Elsevier eBooks, Год журнала: 2023, Номер unknown, С. 467 - 508
Опубликована: Янв. 1, 2023
Язык: Английский
Trends in Microbiology, Год журнала: 2022, Номер 31(4), С. 346 - 355
Опубликована: Дек. 5, 2022
Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how is transmitted maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct play unique role by linking one generation to next. Studies microbial inheritance, process we suggest including both vertical transmission subsequent migration of seed microorganisms new plant, thus become essential for our understanding evolutionary potential host–microbiome coevolution. We propose dividing inheritance into three stages: (i) plant seed, (ii) dormancy, (iii) seedling. discuss factors affecting assembly during stages, highlight future research directions, emphasize implications fundamental science society.
Язык: Английский
Процитировано
91
Nature, Год журнала: 2024, Номер 626(8001), С. 1125 - 1132
Опубликована: Фев. 14, 2024
Abstract To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis protect their ribosomes from damage 1,2 . In bacteria, two families of factors have been described, but the low conservation these huge diversity species, habitats environmental stressors confounded discovery 3–6 Here, by combining cryogenic electron microscopy, genetics biochemistry, we identify Balon, a new in cold-adapted bacterium Psychrobacter urativorans We show that Balon is distant homologue archaeo-eukaryotic translation aeRF1 found 20% representative bacteria. During cold shock or stationary phase, occupies ribosomal A site both vacant actively translating complex with EF-Tu, highlighting an unexpected role for EF-Tu cellular stress response. Unlike typical A-site substrates, binds mRNA-independent manner, initiating mode ribosome can commence while are still engaged synthesis. Our work suggests Balon–EF-Tu-regulated ubiquitous bacterial stress-response mechanism, demonstrate putative homologues Mycobacteria bind similar fashion. This finding calls revision current model inferred common holds numerous implications how understand study hibernation.
Язык: Английский
Процитировано
17
Journal of Biological Chemistry, Год журнала: 2023, Номер 299(9), С. 105163 - 105163
Опубликована: Авг. 14, 2023
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, degradation. Regulation of ribosome biogenesis synthesis are cornerstones this cellular adaptation all domains life, which rationalized by the high energy demand both processes increased resistance translationally silent cells against internal or external poisons. Reduced ultimately also reduces substrate load transport systems, required maintaining periplasmic, inner, outer membrane subproteomes. Consequences impaired have been analyzed several studies generally induce multifaceted response includes upregulation chaperones proteases simultaneous downregulation synthesis. contrast, less known how adjust targeting machineries reduced synthesis, e.g., when encounter face nutrient deprivation. current review, mainly focused using Escherichia coli model we summarize basic concepts activity regulated conditions. addition, highlight some recent developments directly impair bacterial membrane. Finally, describe mechanisms allow maintain stress-responsive proteins canonical pathways impaired. The dynamic regulation balanced compartmentalized essential organism depends network molecular aspects life cycle proteins. This at ribosome, co- posttranslational transport, finally degradation (1Mogk A. Huber D. Bukau B. Integrating homeostasis strategies prokaryotes.Cold Spring Harb. Perspect. Biol. 2011; 3a004366Crossref PubMed Scopus (75) Google Scholar, 2Powers E.T. Powers D.L. Gierasch L.M. FoldEco: E. coli.Cell Rep. 2012; 1: 265-276Abstract Full Text PDF (55) 3Bittner Arends J. Narberhaus F. When, why? proteolysis FtsH protease coli.Biol. Chem. 2017; 398: 625-635Crossref (59) 4Rosenzweig R. Nillegoda N.B. Mayer M.P. Hsp70 chaperone network.Nat. Rev. Mol. Cell 2019; 20: 665-680Crossref (525) 5Denks K. Vogt Sachelaru I. Petriman N.A. Kudva Koch H.G. Sec translocon mediated prokaryotes eukaryotes.Mol. Membr. 