An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum

Bock, Thomas; Chen, Weihua; Ori, Alessandro; Malik, Nayab; Silva-Martin, N.; Huerta-Cepas, Jaime; Powell, Sean; Kastritis, Panagiotis L.; Smyshlyaev, Georgy; Vonkova, Ivana; Kirkpatrick, Joanna; Doerks, Tobias; Nesme, Leo; Baßler, Jochen; Koš, Martin; Hurt, Ed; Carlomagno, Teresa; Gavin, Anne‐Claude; Barábas, O.; Müller, Christoph W.; Noort, Vera van; Beck, Martin; Bork, Peer

doi:10.1093/nar/gku1147

Cited by 54 publications

(58 citation statements)

References 33 publications

(42 reference statements)

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“…The lysate was subjected to click reaction with biotin azide, and protein−lipid complexes were enriched using NeutrAvidin. Proteins were digested according to a recently developed protocol (23) and subjected to high-pH fractionation (38). Peptides were separated using the nanoAcquity ultra performance liquid chromatography (UPLC) system coupled directly to a linear trap quadrupole (LTQ) OrbitrapVelos Pro using the Proxeon nanospray source.…”

Section: Methodsmentioning

confidence: 99%

Trifunctional lipid probes for comprehensive studies of single lipid species in living cells

Höglinger

Nadler

Haberkant

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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110

105

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Lipid-mediated signaling events regulate many cellular processes. Investigations of the complex underlying mechanisms are difficult because several different methods need to be used under varying conditions. Here we introduce multifunctional lipid derivatives to study lipid metabolism, lipid−protein interactions, and intracellular lipid localization with a single tool per target lipid. The probes are equipped with two photoreactive groups to allow photoliberation (uncaging) and photo-cross-linking in a sequential manner, as well as a click-handle for subsequent functionalization. We demonstrate the versatility of the design for the signaling lipids sphingosine and diacylglycerol; uncaging of the probe for these two species triggered calcium signaling and intracellular protein translocation events, respectively. We performed proteomic screens to map the lipid-interacting proteome for both lipids. Finally, we visualized a sphingosine transport deficiency in patient-derived Niemann−Pick disease type C fibroblasts by fluorescence as well as correlative light and electron microscopy, pointing toward the diagnostic potential of such tools. We envision that this type of probe will become important for analyzing and ultimately understanding lipid signaling events in a comprehensive manner.

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Section: Methodsmentioning

confidence: 99%

Trifunctional lipid probes for comprehensive studies of single lipid species in living cells

Höglinger

Nadler

Haberkant

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

110

105

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“…A recent study based on thermophilic yeast genomes also shed some light on the thermal fingerprint on their proteomes (van Noort et al. 2013; Bock et al. 2014), depicting strategies adopted by these strains when facing high temperature (i.e.…”

Section: Introductionmentioning

confidence: 99%

Proteome evolution of deep-sea hydrothermal vent alvinellid polychaetes supports the ancestry of thermophily and subsequent adaptation to cold in some lineages

et al. 2017

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Temperature, perhaps more than any other environmental factor, is likely to influence the evolution of all organisms. It is also a very interesting factor to understand how genomes are shaped by selection over evolutionary timescales, as it potentially affects the whole genome. Among thermophilic prokaryotes, temperature affects both codon usage and protein composition to increase the stability of the transcriptional/translational machinery, and the resulting proteins need to be functional at high temperatures. Among eukaryotes less is known about genome evolution, and the tube-dwelling worms of the family Alvinellidae represent an excellent opportunity to test hypotheses about the emergence of thermophily in ectothermic metazoans. The Alvinellidae are a group of worms that experience varying thermal regimes, presumably having evolved into these niches over evolutionary times. Here we analyzed 423 putative orthologous loci derived from 6 alvinellid species including the thermophilic Alvinella pompejana and Paralvinella sulfincola. This comparative approach allowed us to assess amino acid composition, codon usage, divergence, direction of residue changes and the strength of selection along the alvinellid phylogeny, and to design a new eukaryotic thermophilic criterion based on significant differences in the residue composition of proteins. Contrary to expectations, the alvinellid ancestor of all present-day species seems to have been thermophilic, a trait subsequently maintained by purifying selection in lineages that still inhabit higher temperature environments. In contrast, lineages currently living in colder habitats likely evolved under selective relaxation, with some degree of positive selection for low-temperature adaptation at the protein level.

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“…Hence, partial rather than global retro-inverso isomers to stabilize hydrolysis-prone peptide bonds while maintaining the side chain topology that closely resembles the native sequence has been suggested as a better strategy for developing therapeutic peptides [58]. Icatibant is a partial retro-inverso interface peptide drug with a half-life of over 1 hr for the treatment of angioedema [59]. Developed to block the interaction between the prostaglandin and the bradykinin receptor-2 (BR-2), lcatibant is a peptide mimic of the amino terminus of BR-2 with four substituted non-natural amino acids and one D amino acid.…”

Section: Retro-inverso Peptidesmentioning

confidence: 99%

Interface Peptide Mimetics-Rationale and Application as Therapeutic Agents

Srinivasan¹

2016

Med chem

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Biomolecular recognition via protein-protein interactions (PPI) is central to the signaling events in most physiological and pathological processes. Hence PPI are considered excellent targets for drug development. In recent years there is considerable interest in the design and development of peptide based drugs as antagonists or agonists of PPI. High potency, great selectivity and better safety profile are significant advantages of peptide therapeutics. The following is a brief review of the rationale and modifications in the design of peptide mimetics of PPI interface.

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An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum

Cited by 54 publications

References 33 publications

Trifunctional lipid probes for comprehensive studies of single lipid species in living cells

Trifunctional lipid probes for comprehensive studies of single lipid species in living cells

Proteome evolution of deep-sea hydrothermal vent alvinellid polychaetes supports the ancestry of thermophily and subsequent adaptation to cold in some lineages

Interface Peptide Mimetics-Rationale and Application as Therapeutic Agents

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