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Is Pyrococcus furiosus dolichylphosphate mannose synthase moonlighting as a biogenic flippase for dolichylphosphate mannose?
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology. (Divne group)ORCID iD: 0000-0001-5156-4592
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.ORCID iD: 0000-0003-4171-0693
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.ORCID iD: 0000-0001-5829-9357
KTH, Superseded Departments (pre-2005), Biotechnology. KTH, School of Biotechnology (BIO), Centres, Swedish Center for Biomimetic Fiber Engineering, BioMime. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, Superseded Departments (pre-2005), Biochemistry and Biotechnology.ORCID iD: 0000-0002-5805-2693
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Dolichylphosphate mannose synthase (DPMS) performs an essential function by synthesizing the activated lipid-linked sugar intermediated required by non-Leloir mannosyltransferases involved in protein glycosylation pathways. In eukaryotes and archaea, DPMS catalyzes the transfer of a mannose unit from GDP-mannose to dolichylphosphate to generate dolichylphosphate mannose (Dol-P-Man). DPMS from the extremophilic archaeon Pyrococcus furiosus (PfDPMS) belongs to the type-III class of DPMSs with a large catalytic domain attached to a transmembrane (TM) domain with two dimers of TM helices, TMD1 and TMD2, oriented such that TMD2 forms a 45° angle with TMD1. Our earlier work showed that the TM domain is dispensable for Dol-Pmannosylation, which brought its biological relevance into question. Here, we present crystallographic and bioinformatic evidence for a role for the TM domain in membrane translocation of Dol-P-Man. We crystallized a reaction performed at a temperature where PfDPMS activity is low, and determined the crystal structure at 2.9 Å resolution. Although the experimental data is deeply convoluted by traces of different structural states, we observed a strong signal for a Dol-P-Man molecule flipped inside the protein. Dol-P-Man is found to be flipped across TMD2 to position the mannosylphosphate head group in a polar pocket between TMD1 and TMD2. A role of the TM domain in glycolipid translocation is further discussed based on its topological resemblance to the GtrA family of small membrane transporters. Additionally, we identfied a dpm2 gene candidate that may serve as the missing translocation domain for the previously characterized type-I DPMS from Saccharmomyces cerevisiae.

National Category
Structural Biology Biochemistry Molecular Biology
Research subject
Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-281709OAI: oai:DiVA.org:kth-281709DiVA, id: diva2:1469353
Note

QC 20200922

Available from: 2020-09-21 Created: 2020-09-21 Last updated: 2025-02-20Bibliographically approved
In thesis
1. Structural and biochemical insights into biosynthesis and degradation of N-glycans
Open this publication in new window or tab >>Structural and biochemical insights into biosynthesis and degradation of N-glycans
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Carbohydrates are a primary energy source for all living organisms, but importantly, they also participate in a number of life-sustaining biological processes, e.g. cell signaling and cell-wall synthesis. The first part of the thesis examines glycosyltransferases that play a crucial role in the biosynthesis of N-glycans. Precursors to eukaryotic N-glycans are synthesized in the endoplasmic reticulum (ER) in the form of a lipid-bound oligosaccharide, which is then transferred to a nascent protein. The first seven sugar units are assembled on the cytoplasmic side of the ER, which is performed by glycosyltransferases that use nucleotide sugars as donors. The mannosyl transferase PcManGT is produced by the archaeon Pyrobaculum calidifontis, and the biochemical and structural results presented in the thesis suggest that the enzyme may be a counterpart to the glycosyltransferase Alg1 that participates in the biosynthesis of N-glycans in eukaryotes. Within the ER (in the lumen), activated dolichol-bound sugars are used as donor substrates instead of nucleotide sugars for glycosyltransferases that synthesize N-glycans. The glycosyltransferase dolichylphosphate mannose synthase (DPMS) catalyzes the formation of dolichylphosphate mannose, which is one of these dolichyl-bound sugars. The structure and function were studied for DPMS from Pyrococcus furiosus using protein X-ray crystallographic and biochemical methods and a new assay based on proteoliposomes was designed. The second part of the thesis focuses on glycoside hydrolases from bacteria that break down oligo- and polysaccharides. In one of the studies, a bacterial glycoside hydrolase from the acne bacterium Cutibacterium acnes was characterized. The enzyme was shown to be able to break down the host's N-glycans, which can be used as nutrients or perhaps even evade detection of the immune system. This study also suggests a cytoplasmic biosynthetic pathway for the formation of N-glycans in the acne bacterium. In another study, a glycoside hydrolase from a bacterium living in the moose rumen was characterized. The enzyme was shown to be able to break down β-1,3-glucans, which is a property that can be used industrially for biomass treatment.