2014; 31: 58-84Crossref (125) 6Kudva Denks Kuhn P. Muller M. Protein translocation across inner Gram-negative bacteria: Tat dependent pathways.Res. Microbiol. 2013; 164: 505-534Crossref (129) 7Gloge Becker A.H. Kramer G. Co-translational maturation.Curr. Opin. Struct. 24c: 24-33Crossref (96) 8Rodnina M.V. Wintermeyer W. elongation, co-translational folding targeting.J. 2016; 428: 2165-2185Crossref (50) Scholar) (Fig. 1). Ribosomes serve major checkpoints pro- eukaryotes crucial targets stress-induced nonfavorable (9Starosta A.L. Lassak Jung Wilson D.N. translation response.FEMS 38: 1172-1201Crossref (132) 10Albert Kos-Braun I.C. Henras A.K. Dez C. Rueda Zhang X. et al.A assembly regulates transcription homeostasis.Elife. 8e45002Crossref (73) 11Zegarra V. Bedrunka Bange Czech L. How save times stress.Semin. Dev. 2023; 136: 3-12Crossref (2) Scholar). explained their abundance, high-energy biogenesis, costs (11Zegarra depletion, reduce modify ribosomes components translational machinery, regulate initiation elongation adapting Bacteria silence protecting them damage (12Maki Y. Yoshida H. Ribosomal hibernation-associated factors coli.Microorganisms. 2021; 10: 33Crossref (3) 13Matzov Bashan Yap M.F. Yonath Stress implemented hibernating ribosomes: structural overview.FEBS 286: 3558-3565Crossref (21) 14Prossliner T. Skovbo Winther Sørensen M.A. Gerdes Ribosome hibernation.Annu. Genet. 2018; 52: 321-348Crossref (82) 15Bakshi S. Choi Weisshaar J.C. spatial biology rapidly growing coli.Front. 2015; 6: 636Crossref (67) 16Beck H.J. Moll Leaderless mRNAs spotlight: ancient but not outdated.Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.RWR-0016-2017Crossref (29) 17Cheng-Guang Gualerzi C.O. switchboard response.Front. 2020; 11619038PubMed 18Vinogradova D.S. Zegarra Maksimova Nakamoto J.A. Kasatsky Paleskava al.How initiating copes ppGpp translate mRNAs.PLoS 18e3000593Crossref (30) 19Trösch Willmund conserved theme hibernation: from chloroplasts plants.Biol. 400: 879-893Crossref 20Wang Liang Zheng Liu An Xu al.Ribosome hibernation bacteria.Protein Pept. Lett. 27: 1082-1091Crossref complemented production proteases, support correct suboptimal degrade aggregated damaged (3Bittner 21Mahmoud S.A. Chien Regulated bacteria.Annu. Biochem. 87: 677-696Crossref (87) 22Bukau Weissman Horwich Molecular quality control.Cell. 2006; 125: 443-451Abstract (1233) A similar initiated membranes saturated due limiting number channels (6Kudva 23Baars Wagner Wickstrom Klepsch Ytterberg A.J. van Wijk K.J. al.Effects SecE depletion proteomes coli.J. Bacteriol. 2008; 190: 3505-3525Crossref (39) 24Wickstrom Simonsson Pop O. Baars al.Characterization consequences YidC 2D blue native/SDS-PAGE.J. 409: 124-135Crossref (34) 25Wang Dalbey R.E. Global change gene expression cell physiology YidC-depleted 2010; 192: 2193-2209Crossref (42) 26Price C.E. Otto Fusetti Becher Hecker Driessen Differential effect aerobic anaerobic growth conditions.Proteomics. 3235-3247Crossref (31) Enhanced cytosolic aggregation cannot be transported induces (26Price 27Bernstein H.D. Hyndman J.B. Physiological basis conservation signal recognition particle pathway 2001; 183: 2187-2197Crossref (53) 28Qi H.Y. Bernstein DnaK promotes selective export precursors SecA-deficient 2002; 277: 51077-51083Abstract (0) 29Baars Drew Thilo al.Defining role SecB comparative proteomics.J. 281: 10024-10034Abstract (69) Simultaneously, membrane-bound clears jammed (30Ito Akiyama Cellular functions, mechanism action, protease.Annu. 2005; 59: 211-231Crossref (316) 31van Stelten Silva Belin Silhavy T.J. Effects antibiotics proto-oncogene homolog destruction translocator SecY.Science. 2009; 325: 753-756Crossref (90) surface enlarged result phospholipid biosynthesis (32Herskovits A.A. Shimoni Minsky Bibi Accumulation endoplasmic novel ribosome-signal receptor complexes 159: 403-410Crossref 33Arechaga Miroux Karrasch Huijbregts de Kruijff Runswick M.J. al.Characterisation new intracellular accompanying large scale over-production b subunit F(1)F(o) ATP synthase.FEBS 2000; 482: 215-219Crossref (127) 34Weiner J.H. Lemire B.D. Elmes M.L. Bradley R.D. Scraba D.G. Overproduction fumarate reductase lipid-protein organelle.J. 1984; 158: 590-596Crossref downregulated ribosomal sequestered inactive aggregates (35Bürk Weiche Wenk Boy Nestel Heimrich al.Depletion inactivates 191: 7017-7026Crossref (20) 36Wickstrom al.Consequences 4598-4609Abstract (32) 37Wagner Klussmeier C.S. Nord overexpression coli.Mol. Cell. Proteomics. 2007; 1527-1550Abstract (269) induced via RNA polymerase (RNAP) RpoH (σ32) (38Oswald Njenga Natriashvili Sarmah SecYEG translocon.Front. Biosci. 8664241Crossref 39Guo M.S. Gross C.A. Stress-induced remodeling proteome.Curr. 24: R424-R434Abstract For executing its function, σ32 needs out-compete housekeeping σ70 subunit, requires presence hyperphosphorylated guanine nucleotides pppGpp, collectively called alarmones (40Jishage Kvint Shingler Nyström sigma factor competition alarmone ppGpp.Genes 16: 1260-1270Crossref (267) 41Steinchen ppGpp: magic modulators metabolism.Front. 11: 2072Crossref Nucleotide second messengers (p)ppGpp act critical signaling molecules during redirect metabolism toward factors, while inhibiting (rRNA) 42Leiva L.E. Ibba At crossroad nucleotide dynamics bacteria.Microbiol. 87e0004422Crossref (1) 43Gottesman Trouble coming: general responses bacteria.J. 294: 11685-11700Abstract (111) Considering approximately one-third entire 44Milo What total per volume? call rethink published values.Bioessays. 35: 1050-1055Crossref (357) 45Li G.W. Burkhardt J.S. Quantifying absolute rates reveals principles underlying allocation resources.Cell. 157: 624-635Abstract (845) execute function outside cytosol, preventing On other hand, it largely unknown activities adapted enter stationary phase starvation. Intriguingly, study has demonstrated accumulation only shuts down (SRP)-dependent (46Czech Mais C.N. Kratzat Giammarinaro Freibert al.Inhibition SRP-dependent secretion (p)ppGpp.Nat. Commun. 2022; 13: 1069Crossref (9) first part use they engage silencing ribosomes. briefly highlights Sec-dependent then describes machinery responds enables coordinate single can contain up 70,000 ribosomes, account 50% content 85% Adjusting turnover available nutrients status therefore critically important survival. reflected rapid increase exponential decline transition into (47Failmezger Ludwig Nieß Siemann-Herzberg fluorescence.FEMS 364: fnx055Crossref (10) (Table primarily determined rate rRNA (42Leiva 48Nomura Saccharomyces cerevisiae: diversity common principles.J. 1999; 181: 6857-6864Crossref Scholar), linked levels (49Deng Beahm D.R. Ionov Sarpeshkar Measuring modeling power consumption living microbial synthetic reporter.BMC 19: 101Crossref (26) 50Schneider D.A. Gaal Gourse R.L. NTP-sensing promoters direct.Proc. Natl. Acad. Sci. U. 99: 8602-8607Crossref (86) contains seven operons, each encoding 16S rRNA, 23S 5S variable tRNA genes (51Maeda Shimada Ishihama Strength coli.PLoS One. 10e0144697Crossref Each operon transcribed two promotors; upstream P1 promoter responsible high-level downstream P2 accounts basal low 2). Transcription portion global transcriptome (52Dennis P.P. Ehrenberg Bremer Control coli: systems approach.Microbiol. 2004; 68: 639-668Crossref (136) Stable binding RNAP promotor operons millimolar concentrations thus diminished drop 2).Table 1Abundance ribosome-hibernation coliProteinProtein abundance (proteins/cell)Ribosome profiling dataaE. MG1655 were grown (A600 = 0.3) Mops medium 2% glucose (347). (45Li Scholar)Protein mass spectrometry dataIBAQIBAQExponential phasebE. BW25113 M9 + 5 g/l glucose. (346Schmidt Kochanowski Vedelaar Ahrné Volkmer Callipo al.The quantitative condition-dependent proteome.Nat. Biotechnol. 34: 104-110Crossref (453) Scholar)Stationary phasecE. (24 h) Scholar)Ribosomal uS2 (RpsB)23,48713,9572432 uL4 (RplD)18,68811,4781409Hibernation RMF16,1221383538 HPF291723124011 RaiA5010304511,711 Sra15,79218355851 RsfA/RsfS796694 YqjD10,88621466209 ElaB11,47723984052 YgaM4734762793 EttA2080n.d.n.d.In general, based data most cases higher than spectrometry. potentially fact does consider degradation, particularly these experiments performed identical strains.Abbreviations: IBAQ, intensity-based quantification; n.d., determined/not detected.a (347Neidhardt F.C. Bloch P.L. Smith D.F. Culture enterobacteria.J. 1974; 119: 736-747Crossref Scholar).b glucose.c Open table tab strains. Abbreviations: detected. Transition further accompanied an polyphosphorylated pppGpp termed stringent 53Bange Brodersen D.E. Liuzzi Steinchen Two P P: understanding (p)ppGpp.Annu. 75: 383-406Crossref (16) 54Bennison D.J. Irving S.E. Corrigan R.M. impact TRAFAC GTPases prokaryotic assembly.Cells. 8: 1313Crossref 55Ferullo Lovett S.T. arrest 4e1000300Crossref (103) 56Irving Choudhury N.R. physiological roles (pp)pGpp bacteria.Nat. 256-271Crossref (119) 57Potrykus Cashel (p)ppGpp: still magical?.Annu. 62: 35-51Crossref (890) 58Hauryliuk Atkinson G.C. Murakami K.S. Tenson Recent insights physiology.Nat. 298-309Crossref controlled GDP/GTP pyrophosphokinase RelA bifunctional synthetase/hydrolase SpoT (41Steinchen 59Pausch Abdelshahid Schäfer Gratani F.L. al.Structural opposing synthetase hydrolase within orchestrator Rel.Cell 32108157Abstract (28) 3A). show very amino acid sequence likely evolved duplication ancestral Rel (60Mittenhuber Comparative genomics evolution synthetases/hydrolases (the Rel, proteins).J. 3: 585-600PubMed domain (53Bange Under nonstress acquires synthetase-off conformation, N-terminal catalytic inhibited C-terminal regulatory domain. However, starvation, interacts uncharged A-site releases 61Brown Fernández I.S. Gordiyenko Ramakrishnan Ribosome-dependent activation control.Nature. 534: 277-280Crossref (144) 3, B C). Among many itself because affinity dissociation ribosome. turn allows reactivation next stalled "hopping model" postulates provides interact tRNAs absence possible binds transfers vacant (62Winther Roghanian Activation loading RelA-tRNA A-site.Mol. 70: 95-105.e4Abstract (62) 63Kushwaha G.S. Bhavesh N.S. Interaction provide evidence prerequisite complex binding.Curr. 65: 1173-1184Crossref (13) Nevertheless, contact appears (64Li Bouveret Wang J.D. starvation diffusive behavior live 571-585Crossref synthesized transferring pyrophosphate 3′-hydroxyl group GDP GTP, respectively. T
Язык: Английский
Процитировано
38
Nature Communications, Год журнала: 2022, Номер 13(1)
Опубликована: Фев. 1, 2022
Abstract The evolution of microbial parasites involves the counterplay between natural selection forcing to improve and genetic drifts lose genes accumulate deleterious mutations. Here, understand how this occurs at scale individual macromolecules, we describe cryo-EM structure ribosomes from Encephalitozoon cuniculi , a eukaryote with one smallest genomes in nature. extreme rRNA reduction E. is accompanied unparalleled structural changes, such as previously unknown molten linkers bulgeless rRNA. Furthermore, withstand loss protein segments by evolving an ability use small molecules mimics degenerated segments. Overall, show that molecular structures long viewed reduced, degenerated, suffering debilitating mutations possess array compensatory mechanisms allow them remain active despite reduction.
Язык: Английский
Процитировано
30
Experientia supplementum, Год журнала: 2022, Номер unknown, С. 1 - 42
Опубликована: Янв. 1, 2022
Microsporidia represent an evolutionary outlier in the tree of life and occupy extreme edge eukaryotic domain with some their biological features. Many these unicellular fungi-like organisms have reduced genomic content to potentially lowest limit. With most compacted genomes, microsporidia are excellent model study reductive evolution its functional consequences. While growing number sequenced microsporidian genomes elucidated genome composition organization, a recent increase complementary post-genomic studies has started shed light on impacts reduction unique pathogens. This chapter will discuss framework enabling minimization use one ancient essential macromolecular complexes, ribosome, illustrate effects structural, molecular, cellular level. We outline how shaped DNA function complexity ribosome biogenesis process. Studying mechanisms, processes, or machines illuminates lifestyle provides valuable insights for comparative structural biology.
Язык: Английский
Процитировано
22
Nucleic Acids Research, Год журнала: 2025, Номер 53(2)
Опубликована: Янв. 11, 2025
Abstract Protein synthesis (translation) consumes a substantial proportion of cellular resources, prompting specialized mechanisms to reduce translation under adverse conditions. Ribosome inactivation often involves ribosome-interacting proteins. In both bacteria and eukaryotes, various proteins facilitate ribosome dimerization or hibernation, and/or prevent ribosomal subunits from associating, enabling the organisms adapt stress. Despite extensive studies on understanding factor-mediated anti-association in archaea remains elusive. Here, we present cryo-electron microscopy structures an archaeal 30S dimer complexed with factor (designated aRDF), Pyrococcus furiosus, resolved at resolution 3.2 Å. The complex features two stabilized by aRDF homodimers unique head-to-body architecture, which differs disome architecture observed during hibernation eukaryotes. interacts directly eS32 protein, is essential for subunit association. binding mode elucidates its properties, assembly 70S ribosomes.
Язык: Английский
Процитировано
0
Molecular & Cellular Proteomics, Год журнала: 2019, Номер 18(7), С. 1345 - 1362
Опубликована: Апрель 26, 2019
Mitochondrial transcripts are subject to a wealth of processing mechanisms including cis- and trans-splicing events, as well base modifications (RNA editing). Hundreds proteins required for these processes in plant mitochondria, many which belong the pentatricopeptide repeat (PPR) protein superfamily. The structure, localization, function is only poorly understood. Here we present evidence that several PPR bound mitoribosomes plants. A novel complexome profiling strategy combination with chemical crosslinking has been employed systematically define constituents large small ribosomal subunits mitochondria We identified more than 80 proteins, include other non-conventional proteins. These findings reveal potential coupling transcriptional translational events Furthermore, data indicate an extremely high molecular mass "small" subunit, even exceeding "large" subunit. Correction: Complexome Profiling Reveals Association Proteins Ribosomes Mitochondria Plants.Molecular & Cellular ProteomicsVol. 18Issue 8PreviewVOLUME 18 (2019) PAGES 1345–1362 Full-Text PDF Open Access semi-autonomous organelles eukaryotic cells produce some their using innate ribosomes (mitoribosomes). Aside from RNA-moieties (rRNAs) dedicated tRNAs, also encode involved mRNA maturation, translation, cytochrome c maturation oxidative phosphorylation (1Kubo T. Newton K.J. Angiosperm mitochondrial genomes mutations.Mitochondrion. 