scholarly journals Genome of Methylobacillus flagellatus, Molecular Basis for Obligate Methylotrophy, and Polyphyletic Origin of Methylotrophy

2007 ◽  
Vol 189 (11) ◽  
pp. 4020-4027 ◽  
Author(s):  
Ludmila Chistoserdova ◽  
Alla Lapidus ◽  
Cliff Han ◽  
Lynne Goodwin ◽  
Liz Saunders ◽  
...  
Keyword(s):  
Formate Dehydrogenase ◽  
Tricarboxylic Acid Cycle ◽  
Methylococcus Capsulatus ◽  
Methylobacterium Extorquens ◽  
Circular Chromosome ◽  
Transport Chain ◽  
Carbon Compounds ◽  
Formaldehyde Oxidation ◽  
Global Carbon ◽  
Single Circular Chromosome

ABSTRACT Along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. The complete genome of a model obligate methanol and methylamine utilizer, Methylobacillus flagellatus (strain KT) was sequenced. The genome is represented by a single circular chromosome of approximately 3 Mbp, potentially encoding a total of 2,766 proteins. Based on genome analysis as well as the results from previous genetic and mutational analyses, methylotrophy is enabled by methanol and methylamine dehydrogenases and their specific electron transport chain components, the tetrahydromethanopterin-linked formaldehyde oxidation pathway and the assimilatory and dissimilatory ribulose monophosphate cycles, and by a formate dehydrogenase. Some of the methylotrophy genes are present in more than one (identical or nonidentical) copy. The obligate dependence on single-carbon compounds appears to be due to the incomplete tricarboxylic acid cycle, as no genes potentially encoding alpha-ketoglutarate, malate, or succinate dehydrogenases are identifiable. The genome of M. flagellatus was compared in terms of methylotrophy functions to the previously sequenced genomes of three methylotrophs, Methylobacterium extorquens (an alphaproteobacterium, 7 Mbp), Methylibium petroleiphilum (a betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (a gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or phylogenetically, the methylotrophy functions in M. flagellatus were more similar to those in M. capsulatus and M. extorquens than to the ones in the more closely related M. petroleiphilum species, providing the first genomic evidence for the polyphyletic origin of methylotrophy in Betaproteobacteria.

scholarly journals Draft Genome Sequence of the Methane-Oxidizing Bacterium Methylococcus capsulatus (Texas)

2012 ◽  
Vol 194 (23) ◽  
pp. 6626-6626 ◽  
Author(s):  
Charlotte R. Kleiveland ◽  
Lene T. Olsen Hult ◽  
Katarzyna Kuczkowska ◽  
Morten Jacobsen ◽  
Tor Lea ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Type Strain ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Methylococcus Capsulatus ◽  
Content Type ◽  
Carbon Cycles ◽  
Carbon Compounds ◽  
Sewer Sludge ◽  
Global Carbon

ABSTRACTMethanotrophic bacteria perform major roles in global carbon cycles via their unique enzymatic activities that enable the oxidation of one-carbon compounds, most notably methane. Here we describe the annotated draft genome sequence of the aerobic methanotrophMethylococcus capsulatus(Texas), a type strain originally isolated from sewer sludge.

scholarly journals Whole-Genome Sequence of Mycoplasma bovis Strain Ningxia-1

2018 ◽  
Vol 6 (4) ◽  
Author(s):  
Peng Sun ◽  
Haifeng Luo ◽  
Xin Zhang ◽  
Jingyi Xu ◽  
Yanan Guo ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Whole Genome Sequence ◽  
Mycoplasma Bovis ◽  
Sequencing Technology ◽  
Circular Chromosome ◽  
A Genome ◽  
Variable Surface ◽  
Integrative Conjugative Elements ◽  
Single Circular Chromosome

ABSTRACT A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology. The strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia, China. The single circular chromosome of 1,033,629 bp shows differences between complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins (VSPs), pathogenicity islands (PAIs), etc.

scholarly journals Draft Genome Sequence of the Psychrophilic Gliding Species Gelidibacter algens ACAM 536

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
John P. Bowman
Keyword(s):  
Sea Ice ◽  
Genome Sequence ◽  
Type Strain ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Diatom Assemblages ◽  
Circular Chromosome ◽  
Single Circular Chromosome

