20.500.12556/RUL-164757 Prepoznava genskih skupkov za razgradnjo hemiceluloz in pektinov v bakterijskem rodu Prevotella s transkriptomskim pristopom doktorska disertacija Identification of hemicellulose and pectin ultilization loci in Prevotella using transcriptomics doctoral dissertation Bakterije iz rodu Prevotella so ena najbolj dominantnih skupin v mikrobioti vampa. Njihova glavna funkcija je razgradnja hemiceluloz in pektinov rastlinske celične stene ter založnih polisaharidov. Te substrate razgrajujejo s pestrim naborom encimov, ki so kodirani v skupkih, odgovornih za razgradnjo polisaharidov (angl. Polysaccharide Utilisation Loci – PULs). To so lokusi ko-reguliranih genov, katerih produkti zaznavajo, vežejo, prenašajo in encimsko razgrajujejo kompleksne ogljikove hidrate. S konstituivno ekspresijo genov sistema PUL lahko te bakterije spremljajo substrate v okolju in če jih zaznajo, začnejo z ekspresijo genov na višjem nivoju. PUL se aktivira ob zaznavi substrata, katerega so produkti aktiviranega PULa sposobni razgraditi. Bioinformacijske analize vampnih vrst Prevotella so pokazale, da vsebujejo raznolik nabor PULov v svojih genomih, transkriptomski in genetski pristopi pa so napovedi potrdili na omejenem številu substratov. V tej študiji smo transkriptomsko identificirali različne PULe v Prevotella ruminicola KHP1 in Prevotella bryantii TF1-3, da bi potrdili njihovo specifičnost in preiskali raznolikost prisotnih PULov. Poleg tega smo z RT-qPCR preverili substratne preference in ocenili, da specifična hitrost rasti in količina biomase, ki jo sev lahko pridobi na substratu, vplivata na izbiro substratov za rast. Preferenčni substrati so bili uporabljeni v obeh bakterijah istočasno. Opazili smo tudi izrabljanje substratov, za katere ni bilo napovedanih in identificiranih PULov s transkriptomiko. V takšnem primeru sklepamo, da razgradnja substrata poteka z delovanjem več PULov hkrati. Prav tako smo preverjali homologijo in strukturno podobnost odkritih PULov s transkriptomiko še v 75 sevih Prevotella, da smo dobili vpogled v dinamiko spreminjanja genoma v tem rodu. Bacteria of the genera Prevotella are among the most dominant groups in the rumen microbiota. They are characterized by the ability to utilize different hemicelluloses and pectin of plant cell-wall as well as plant energy storage polysaccharides. The degradation is possible with the use of cell envelope bound multiprotein apparatuses coded in polysaccharide utilization loci (PULs), which have been shown to be substrate specific. PULs are constitutively expressed at low levels, but when they detect their cognate substrate, the expression of PUL genes increases singnificantly. The knowledge of PUL presence in rumen Prevotella based on bioinformatic analyses is already established and transcriptomic and genetic approaches confirmed predicted PULs for a limited number of substrates. In this study, we transcriptomically identified additional different PULs in Prevotella ruminicola KHP1 and Prevotella bryantii TF1-3. We also identified substrate preferences and found that specific growth rate and extent of growth impacted the choice of substrates preferentially used for degradation. These preferred substrates were used by both strains simultaneously as judged by their PUL upregulation. Lastly, β-glucan and xyloglucan were used by these strains in the absence of bioinformatically and transcriptomically identifiable PUL systems. We also analysed homology and synteny of transcriptomicaly confirmed PULs in 75 more strains of Prevotella to gain the insight of dynamics of PUL evolution in this genus. polisaharidi transkriptomika Prevotella vamp prežvekovalci hemiceluloze pektin RNAseq bioinformacijska analiza genski skupki polysaccharides transcriptomics Prevotella rumen ruminants hemicellulose pectin RNAseq bioinformatic analysis genetic loci true false false Slovenski jezik Angleški jezik Doktorsko delo/naloga 2024-11-11 07:15:24 2024-11-11 07:15:41 2024-11-22 14:56:01 0000-00-00 00:00:00 2024 0 0 0000-00-00 NiDoloceno NiDoloceno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 254241 214812675 44151.pdf 44151.pdf 1 3080A95A2B4DB474C84BADB4FD124D87 b1faf6e6e93f8da25cf25955fe4e62919ff54f320ac75391bad07c2731dc7f4e 0ac8e08f-9ff4-11ef-b232-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=195392 44152.xlsx 44152.xlsx 1 DDE3400F6CD0FD1D7C3C16C2980A9CD1 d5e074214f84d84a7e23643b5ab25f1c866d3cfe0db262f28f6fcb263ad85d0f 0ad7ffe5-9ff4-11ef-b232-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=195393 44153.xlsx 44153.xlsx 1 9949D3BD40F3E5B180C39BD2F9E53572 69c04f12af81fa7faa04c14b6339d1d5902fb6b9b5fe72785d91ab4d0a8b7ec3 0ad8613b-9ff4-11ef-b232-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=195394 44154.xlsx 44154.xlsx 1 FA705C65D928FE4C5BCC8F1403264234 f97b05a055c309fc15cdf9a0fca0b257d6f833e6e8fd71f8045b4ad93da97859 0ad96061-9ff4-11ef-b232-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=195395 44155.xlsx 44155.xlsx 1 B13F0D90F834E9C29C41C5F719B221ED 04b8f338cc37bc0c6f3841410aef3b451d4df6fadb80ba5ed1a08e34a0459f6d 0ad9ae17-9ff4-11ef-b232-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=195396 Biotehniška fakulteta 0 0 0