2008; 8: 5-14Crossref PubMed Scopus (207) Google Scholar). Several form complexes contain encoded nucleus. Therefore, components derived two different genomes, located nucleus themselves, thus defining chimeras. Due α-proteobacterial origin, largely resemble bacterial 70S respect sedimentation behavior, RNA content, susceptibility certain antibiotics (2Hamilton M.G. O'Brien T.W. Ultracentrifugal characterization ribosome subribosomal particles bovine liver: size composition.Biochemistry. 1974; 13: 5400-5403Crossref (39) They use similar initiation elongation factors (3Zhang Y. Spremulli L.L. Roles residues mammalian factor Ts interaction Tu.J. Biol Chem. 1998; 273: 28142-28148Abstract Full Text (17) Scholar, 4Gaur R. Grasso D. Datta P.P. Krishna P.D. Das G. Spencer A. Agrawal R.K. L. Varshney U. single translation functionally replaces factors.Mol. Cell. 29: 180-190Abstract (75) However, have evolved considerably lineage. Reconstruction Last Eukaryotic Common Ancestor (LECA) 1The abbreviations used are:LECAlast common ancestoriBAQintensity-based absolute quantificationlpBN-PAGElarge pore Blue-Native PAGEmtLSUmitoribosomal subunitmtSSUmitoribosomal subunitPPRpentatricopeptide repeatrRNAribosomal RNASLPstomatin-like proteinTAIRthe arabidopsis information resource. revealed were initially larger possessed counterpart (5Desmond E. Brochier-Armanet C. Forterre P. Gribaldo S. On last ancestor early evolution eukaryotes: reconstructing history ribosomes.Res. Microbiol. 2011; 162: 53-70Crossref (74) In addition, mitoribosomal polypeptide exit tunnel possesses hydrophobic surface caters proportion respiratory chain produced (6Brown Amunts Bai X.C. Sugimoto Edwards P.C. Murshudov Scheres S.H.W. Ramakrishnan V. Structure subunit human mitochondria.Science. 2014; 346: 718-722Crossref (205) intensity-based quantification PAGE stomatin-like yeast, mammals, trypanosomes characterized respective structures determined at near-atomic resolution cryo-electron microscopy (7Amunts Brown Toots J. Ribosome. structure ribosome.Science. 2015; 348: 95-98Crossref (326) 8Desai N. yeast 2017; 355: 528-531Crossref (114) 9Ramrath D.J.F. Niemann M. Leibundgut Bieri Prange Horn E.K. Leitner Boehringer Schneider Ban Evolutionary shift toward protein-based architecture trypanosomal ribosomes.Science. 2018; 362: eaau7735Crossref (71) 74S composed 54S (mtLSU) 37S (mtSSU). Together, they 73 (34 mtSSU, 39 mtLSU) rRNAs (15S mtSSU 21S mtLSU). Both, rRNA LSU 15S SSU consist nucleotides coli counterparts (8Desai 10Amunts Llácer J.L. Hussain Emsley Long F. subunit.Science. 343: 1485-1489Crossref (404) 11Greber B.J. Function ribosome.Annu. Rev. Biochem. 2016; 85: 103-132Crossref (145) Yeast mitoribosomes, however, lack 5S found LSU, binding (10Amunts Mammalian possess lower coefficient 55S dissociate into 28S 39S Together ∼80 30 50 mtLSU (12O'Brien general occurrence 55 S liver mitochondria.J. Biol. 1971; 246: 3409-3417Abstract 13Cahill Baio D.L. Cunningham C.C. Isolation Characterization rat ribosomes.Anal. 1995; 232: 47-55Crossref (37) 14Amunts (248) 15Greber Aebersold complete 303-308Crossref (269) Limited synthesis subunits, portion interact inner membrane (16Liu Interaction membrane.J. 2000; 275: 29400-29406Abstract (84) 17Pfeffer Woellhaf M.W. Herrmann J.M. Forster Organization machinery studied situ by cryoelectron tomography.Nat. Commun. 6: 6019Crossref (72) Only containing 16S 12S (mtSSU) rRNA, instead utilizing mt-tRNAVal (18Greber Schmitz ribosome.Nature. 