A draft genome sequence was obtained from the type strain of Gelidibacter algens (ACAM 536). This species was isolated from sea-ice diatom assemblages collected from Ellis Fjord, Eastern Antarctica. The genome of ACAM 536 is a single circular chromosome with an estimated size of 4.50 Mbp.

scholarly journals Whole-Genome Sequence of Lactobacillus salivarius DJ-sa-01, Isolated from Chicken Small Intestine

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Dongjun Kim ◽  
Mun-Ju Cho ◽  
Seungchan Cho ◽  
Yongjun Lee ◽  
Sung June Byun ◽  
...  
Keyword(s):  
Small Intestine ◽  
Genome Sequence ◽  
Probiotic Strain ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Lactobacillus Salivarius ◽  
Circular Chromosome ◽  
Content Type ◽  
Single Circular Chromosome

We have identified the whole-genome sequence of Lactobacillus salivarius DJ-sa-01, a potential probiotic strain for poultry, isolated from a chicken small intestine. We used the PacBio and Illumina platforms to obtain the sequence of the entire single circular chromosome.

scholarly journals Effects of L-Malate on Mitochondrial Oxidoreductases in Liver of Aged Rats

2011 ◽  
pp. 329-336 ◽  
Author(s):  
J.-L. WU ◽  
Q.-P. WU ◽  
Y.-P. PENG ◽  
J.-M. ZHANG
Keyword(s):  
Electron Transport ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Electron Transport Chain ◽  
Nadh Dehydrogenase ◽  
Tricarboxylic Acid Cycle ◽  
Radical Scavenger ◽  
Aged Rats ◽  
Transport Chain ◽  
Nadh Cytochrome

Accumulation of oxidative damage has been implicated to be a major causative factor in the decline in physiological functions that occur during the aging process. The mitochondrial respiratory chain is a powerful source of reactive oxygen species (ROS), considered as the pathogenic agent of many diseases and aging. L-malate, a tricarboxylic acid cycle intermediate, plays an important role in transporting NADH from cytosol to mitochondria for energy production. Previous studies in our laboratory reported L-malate as a free radical scavenger in aged rats. In the present study we focused on the effect of L-malate on the activities of electron transport chain in young and aged rats. We found that mitochondrial membrane potential (MMP) and the activities of succinate dehydrogenase, NADH-cytochrome c oxidoreductase and cytochrome c oxidase in liver of aged rats were significantly decreased when compared to young control rats. Supplementation of L-malate to aged rats for 30 days slightly increased MMP and improved the activities of NADH-dehydrogenase, NADH-cytochrome c oxidoreductase and cytochrome c oxidase in liver of aged rats when compared with aged control rats. In young rats, L-malate administration increased only the activity of NADH-dehydrogenase. Our result suggested that L-malate could improve the activities of electron transport chain enzymes in aged rats

scholarly journals The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli

2004 ◽  
Vol 17 (8) ◽  
pp. 827-836 ◽  
Author(s):  
Claudia B. Monteiro-Vitorello ◽  
Luis E. A. Camargo ◽  
Marie A. Van Sluys ◽  
João P. Kitajima ◽  
Daniela Truffi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gc Content ◽  
Open Reading Frames ◽  
Circular Chromosome ◽  
Free Sugars ◽  
Sugar Transporters ◽  
Living Organisms ◽  
Bacterial Plant Pathogen ◽  
Single Circular Chromosome ◽  
Reading Frames

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

scholarly journals Complete Genome Sequence of the Carotenoid-Producing Deinococcus sp. Strain AJ005

2019 ◽  
Vol 8 (48) ◽  
Author(s):  
Jun Young Choi ◽  
Kunjoong Lee ◽  
Pyung Cheon Lee
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Novel Species ◽  
The Novel ◽  
King George Island ◽  
Circular Chromosome ◽  
Single Circular Chromosome

The novel species Deinococcus sp. strain AJ005, isolated from King George Island, synthesizes a red carotenoid. Its complete genome is made up of a single circular chromosome (3,380,712 bp, 64.2% G+C content) and four circular plasmids.

