] (L.P.); [email protected] (B.O.) 2 Dipartimento di Scienze della Vita (DSV), University of Modena e Reggio Emilia, I-41125 Modena, Italy; [email protected] * Correspondence: [email protected] (E.G.); [email protected] (A.A.) Received: 5 August 2020; Accepted: 1 September 2020; Published: 5 September 2020 Simple Summary: Phytoplasmas are a group of phloem-restricted phytopathogens that attack a huge number of wild and cultivated plants, causing heavy economic losses. They are transmitted by phloem-feeding insects of the order Hemiptera; the transmission process requires the vector to orally acquire the phytoplasma by feeding on an infected plant, becoming infective once it reaches the salivary glands after quite a long latency period. Since infection is retained for all of the insect’s life, acquisition at the nymphal stage is considered to be most effective because of the long time needed before pathogen inoculation. This work provides evidence for the reduced latency period needed by adults of the phytoplasma vector Euscelidius variegatus from flavescence dorée phytoplasma acquisition to transmission. Indeed, we demonstrate that adults can become infective as soon as 9 days from the beginning of phytoplasma acquisition. Our results support a reconsideration of the role of adults in phytoplasma epidemiology, by indicating their extended potential ability to complete the full transmission process. -
Insect Vectors of Phytoplasmas - R
TROPICAL BIOLOGY AND CONSERVATION MANAGEMENT – Vol.VII - Insect Vectors of Phytoplasmas - R. I. Rojas- Martínez INSECT VECTORS OF PHYTOPLASMAS R. I. Rojas-Martínez Department of Plant Pathology, Colegio de Postgraduado- Campus Montecillo, México Keywords: Specificity of phytoplasmas, species diversity, host Contents 1. Introduction 2. Factors involved in the transmission of phytoplasmas by the insect vector 3. Acquisition and transmission of phytoplasmas 4. Families reported to contain species that act as vectors of phytoplasmas 5. Bactericera cockerelli Glossary Bibliography Biographical Sketch Summary The principal means of dissemination of phytoplasmas is by insect vectors. The interactions between phytoplasmas and their insect vectors are, in some cases, very specific, as is suggested by the complex sequence of events that has to take place and the complex form of recognition that this entails between the two species. The commonest vectors, or at least those best known, are members of the order Homoptera of the families Cicadellidae, Cixiidae, Psyllidae, Cercopidae, Delphacidae, Derbidae, Menoplidae and Flatidae. The family with the most known species is, without doubt, the Cicadellidae (15,000 species described, perhaps 25,000 altogether), in which 88 species are known to be able to transmit phytoplasmas. In the majority of cases, the transmission is of a trans-stage form, and only in a few species has transovarial transmission been demonstrated. Thus, two forms of transmission by insects generally are known for phytoplasmas: trans-stage transmission occurs for most phytoplasmas in their interactions with their insect vectors, and transovarial transmission is known for only a few phytoplasmas. UNESCO – EOLSS 1. Introduction The phytoplasmas are non culturable parasitic prokaryotes, the mechanisms of dissemination isSAMPLE mainly by the vector insects. -
154 Detection of Phytoplasmas Associated with Kalimantan Wilt Disease of Coconut by the Polymerase Chain Reaction
Jurnal Littri 12(4), Desember 2006. Hlm. 154 –JURNAL 160 LITTRI VOL. 12 NO 4, DESEMBER 2006 : 154 - 160 ISSN 0853 - 8212 DETECTION OF PHYTOPLASMAS ASSOCIATED WITH KALIMANTAN WILT DISEASE OF COCONUT BY THE POLYMERASE CHAIN REACTION J.S. WAROKKA1, P. JONES2, and M.J. DICKINSON3 1 Indonesian Coconut and Other Palms Research Institute. PO Box 1004 Manado 95001, Indonesia. 2 Bio-Imaging unit, Rothamsted Research. Harpenden Herts AL5 2JQ, UK. 3 School of Biosciences, University of Nottingham, Loughborough Leicestershire LE12 5RD, UK. ABSTRACT penyebab penyakit layu Kalimantan adalah phytoplasma. Teknik ini juga secara efektif dapat mendeteksi phytoplasma dalam jaringan tanaman Coconut is the second Indonesia’s most important social commodity kelapa yang sudah terinfeksi maupun yang belum menunjukkan gejala after rice. There are more than 3.6 million hectares of coconut plantations penyakit. DNA phytoplasma dapat dideteksi pada 95 sampel dari 116 in Indonesia equivalent to one third of the total world coconut area. sampel (81.9%) yang dianalisis. Berdasarkan jenis sample yang diperiksa However, the production and productivity of the coconut are very low and ternyata phytoplasma dapat dideteksi pada sample yang terinfeksi maupun unstable for various reasons, including pests and diseases. Kalimantan wilt yang belum menunjukkan gejala penyakit masing-masing 95.1% dan (KW) disease causes extensive damage to coconut plantation. In previous 67.3%. Hasil penelitian ini mengkonfirmasi bahwa penyakit layu investigations, bacteria, fungi, viruses, viroids and soil-borne pathogens Kalimantan disebabkan oleh phytoplasma. such as nematodes were tested, but none of them were consistently associated with the disease. The objective of this research was to detect Kata kunci: Kelapa, Cocos nucifera L., penyakit tanaman, penyakit layu and diagnose the phytoplasma associating with KW. -
Wait to Open the Exam Until the Bell Rings
PRINTED NAME BIO 226R SPRING 05 DR BLINKOVA EXAM 4 INSTRUCTIONS: FILL IN NAME AND UTEID ON THE SCANTRON, NOW. FILL IN NAME ON THIS PAGE, NOW. READ THE INSTRUCTIONS BELOW, NOW. Answers. Answer on the answer sheet. 2.5 pts each. Read the questions carefully and choose the best answer. Understanding the questions is part of the exam. Therefore, no questions about the exam will be answered, unless some of the exam questions are ambiguous, in which case, the entire class will be interrupted and the same explanation made to everyone. If you think that a question is ambiguous, inform the TA or instructor. Several questions ask you to analyze lecture material and formulate an answer, rather than just to repeat material from memory. WAIT TO OPEN THE EXAM UNTIL THE BELL RINGS 1. Generalized transduction is distinguishable from specialized transduction by the fact that a. generalized transduction may be used to move any gene, whereas specialized transduction moves only certain genes. b. selective medium is required for generalized transduction, whereas selective medium is not required for specialized transduction. c. donor DNA must be purified from the donor for generalized transduction, whereas specialized transduction involves movement of DNA by phages. d. generalized transduction is possible in generally all organisms, whereas specialized transduction is possible only in special groups of organisms. 2. Generalized transducing particles a. are formed by packaging host chromosomal fragments after phage infection b. are formed during growth of a phage in a bacterial host c. carry donor genes to recipient cells d. all the above 3. -
(Gid ) Genes Coding for Putative Trna:M5u-54 Methyltransferases in 355 Bacterial and Archaeal Complete Genomes
Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Archaea Crenarchaea Aeropyrum pernix_K1 Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; Cenarchaeales; Cenarchaeaceae Pyrobaculum aerophilum_str_IM2 Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae Sulfolobus acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus solfataricus Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus tokodaii Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae Haloarcula marismortui_ATCC_43049 Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Halobacterium sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Haloquadratum walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanococcoides burtonii_DSM_6242 Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanococcus jannaschii Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci;