scholarly journals Complete Genome Sequence of Nitrosospira multiformis, an Ammonia-Oxidizing Bacterium from the Soil Environment

2008 ◽  
Vol 74 (11) ◽  
pp. 3559-3572 ◽  
Author(s):  
Jeanette M. Norton ◽  
Martin G. Klotz ◽  
Lisa Y. Stein ◽  
Daniel J. Arp ◽  
Peter J. Bottomley ◽  
...  
Keyword(s):  
Complete Genome ◽  
Cell Envelope ◽  
Gene Clusters ◽  
Homoserine Lactone ◽  
Sensory Transduction ◽  
Ammonia Oxidizing Bacteria ◽  
Ribulose Bisphosphate Carboxylase ◽  
Circular Chromosome ◽  
Bisphosphate Carboxylase ◽  
Ammonia Oxidizing Bacterium

ABSTRACT The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196T) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and Nitrosomonas eutropha were the best match for 42% of the predicted genes in N. multiformis. The N. multiformis genome contains three nearly identical copies of amo and hao gene clusters as large repeats. The features of N. multiformis that distinguish it from N. europaea include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.

scholarly journals Complete Genome Sequence of Pseudomonas syringae pv. lapsa Strain ATCC 10859, Isolated from Infected Wheat

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Jun Kong ◽  
Hongshan Jiang ◽  
Baiyun Li ◽  
Wenjun Zhao ◽  
Zhihong Li ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Gene Clusters ◽  
Strain Atcc ◽  
Circular Chromosome ◽  
Coding Sequences

Pseudomonas syringae pv. lapsa is a pathovar of Pseudomonas syringae that can infect wheat. The complete genome of P. syringae pv. lapsa strain ATCC 10859 contains a 5,918,899-bp circular chromosome with 4,973 coding sequences, 16 rRNAs, 69 tRNAs, and an average GC content of 59.13%. The analysis of this genome revealed several gene clusters that are related to pathogenesis and virulence.

scholarly journals Insights into the Microbial Degradation of Rubber and Gutta-Percha by Analysis of the Complete Genome of Nocardia nova SH22a

2014 ◽  
Vol 80 (13) ◽  
pp. 3895-3907 ◽  
Author(s):  
Quan Luo ◽  
Sebastian Hiessl ◽  
Anja Poehlein ◽  
Rolf Daniel ◽  
Alexander Steinbüchel
Keyword(s):  
Microbial Degradation ◽  
Complete Genome ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Cell Envelope ◽  
Experimental Studies ◽  
Substrate Uptake ◽  
Circular Chromosome ◽  
Content Type ◽  
Gutta Percha ◽  
Protein Encoding

ABSTRACTThe complete genome sequence ofNocardia novaSH22a was determined in light of the remarkable ability of rubber and gutta-percha (GP) degradation of this strain. The genome consists of a circular chromosome of 8,348,532 bp with a G+C content of 67.77% and 7,583 predicted protein-encoding genes. Functions were assigned to 72.45% of the coding sequences. Among them, a large number of genes probably involved in the metabolism of xenobiotics and hardly degradable compounds, as well as genes that participate in the synthesis of polyketide- and/or nonribosomal peptide-type secondary metabolites, were detected. Based onin silicoanalyses and experimental studies, such as transposon mutagenesis and directed gene deletion studies, the pathways of rubber and GP degradation were proposed and the relationship between both pathways was unraveled. The genes involved include,inter alia, genes participating in cell envelope synthesis (long-chain-fatty-acid–AMP ligase and arabinofuranosyltransferase), β-oxidation (α-methylacyl-coenzyme A [α-methylacyl-CoA] racemase), propionate catabolism (acyl-CoA carboxylase), gluconeogenesis (phosphoenolpyruvate carboxykinase), and transmembrane substrate uptake (Mce [mammalian cell entry] transporter). This study not only improves our insights into the mechanism of microbial degradation of rubber and GP but also expands our knowledge of the genusNocardiaregarding metabolic diversity.

scholarly journals Complete Genome Sequence of the Cytokinin-Producing Biocontrol Strain Pseudomonas fluorescens G20-18