scholarly journals Mitocans Revisited: Mitochondrial Targeting as Efficient Anti-Cancer Therapy

2020 ◽  
Vol 21 (21) ◽  
pp. 7941 ◽  
Author(s):  
Lanfeng Dong ◽  
Vinod Gopalan ◽  
Olivia Holland ◽  
Jiri Neuzil
Keyword(s):  
Cancer Progression ◽  
Tricarboxylic Acid Cycle ◽  
Cancer Therapeutics ◽  
Mitochondrial Metabolism ◽  
Signalling Pathways ◽  
Transport Chain ◽  
Ros Homeostasis ◽  
Mitochondrial Functions ◽  
Anti Cancer ◽  
Selective Targeting

Mitochondria are essential cellular organelles, controlling multiple signalling pathways critical for cell survival and cell death. Increasing evidence suggests that mitochondrial metabolism and functions are indispensable in tumorigenesis and cancer progression, rendering mitochondria and mitochondrial functions as plausible targets for anti-cancer therapeutics. In this review, we summarised the major strategies of selective targeting of mitochondria and their functions to combat cancer, including targeting mitochondrial metabolism, the electron transport chain and tricarboxylic acid cycle, mitochondrial redox signalling pathways, and ROS homeostasis. We highlight that delivering anti-cancer drugs into mitochondria exhibits enormous potential for future cancer therapeutic strategies, with a great advantage of potentially overcoming drug resistance. Mitocans, exemplified by mitochondrially targeted vitamin E succinate and tamoxifen (MitoTam), selectively target cancer cell mitochondria and efficiently kill multiple types of cancer cells by disrupting mitochondrial function, with MitoTam currently undergoing a clinical trial.

scholarly journals Complete Genome Sequence ofBacteroides ovatusV975

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Udo Wegmann ◽  
Alexander Goesmann ◽  
Simon R. Carding
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Bacteroides Ovatus ◽  
Single Circular Chromosome

The complete genome sequence ofBacteroides ovatusV975 was determined. The genome consists of a single circular chromosome of 6,475,296 bp containing five rRNA operons, 68 tRNA genes, and 4,959 coding genes.

Control of lipid oxidation at the mitochondrial levelThis paper article is one of a selection of papers published in this Special Issue, entitled 14th International Biochemistry of Exercise Conference – Muscles as Molecular and Metabolic Machines, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 34 (3) ◽  
pp. 382-388 ◽  
Author(s):  
Kent Sahlin
Keyword(s):  
Lipid Oxidation ◽  
Feedback Inhibition ◽  
Peer Review Process ◽  
Energy State ◽  
Tricarboxylic Acid Cycle ◽  
Low Energy ◽  
Acetyl Coa ◽  
Intensive Exercise ◽  
Transport Chain ◽  
Electron Carriers

The rate of lipid oxidation during exercise is controlled at several sites, and there is a reciprocal dependency between oxidation of lipids and carbohydrates (CHO). It is well known that the proportion of the 2 fuels oxidized is influenced by substrate availability and exercise intensity, but the mechanisms regulating fuel preferences remain unclear. During intense exercise, oxidation of long-chain fatty acids (LCFAs) decreases, and the major control is likely to be at the mitochondrial level. Potential mitochondrial sites for control of lipid oxidation include transport of LCFAs into mitochondrial matrix, β-oxidation, the tricarboxylic acid cycle, and the electron transport chain (ETC). CHO catabolism may impair lipid oxidation by interfering with the transfer of LCFAs into mitochondria and by competing for mutual cofactors (i.e., nicotinamide adenine dinucleotide and (or) coenzyme A (CoA)). The different effect of energy state on the catabolism of CHO and lipids is likely to be of major importance in explaining the shift in fuel utilization during intensive exercise. Formation of acetyl-CoA from CHO is activated by a low energy state, and will lead to accumulation of products that are inhibitory to lipid oxidation. In contrast, β-oxidation of LCFAs to acetyl-CoA is not stimulated by a low energy state. Further interaction between CHO and LCFAs may occur by substrate competition for electron carriers at ETC, due to provisions of electrons through different complexes. Feedback inhibition of β-oxidation by redox state is thought to be an important mechanism for the slowing of lipid oxidation during intensive exercise.

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