The gene of an archaeal α-l-fucosidase is expressed by translational frameshifting

Cobucci‐Ponzano, Beatrice; Conte, Fiorella; Benelli, Dario; Londei, Paola; Flagiello, Angela; Monti, Maria; Pucci, Piero; Rossi, Mosè; Moracci, Marco

doi:10.1093/nar/gkl574

Cited by 23 publications

(42 citation statements)

References 42 publications

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“…that are the two most abundant polymers on Earth (global cellulose production estimates range between 9 9 10 12 and 1.5 9 10 12 tons/year Pinkert et al 2009) and are remarkably stable to spontaneous hydrolysis (half-life of the glycosidic bond is 4.7 9 10 6 years, Wolfenden et al 1998). Thus, carbohydrate active enzymes (cazymes) from (hyper)thermophiles have interesting biotechnological potential (Cobucci-Ponzano et al 2006, 2010a. In fact, their impressive stability (Ausili et al 2004) at the conditions at which plant lignocellulose is pretreated in second generation biorefineries (steamexplosion at extremes of temperatures and pHs), make them the ideal catalysts for the hydrolysis of (hemi)-cellulose into fermentable sugars for the production of bioethanol and plastic precursors (Castiglia et al 2016;Cobucci-Ponzano et al 2013Iacono et al 2016;Aulitto et al 2017).…”

Section: Extremophilic Microbiome Enrichmentsmentioning

confidence: 99%

Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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Geothermally heated regions of Earth, such as terrestrial volcanic areas (fumaroles, hot springs, and geysers) and deep-sea hydrothermal vents, represent a variety of different environments populated by extremophilic archaeal and bacterial microorganisms. Since most of these microbes thriving in such harsh biotopes, they are often recalcitrant to cultivation; therefore, ecological, physiological and phylogenetic studies of these microbial populations have been hampered for a long time. More recently, culture-independent methodologies coupled with the fast development of next generation sequencing technologies as well as with the continuous advances in computational biology, have allowed the production of large amounts of metagenomic data. Specifically, these approaches have assessed the phylogenetic composition and functional potential of microbial consortia thriving within these habitats, shedding light on how extreme physico-chemical conditions and biological interactions have shaped such microbial communities. Metagenomics allowed to better understand that the exposure to an extreme range of selective pressures in such severe environments, accounts for genomic flexibility and metabolic versatility of microbial and viral communities, and makes extreme-and hyper-thermophiles suitable for bioprospecting purposes, representing an interesting source for novel thermostable proteins that can be potentially used in several industrial processes.Keywords Hyperthermophiles Á Geothermal environments Á Microbial and viral metagenomics Á CRISPR Á Enzyme discovery BackgroundHot springs populated by extreme thermophiles (T opt : 65-79°C) and hyperthermophiles (T opt [ 80°C) (DeCastro et al. 2016) are very diverse and some of them show combinations of extreme chemo-physical conditions, such as temperature, acidic or alkaline pHs, high pressure, and high concentrations of salts and heavy metals (López-López et al. 2013). As with all studies of environmental microbiology, our understanding of the composition, functional and physiological dynamics, and evolution of extreme-and hyper-thermophilic microbial consortia has lagged A. Strazzulli Á M. Moracci Á P. Contursi

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Section: Extremophilic Microbiome Enrichmentsmentioning

confidence: 99%

Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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“…Previous studies claimed that the thermoacidophilic archaeon Thermoplasma acidophilum is able to grow on deoxysugars like, L‐fucose or L‐rhamnose, however, the underlying pathway of L‐fucose degradation is still unknown (Kim et al ., ). In the genome of S. solfataricus , only an α‐L‐fucosidase presumably regulated by translational frameshifting was identified so far (Cobucci‐Ponzano et al ., ). In addition no homologs to any of the known enzymes of the E. coli L‐fucose degradation pathway were identified.…”

Section: Introductionmentioning

confidence: 97%

A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L‐fucose versus D‐glucose

Wolf

Stark

Fafenrot

et al. 2016

Molecular Microbiology

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SummaryArchaea are characterised by a complex metabolism with many unique enzymes that differ from their bacterial and eukaryotic counterparts. The thermoacidophilic archaeon Sulfolobus solfataricus is known for its metabolic versatility and is able to utilize a great variety of different carbon sources. However, the underlying degradation pathways and their regulation are often unknown. In this work, the growth on different carbon sources was analysed, using an integrated systems biology approach. The comparison of growth on L-fucose and D-glucose allows first insights into the genome-wide changes in response to the two carbon sources and revealed a new pathway for L-fucose degradation in S. solfataricus. During growth on L-fucose major changes in the central carbon metabolic network, as well as an increased activity of the glyoxylate bypass and the 3-hydroxypropionate/4-hydroxybutyrate cycle were observed. Within the newly discovered pathway for L-fucose degradation the following key reactions were identified: (i) L-fucose oxidation to L-fuconate via a dehydrogenase, (ii) dehydration to 2-keto-3-deoxy-Lfuconate via dehydratase, (iii) 2-keto-3-deoxy-Lfuconate cleavage to pyruvate and L-lactaldehyde via aldolase and (iv) L-lactaldehyde conversion to Llactate via aldehyde dehydrogenase. This pathway as well as L-fucose transport shows interesting overlaps to the D-arabinose pathway, representing another example for pathway promiscuity in Sulfolobus species.

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“…Studies on the S. solfataricus P2 a-fucosidase gene (fucI) have shown that this organism is capable of reading through such deletions, thereby producing full-length, active products through a process known as programmed ribosomal frame shifting [16]. One possibility is that the E2 gene is translated in a similar manner.…”

Section: Discussionmentioning

confidence: 99%

Discovery of a putative acetoin dehydrogenase complex in the hyperthermophilic archaeon Sulfolobus solfataricus

2010

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Edited by Stuart FergusonKeywords: Acetoin 2-Oxoacid dehydrogenase complex Archaea Thermophile Metabolism a b s t r a c t Like many other aerobic archaea, the hyperthermophile Sulfolobus solfataricus possesses a gene cluster encoding components of a putative 2-oxoacid dehydrogenase complex. In the current paper, we have cloned and expressed the first two genes of this cluster and demonstrate that the protein products form an a 2 b 2 hetero-tetramer possessing the catalytic activity characteristic of the first component enzyme of an acetoin dehydrogenase multienzyme complex. This represents the first report of an acetoin multienzyme complex in archaea, and contrasts with the branched-chain 2-oxoacid dehydrogenase complex activities characterised in two other archaea, Thermoplasma acidophilum and Haloferax volcanii.

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The gene of an archaeal α-l-fucosidase is expressed by translational frameshifting

Cited by 23 publications

References 42 publications

Metagenomics of microbial and viral life in terrestrial geothermal environments

Metagenomics of microbial and viral life in terrestrial geothermal environments

A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L‐fucose versus D‐glucose

Discovery of a putative acetoin dehydrogenase complex in the hyperthermophilic archaeon Sulfolobus solfataricus

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