2021 ◽  
Vol 10 (30) ◽  
Author(s):  
Tue K. Nielsen ◽  
Mengistu F. Mekureyaw ◽  
Lars H. Hansen ◽  
Mette H. Nicolaisen ◽  
Thomas G. Roitsch ◽  
...  
Keyword(s):  
Plant Growth ◽  
Pseudomonas Fluorescens ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gene Clusters ◽  
Circular Chromosome ◽  
Content Type ◽  
Plant Growth Promoting ◽  
Growth Promoting

Here, we report the complete genome sequence of the cytokinin-producing plant growth-promoting strain Pseudomonas fluorescens G20-18. The complete genome assembly resulted in a single, circular chromosome of 6.48 Mbp and harbors several secondary metabolite biosynthesis gene clusters that are potentially involved in its plant growth-promoting function.

scholarly journals Complete Genome Resource of Bacillus velezensis J17-4, an Endophyte Isolated from Stem Tissues of Rice

Plant Disease ◽  
2021 ◽  
Author(s):  
Z.R. Shi ◽  
Wanwen Hong ◽  
Qingwei Wang
Keyword(s):  
Root Rot ◽  
Complete Genome ◽  
Gene Clusters ◽  
Underlying Mechanism ◽  
Economic Losses ◽  
Bacillus Velezensis ◽  
Circular Chromosome ◽  
Root Rot Disease ◽  
Genome Data ◽  
Rot Disease

Dickeya zeae is the causative agent of rice root rot disease and causes severe harvest and economic losses. In this study, the Bacillus velezensis strain J17-4 with significant antagonist against D. zeae was used to generate DNA for sequencing. After assembly, a high-quality complete genome comprising only a circular chromosome was available. The genome sequence consists of a total of 3877 prediction coding sequences and nine types of gene clusters involved in secondary metabolite production. This genome data will provide information for understanding the underlying mechanism of strain J17-4 antagonist against D. zeae and a new useful source for comparative genomics studies between strains isolated from various habitats.

scholarly journals The complete genome sequence of Hafnia alvei A23BA; a potential antibiotic-producing rhizobacterium

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Opeyemi K. Awolope ◽  
Noelle H. O’Driscoll ◽  
Alberto Di Salvo ◽  
Andrew J. Lamb
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Growth Promotion ◽  
Gc Content ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Circular Chromosome ◽  
Hafnia Alvei

Abstract Objectives The urgent need for novel antibiotics cannot be overemphasized. Hafnia alvei A23BA was isolated from plant rhizosphere as part of an effort to recover novel antibiotic-producing bacterial strains from soil samples. The genome of the isolate was sequenced to facilitate mining for potential antibiotic-encoding biosynthetic gene clusters and to gain insights into how these gene clusters could be activated. Data description Here, we report the complete genome sequence of H. alvei A23BA obtained from the hybrid assembly of Illumina HiSeq and GridION reads. The genome, consisting of a circular chromosome and a circular plasmid, is 4.77 Mb in size with a GC content of 48.77%. The assembly is 99.5% complete with genomic features including 4,217 CDSs, 125 RNAs, and 30 pseudogenes. Thiopeptide, beta-lactone, siderophore, and homoserine lactone biosynthetic gene clusters were also identified. Other gene clusters of interest include those associated with bioremediation, biocontrol, and plant growth promotion- all of which are reported for H. alvei for the first time. This dataset serves to expedite the exploration of the biosynthetic and metabolic potentials of the species. Furthermore, being the first published genome sequence of a soil isolate, this dataset enriches the comparative genomics study of H. alvei strains.

scholarly journals Complete Genome Sequence of the Ammonia-Oxidizing Bacterium Nitrosospira sp. Strain NRS527, Isolated from the Rhizoplane of Paddy Rice

2021 ◽  
Vol 10 (28) ◽  
Author(s):  
Tatsunori Nakagawa ◽  
Yuki Tsuchiya ◽  
Reiji Takahashi
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Paddy Rice ◽  
Circular Chromosome ◽  
Ammonia Oxidizing Bacterium

This work reports the complete genome sequence of the chemoautotrophic ammonia-oxidizing bacterium Nitrosospira sp. strain NRS527. The assembled genome is composed of a circular chromosome and two plasmids (80,750 bp and 41,389 bp, respectively).