Abstract [sv]

Kolhydrater utgör en primär energikälla för alla levande organismer, man deltar dessutom i mängd livsuppehållande biologiska processer, t.ex. cellsignalering och cellväggssyntes. Den första delen av avhandlingen undersöker glykosyltransferaser som spelar en avgörande roll för biosyntes av N-glykaner. Förstadier till eukaryota N-glykaner syntetiseras i det endoplasmatiska nätverket (ER) i form av en lipidbunden oligosackarid som sedan överförs till ett nybildat protein. De första sju sockerenheterna sätts ihop på den cytoplasmatiska sidan av ER, vilket sker med hjälp av glykosyltransferaser som använder nukleotidsockerföreningar som kan donera sockerenheter. Mannosyltransferaset PcManGT produceras av arkebakterien Pyrobaculum calidifontis och de biokemiska och strukturella resultat som presenteras i avhandlingen tyder på att enzymet kan vara en motsvarighet till glykosyltransferaset Alg1 som deltar i biosyntes av N-glykaner i eukaryoter. Inuti ER (i lumen) används aktiverade dolikolbundna socker istället för nukleotidsockerföreningar som substrat för glykosyltransferaser som syntetiserar N-glykaner. Glykosyltransferaset dolikolfosfatmannossyntas (DPMS) katalyserar bildandet av dolikolfosfatmannos vilket är en av dessa dolikolbundna sockerföreningar. Struktur och funktion studerades för DPMS från Pyrococcus furiosus med hjälp av proteinröntgenkristallografi samt biokemiska metoder samt en ny analysmetid baserad på proteoliposomer. Den andra delen av avhandlingen fokuserar på glykosidhydrolaser från bakterier som bryter ned oligo- och polysackarider. I en av studierna karakteriserades ett bakteriellt glykosidhydrolas från aknebakterien Cutibacterium acnes. Enzymet visade sig kunna bryta ned värdorganismens N-glykaner vilka kan användas som näring eller kanske även i syfte att undgå upptäckt av immunförsvaret. Studien föreslår även en cytoplasmatisk biosyntesväg för bildande av N-glykaner i aknebakterien. I en annan studie karakteriserades ett glykosidhydrolas från en bakterie som lever i älgvåmmen. Enzymet visade sig kunna bryta ned β-1,3- glukaner vilket är en egenskap som kan användas för i industriella tillämpningar för bearbetning av biomassa.

Abstract [de]

Kohlenhydrate sind eine primäre Energiequelle für alle lebenden Organismen, aber vor allem sind sie an einer großen Anzahl von lebensnotwendigen biologischen Prozessen, z.B. Zellsignalwegen und Zellwandaufbau, beteiligt. Der erste Teil dieser Doktorarbeit untersucht Glycosyltransferasen, welche entscheidend für die Synthese von N-Glycanen sind. Die Vorläufer der eukaryotischen N-Glycane werden im endoplasmatischen Retikulum (ER) als Lipid-gebundene Oligosaccharide synthetisiert, bevor sie auf das entstehende Protein transferiert werden. Die ersten sieben Zucker werden auf der zytoplasmatischen Seite der ER-Membran von Glycosyltransferasen, welche Nukleotidzucker als Donor nutzen, transferiert. Die Mannosyltransferase PcManGT wird von den Archaea Pyrobaculum calidifontis produziert, und die in dieser Doktorarbeit präsentierten biochemischen und strukturellen Resultate deuten darauf hin, dass das Enzym ein Pedant zu dem eukaryotischen Enzym Alg1 ist, welches Teil der eukaryotischen N-Glycan Biosynthese ist. Im ER (ERlumen) werden aktivierte Dolichol-gebundene Zucker, statt Nukleotidzuckern als Donor, für N-Glycan synthetisierende Glycosyltransferasen bereitgestellt. Die Glycosyltransferase Dolichylphosphate Mannose Synthase (DPMS) katalysiert mit der Bildung von Dolichylphosphate Mannose, einen dieser Dolicholgebundene Zucker. Die Struktur und Funktion der DPMS von Pyrococcus furiosus wurde mit Hilfe von sowohl X-ray Kristallographie als auch biochemischen Methoden untersucht und ein neuer Assay basierend auf Proteoliposomen designt. Im zweiten Teil der Doktorarbeit fokussiert sich auf bakterielle Glycosidasen welche Oligo- und Polysaccharide abbauen. Charakterisiert wurde die bakterielle Glycosidase von dem Aknebakterium Cutibacterium acnes. Das Enzym kann Teile des Wirt N-Glycans abbauen, wodurch Nährstoffe bereitgestellt werden oder die Erkennung des Immunsystems vermieden wird. Zusätzlich wird auch ein potentieller N-Glycan Abbauweg des Aknebakterium vorgeschlagen. In einer weiteren Studie wurde eine Glucosidase von einem Elchmagenbakterium charakterisiert. Das Enzym war in der Lage β-1,3-Glucane abzubauen, welches Anwendung in der industriellen Biomassebehandlung finden könnte.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2020. p. 59
Series
TRITA-CBH-FOU ; 2020:41
Keywords
N-glycan, biosynthesis, degradation, glycosyltransferase, glycoside hydrolase, biofuel, enzyme, membrane protein
National Category
Biochemistry Molecular Biology Structural Biology
Research subject
Biotechnology
Identifiers
urn:nbn:se:kth:diva-281752 (URN)978-91-7873-660-7 (ISBN)
Public defence
2020-10-16, https://kth-se.zoom.us/meeting/register/u5ErcuqurDMqG9De0JHMgaaxfcnXVREWWX38, Stockholm, 10:00 (English)
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Note

QC 2020-09-25

Available from: 2020-09-25 Created: 2020-09-24 Last updated: 2025-02-20Bibliographically approved

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Reichenbach, TomGandini, RosariaKalyani, DayanandDivne, Christina

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