515: 283-286Crossref (179) 6Brown reduction structural particularly bridging compensated additional (19Sharma M.R. Koc E.C. Booth T.M. reveals expanded functional role its component proteins.Cell. 2003; 115: 97-108Abstract (284) As such, 36 absent (14Amunts 20Greber Voigts-Hoffmann Erzberger J.P. Architecture 505: 515-519Crossref (167) substitution elements through acquisition shown further perpetuated mitoribosomes. Here, reduced (9S 12S) joined 127 (57 70 4.5 MDa ribonucleoprotein complex (9Ramrath significant predicted functions those classical subunits. Striking features trypanosome exceptionally presence tetratricopeptide latter mitochondria. Arabidopsis genome encodes ∼450 majority be imported (21Lurin Andrés Aubourg Bellaoui Bitton Bruyère Caboche Debast Gualberto Hoffmann B. Lecharny Le Ret Martin-Magniette M.L. Mireau H. Peeters Renou Szurek Taconnat Small I. Genome-wide analysis essential organelle biogenesis.Plant 2004; 16: 2089-2103Crossref (999) While mRNAs, currently unknown. PPR-protein polysome fractions isolated suggests participation (22Uyttewaal Rurek Hammani K. Arnal Quadrado Giegé PPR336 associated polysomes mitochondria.Mol. 375: 626-636Crossref (55) Knowledge composition scarce. Mitoribosomes higher plants 70–78S (depending on species assay conditions) 18S 26S (mtLSU). number varies least 68 potato broad bean (23Leaver C.J. Harmey M.A. Plant nucleic acids.Biochem. Soc. Symposia. 1973; 38: 175-193PubMed 24Vasconcelos A.C. Bogorad cytoplasmic, chloroplast, plants.Biochim. Biophys. Acta. 228: 492-502Crossref (27) 25Pinel Douce Mache study Solanum tuberosum L.Mol. Reports. 1986; 11: 93-97Crossref (10) 26Maffey Degand Boutry Partial purification identification genome.Mol. General Gen. 1997; 254: 365-371Crossref (16) since reliable techniques such spectrometry became accessible after studies conducted, minor known. More recently, part proteome shotgun proteomic approaches (27Heazlewood Tonti-Filippini J.S. Gout A.M. Day D.A. Whelan Millar A.H. Experimental highlights signaling regulatory components, provides assessment targeting prediction programs, indicates plant-specific proteins.Plant 241-256Crossref (481) 28Huang Taylor N.L. Narsai Eubel rice proteome, biogenesis, heterogeneity.Plant Physiol. 2009; 149: 719-734Crossref (112) 29Klodmann Senkler Rode Braun H.P. Defining mitochondria.Plant Physiology. 157: 587-598Crossref 30Salvato Havelund J.F. Chen Rao R.S. Rogowska-Wrzesinska Jensen O.N. Gang D.R. Thelen J.J. Møller I.M. tuber proteome.Plant 164: 637-653Crossref (90) 31Senkler Hildebrandt Lengwenus Schertl Schwarzländer Wagner Wittig thaliana.Plant 89: 1079-1092Crossref (129) Salvato et al. (30Salvato Scholar) but among considerable cytosolic It remains unclear constitute ribosome. extent mRNAs mitochondria-encoded genes processed, gene expression differs sequence-specific deamination cytosine editing) frequently occurring process requires specialized RNA-binding editing factors. if occurs bulk phase matrix or intramitochondrial eubacterial showed bind (32Wegrzyn R.D. Deuerling Molecular guardians newborn proteins: ribosome-associated chaperones folding.Cell. Mol. Life Sci. 2005; 62: 2727-2738Crossref Additionally, close proximity membrane, where mediating insertion newly synthesized lipid bilayer (33Pfeffer Förster tomography.Nature (88) can expected (or associate with) not directly synthesis, upstream steps (i.e. processing) downstream translation. Using approach (34Heide Bleier Steger Ackermann Dröse Schwamb Zörnig Reichert A.S. Koch Brandt identifies TMEM126B I assembly complex.Cell Metabolism. 2012; 538-549Abstract (198) Scholar), here report fragments. To this end, formaldehyde cross-linked first separated either large-pore blue-native (lpBN) gels (35Strecker Wumaier Z. Schägger Large separate mega 10 blue native electrophoresis: isolation putative strings patches.Proteomics. 