Low temperature regulated DEAD-box RNA helicase from the antarctic archaeon, Methanococcoides burtonii

Lim, Julianne; Thomas, Torsten; Cavicchioli, Ricardo

doi:10.1006/jmbi.2000.3585

Cited by 136 publications

(114 citation statements)

References 53 publications

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“…Certain cold-induced RNA helicases can un-wind the RNAs or bind to them, which allows translation to proceed (152,153). Fungi that carry these RNA helicases display improved cold tolerance (154)(155)(156)(157)(158)(159) and can be more prevalent in colder environments (157). RNA helicase may form part of a generalized stress response (156,160).…”

Section: Stress Tolerancementioning

confidence: 99%

Fungal Traits That Drive Ecosystem Dynamics on Land

Treseder

Lennon

2015

Microbiol Mol Biol Rev

456

322

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SUMMARY Fungi contribute extensively to a wide range of ecosystem processes, including decomposition of organic carbon, deposition of recalcitrant carbon, and transformations of nitrogen and phosphorus. In this review, we discuss the current knowledge about physiological and morphological traits of fungi that directly influence these processes, and we describe the functional genes that encode these traits. In addition, we synthesize information from 157 whole fungal genomes in order to determine relationships among selected functional genes within fungal taxa. Ecosystem-related traits varied most at relatively coarse taxonomic levels. For example, we found that the maximum amount of variance for traits associated with carbon mineralization, nitrogen and phosphorus cycling, and stress tolerance could be explained at the levels of order to phylum. Moreover, suites of traits tended to co-occur within taxa. Specifically, the genetic capacities for traits that improve stress tolerance—β-glucan synthesis, trehalose production, and cold-induced RNA helicases—were positively related to one another, and they were more evident in yeasts. Traits that regulate the decomposition of complex organic matter—lignin peroxidases, cellobiohydrolases, and crystalline cellulases—were also positively related, but they were more strongly associated with free-living filamentous fungi. Altogether, these relationships provide evidence for two functional groups: stress tolerators, which may contribute to soil carbon accumulation via the production of recalcitrant compounds; and decomposers, which may reduce soil carbon stocks. It is possible that ecosystem functions, such as soil carbon storage, may be mediated by shifts in the fungal community between stress tolerators and decomposers in response to environmental changes, such as drought and warming.

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Section: Stress Tolerancementioning

confidence: 99%

Fungal Traits That Drive Ecosystem Dynamics on Land

Treseder

Lennon

2015

Microbiol Mol Biol Rev

456

322

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Section: Bacterial Megaclassificationmentioning

confidence: 99%

“…Methanogenesis was almost certainly lost by the ancestor of Halobacteriales, but could have been lost several times. Even though the ancestral methanogen was probably, like the ancestral archaebacterium, a hyperthermophile, at least one has secondarily gone to the opposite extreme and evolved adaptations for psychrophily (Lim et al, 2000).' Domain ' is not a taxonomic category and should not be treated as one ; it is a useful informal term, but the three domains have a very different status ; on the present system, eubacteria are a paraphyletic grade but not a taxon, whereas Archaebacteria (division or phylum) and Eukaryota (empire or superkingdom ; Cavalier-Smith, 1998) are both holophyletic taxa but of very unequal rank. The term domain is convenient when, for simplicity, we wish to ignore these distinctions, but in some contexts they are important and the classical ranks more informative.…”

mentioning

confidence: 99%

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Cavalier‐Smith¹

2002

International Journal of Systematic and Evolutionary Microbiology

418

590

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Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms : Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translationarrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids ; flagellar shaft of glycoprotein, not flagellin ; DNA-binding protein 10b ; specially modified tRNA ; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles ; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of T. Cavalier-Smith quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution : the fact that, during major evolutionary transformations, some org...

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“…In the Antarctic archaeon Methanococcoides burtonii, these enzymes are overexpressed at low temperature and are involved in the destabilization of secondary structures of nucleic acids 43 . Differential regulation of gene expression may function in the bacterial adaptation to temperature shifts.…”

Section: A R T I C L E Smentioning

confidence: 99%

Complete genome sequence of the fish pathogen Flavobacterium psychrophilum

et al. 2007

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We report here the complete genome sequence of the virulent strain JIP02/86 (ATCC 49511) of Flavobacterium psychrophilum, a widely distributed pathogen of wild and cultured salmonid fish. The genome consists of a 2,861,988-base pair (bp) circular chromosome with 2,432 predicted protein-coding genes. Among these predicted proteins, stress response mediators, gliding motility proteins, adhesins and many putative secreted proteases are probably involved in colonization, invasion and destruction of the host tissues. The genome sequence provides the basis for explaining the relationships of the pathogen to the host and opens new perspectives for the development of more efficient disease control strategies. It also allows for a better understanding of the physiology and evolution of a significant representative of the family Flavobacteriaceae, whose members are associated with an interesting diversity of lifestyles and habitats.

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Low temperature regulated DEAD-box RNA helicase from the antarctic archaeon, Methanococcoides burtonii

Cited by 136 publications

References 53 publications

Fungal Traits That Drive Ecosystem Dynamics on Land

Fungal Traits That Drive Ecosystem Dynamics on Land

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Complete genome sequence of the fish pathogen Flavobacterium psychrophilum

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