scholarly journals Whole-Genome Sequence of the Ammonia-Oxidizing Bacterium Nitrosomonas stercoris Type Strain KYUHI-S, Isolated from Composted Cattle Manure

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Tatsunori Nakagawa ◽  
Yuki Tsuchiya ◽  
Reiji Takahashi
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Large Plasmid ◽  
Circular Chromosome ◽  
Content Type ◽  
Ammonia Oxidizing Bacterium

This work reports the complete genome sequence of a chemoautotrophic ammonia-oxidizing bacterium, Nitrosomonas stercoris strain KYUHI-ST (= ATCC BAA-2718T and NBRC 110753T). The assembled genome is composed of a circular chromosome and a large plasmid.

scholarly journals Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC 19707

2006 ◽  
Vol 72 (9) ◽  
pp. 6299-6315 ◽  
Author(s):  
Martin G. Klotz ◽  
Daniel J. Arp ◽  
Patrick S. G. Chain ◽  
Amal F. El-Sheikh ◽  
Loren J. Hauser ◽  
...  
Keyword(s):  
Tricarboxylic Acid Cycle ◽  
Reducing Power ◽  
Pentose Phosphate ◽  
Type I ◽  
Circular Chromosome ◽  
Bisphosphate Carboxylase ◽  
Terminal Electron Acceptor ◽  
Genes Encoding ◽  
Pentose Phosphate Pathways ◽  
Ammonia Oxidizing Bacterium

ABSTRACT The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H+-dependent F0F1 type, one Na+-dependent V type).

scholarly journals Amycolatopsis aidingensis sp. nov., a Halotolerant Actinobacterium, Produces New Secondary Metabolites

2021 ◽  
Vol 12 ◽  
Author(s):  
Rui Li ◽  
Meng Wang ◽  
Zhen Ren ◽  
Yang Ji ◽  
Min Yin ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Complete Genome ◽  
Type Strain ◽  
Polyketide Synthase ◽  
Gene Clusters ◽  
Antitumor Agent ◽  
Northwest China ◽  
Rrna Gene ◽  
Circular Chromosome ◽  
Nocardicin A

A novel actinobacterium, strain YIM 96748T, was isolated from a saline soil sample collected from the south bank of Aiding Lake in Xinjiang Province, Northwest China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 96748T is closely related to Amycolatopsis cihanbeyliensis BNT52T (98.9%) and Amycolatopsis jiangsuensis KLBMP 1262T (97.2%). The DNA–DNA relatedness between strain YIM 96748T and its closest type strain A. cihanbeyliensis BNT52T was 59.6%. The average nucleotide identity between strain YIM 96748T and its neighbor strain was 88.97%. Based on the genotypic and phenotypic characteristics, it is concluded that strain YIM 96748T represents a novel species of the genus Amycolatopsis, whose name was proposed as Amycolatopsis aidingensis sp. nov. The type strain is YIM 96748T. To investigate the biosynthetic potential of producing secondary metabolites, the complete genome of YIM 96748T was sequenced and analyzed. The complete genome sequence of YIM 96748T consists of a 7,657,695-bp circular chromosome, comprising 7,162 predicted genes with a DNA G + C content of 70.21 mol%. Fifty-one putative biosynthetic gene clusters of secondary metabolites were found, including the antibacterial/antitumor agent TLN-05220, the antibacterial agent nocardicin A, the antifungal agent nystatin A1, and the osmolyte ectoine. The investigation of the secondary metabolites of A. aidingensis YIM96748T led to the discovery of two new phenylpropyl acetate enantiomers, amycoletates A (1) and B (2), and five known compounds: 4-hydroxy phenethyl acetate (3), 2-p-acetoxyphenylethanol (4), (S)-ethyl indole-3-lactate (5), (R)-ethyl indole-3-lactate (6), and p-hydroxybenzoic acid (7). One of the gene clusters 14, 36, and 43, which contain a single module of polyketide synthase, might be responsible for the biosynthesis of compounds 1 and 2 from compound 7 as a precursor. Further studies, including the one strain many compounds approach (OSMAC) and genetic modification, are needed to explore novel compounds from this talented halophilic Amycolatopsis strain.

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