The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Schulze, Stefan; Adams, Zachary; Cerletti, Micaela; Castro, Rosana de Carvalho; Ferreira-Cerca, Sébastien; Fufezan, Christian; Giménez, María Inés; Hippler, Michael; Jevtić, Ž; Knüppel, Robert; Legerme, Georgio; Lenz, Christof; Marchfelder, Anita; Maupin-Furlow, Julie A.; Paggi, Roberto A.; Pfeiffer, Friedhelm; Poetsch, Ansgar; Urlaub, Henning; Pohlschröder, Mechthild

doi:10.1038/s41467-020-16784-7

Cited by 41 publications

(61 citation statements)

References 115 publications

(167 reference statements)

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“…Another example highlighting the potential of hyperthermozymes for industrial application is the development of a continuous process for lactulose production by implementation of immobilized thermostable β-glycosidase from Pyrococcus furiosus [ 137 ]. With the advance of more thorough analyses of archaea, including the Archaeal Proteome Project (ArcPP), further insights into the mechanisms and beneficial properties of archaeal enzymes are expected in the near future [ 102 , 138 ].…”

Section: Protein Engineering To Tailor Plant-degrading Enzymes For Inmentioning

confidence: 99%

Biomass-degrading glycoside hydrolases of archaeal origin

Suleiman

Krüger

Antranikian

2020

Biotechnol Biofuels

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During the last decades, the impact of hyperthermophiles and their enzymes has been intensively investigated for implementation in various high-temperature biotechnological processes. Biocatalysts of hyperthermophiles have proven to show extremely high thermo-activities and thermo-stabilities and are identified as suitable candidates for numerous industrial processes with harsh conditions, including the process of an efficient plant biomass pretreatment and conversion. Already-characterized archaea-originated glycoside hydrolases (GHs) have shown highly impressive features and numerous enzyme characterizations indicated that these biocatalysts show maximum activities at a higher temperature range compared to bacterial ones. However, compared to bacterial biomass-degrading enzymes, the number of characterized archaeal ones remains low. To discover new promising archaeal GH candidates, it is necessary to study in detail the microbiology and enzymology of extremely high-temperature habitats, ranging from terrestrial to marine hydrothermal systems. State-of-the art technologies such as sequencing of genomes and metagenomes and automated binning of genomes out of metagenomes, combined with classical microbiological culture-dependent approaches, have been successfully performed to detect novel promising biomass-degrading hyperthermozymes. In this review, we will focus on the detection, characterization and similarities of archaeal GHs and their unique characteristics. The potential of hyperthermozymes and their impact on high-temperature industrial applications have not yet been exhausted.

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Section: Protein Engineering To Tailor Plant-degrading Enzymes For Inmentioning

confidence: 99%

Biomass-degrading glycoside hydrolases of archaeal origin

Suleiman

Krüger

Antranikian

2020

Biotechnol Biofuels

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“…In addition, the endA mRNA is not detectable on northern blots (data not shown). But proteome data clearly show that the splicing endonuclease is present in the proteome (Jevtić et al, 2019;Schulze et al, 2020).…”

Section: Rna Splicing Endonuclease From Haloferax Volcaniimentioning

confidence: 99%

Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea

et al. 2020

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In all three domains of life, tRNA genes contain introns that must be removed to yield functional tRNA. In archaea and eukarya, the first step of this process is catalyzed by a splicing endonuclease. The consensus structure recognized by the splicing endonuclease is a bulge-helix-bulge (BHB) motif which is also found in rRNA precursors. So far, a systematic analysis to identify all biological substrates of the splicing endonuclease has not been carried out. In this study, we employed CRISPRi to repress expression of the splicing endonuclease in the archaeon Haloferax volcanii to identify all substrates of this enzyme. Expression of the splicing endonuclease was reduced to 1% of its normal level, resulting in a significant extension of lag phase in H. volcanii growth. In the repression strain, 41 genes were down-regulated and 102 were up-regulated. As an additional approach in identifying new substrates of the splicing endonuclease, we isolated and sequenced circular RNAs, which identified excised introns removed from tRNA and rRNA precursors as well as from the 5′ UTR of the gene HVO_1309. In vitro processing assays showed that the BHB sites in the 5′ UTR of HVO_1309 and in a 16S rRNA-like precursor are processed by the recombinant splicing endonuclease. The splicing endonuclease is therefore an important player in RNA maturation in archaea.

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“…volcanii uses two distinct glycosylation pathways which were initially identified as being dependent on environmental salinity: the canonical pathway (AglB-J) and the low-salt pathway (Agl5-15) (Kaminski, Guan, et al, 2013). Unexpectedly, most genes coding for the low-salt N-glycosylation pathway were recently found to be expressed under optimal growth conditions (Schulze et al, 2020).…”

Section: Protein N-glycosylationmentioning

confidence: 99%

“…The Hfx. volcanii annotation referred to as "up-to-date" is that from 6-JUN-2019, which is the basis for the community proteome project arcPP (Schulze et al, 2020).…”

Section: Annotation Of the Hfx Gibbonsii Lr2-5 Genomementioning

confidence: 99%

“…Several haloarchaea are excellent research organisms as they are straightforward to cultivate, have relatively fast doubling times, and for several of them elaborate genetic tools are available (Leigh et al, 2011;Cheng et al, 2017). Haloferax volcanii is widely used as genetically accessible model organism, and different aspects of its biology such as replication, cell division, protein turn-over, transcription, translation and defense against viruses have been studied in detail (Eichler and Maupin-Furlow, 2013;Hawkins et al, 2013;Duggin et al, 2015;Maier et al, 2015;Pohlschroder and Schulze, 2019;Haque et al, 2020;Schulze et al, 2020). Curiously, in contrast to other haloarchaeal genera, viruses for the genus of Haloferax are extremely rare (Atanasova et al, 2012;Atanasova, Demina, et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Cellular and genomic properties ofHaloferax gibbonsiiLR2-5, the host of euryarchaeal virus HFTV1

Tittes

Schwarzer

Pfeiffer

et al. 2020

Preprint

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Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus-host models. Recently a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belonging to the genus Haloferax, but it is not infectious on the widely used model euryarcheon Hfx. volcanii. To gain more insight into the biology of HFTV1 host strain LR2-5, we studied characteristics that might play a role in its virus susceptibility: growth-dependent motility, surface layer, filamentous surface structures and cell shape. Its genome sequence showed that LR2-5 is a new strain of Hfx. gibbonsii. LR2-5 lacks obvious viral defense systems, such as CRISPR-Cas, and the composition of its cell surface is different from Hfx. volcanii, which might explain the different viral host range. This work provides first deep insights into the relationship between the host of halovirus HFTV1 and other members of the genus Haloferax. Given the close relationship to the genetically accessible Hfx. volcanii, LR2-5 has high potential as a new model for virus-host studies in euryarchaea.

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The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Cited by 41 publications

References 115 publications

Biomass-degrading glycoside hydrolases of archaeal origin

Biomass-degrading glycoside hydrolases of archaeal origin

Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea

Cellular and genomic properties ofHaloferax gibbonsiiLR2-5, the host of euryarchaeal virus HFTV1

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