2010; 10: 3379-3387Crossref (46) sucrose velocity gradients. LpBN gel lanes finely cut >40 pieces equal size, each was then analyzed abundance tandem spectrometry. Sucrose gradients fractionated 29 volume subsequently same method. For separation approach, profiles approximately one thousand produced. Hierarchical clustering allowed profiles. Co-migration within gradient indicative complex. Our results suggest unexpectedly surpassing PPR-proteins peptidases proteases observed, extending our current knowledge preparation cell culture leaf material performed described previously (31Senkler 36Cavalcanti J.H.F. Quinhones C.G.S. Brito D.S. Nunes-Nesi Araújo W.L. Differential impact amino acids OXPHOS system activity following carbohydrate starvation suspensions.Physiologia Plantarum. 161: 451-467Crossref (13) except procedure cross-linking step. Cross-linking adding 37% [v/v] solution filtered homogenate final concentration 0.5% [v/v]. After differential isopycnic centrifugation, four washing quantitatively remove Percoll organelles, adjusted 3 mg protein/ml (according Bradford). freshly prepared centrifugation. lpBN-PAGE carried out according Strecker modifications. solubilize membranes, 75 μg (cell mitochondria) 125 (cross-linked treated addition 25 μl 42 μl, respectively, digitonin solubilization buffer (50 mm imidazole, NaCl, 2 aminocaproic acid (ACA), 1 EDTA 5% [w/v] digitonin, pH 7.0), incubated 20 min ice. Coomassie G250 [w/v], loaded onto acrylamide (2% T, 20% C 13% 3% C, 0.5 m 6-aminohexanoic acid, imidazole/HCL, 7.4) overlaid 2.5% 25% (in sample gel. h 100 V, continued another 15 mA max. 500 stabilize fragile molecular-mass gel, firmly attached glass plates silane (GE Healthcare, Uppsala, Sweden) whereas opposite plate releasing agent (Blueslick, SERVA electrophoresis GmbH, Heidelberg, Germany) manufacturer's directions. staining, lane ∼48 top bottom, section subjected in-gel trypsin digestions outlined modified avoid contamination UPLC remnants soft over peptide extraction (now steps, 50% ACN, formic 100% acetonitrile (ACN), 1% acid). suspension) above. layered ml 8% 40% SureSpin 630 tubes, Thermo Scientific, Bremen, centrifuged 6 125,000 × g. piercing bottom tube hot needle create drain hole, 500–600 collected manually, resulting fractions. Of fraction, mixed 4x Laemmli (0.2 Tris, 6.8; sodium dodecylsulfate (SDS); glycerol; β-mercaptoethanol; 0.2% bromphenol blue) Tris-glycin SDS consisting 4% stacking 14% separating reported (37Thal Proteomic dissects nodulation biological nitrogen fixation Vicia faba root nodule physiology.Plant 97: 233-251Crossref (14) run stopped when front reached leaving concentrated band border phases. Following bands excised digestion Thal LC-MS/MS lpBN spectra queried against TAIR10 database additionally contaminations MaxQuant software version 1.6.0.1 (38Cox Mann enables rates, individualized p.p.b.-range accuracies proteome-wide quantification.Nat. Biotechnol. 26: 1367-1372Crossref (6891) parameters selected: carbamidomethyl (C) fixed modification, oxidation (M) acetylation (protein N-term) variable modifications, specific mode (P) missed cleavage sites. FDR applied PSM level. Protein groups contaminants removed manually proteinGroups.txt file. deposited ProteomeXchange Consortium PRIDE partner repository carry dataset identifier PXD011088. Abundance across all (based iBAQ values; (39Schwanhäusser Busse Li Dittmar Schuchhardt Wolf W. Selbach Global control.Nature. 473: 337-342Crossref (4059) Scholar)) NOVA (version 0.5.9.1; (40Giese Heide U NOVA: analyze data.Bioinformatics. 31: 440-441Crossref (51) clustered hierarchically average linkage based Pearson correlation distance. No normalization performed. heatmaps presented manuscript obtained approach. heatmap, 40 readings three gel-based heatmap. overlap neighboring slices, slice x confirmed x-1 x+1. refer independent experiments. Separation successfully past identify stable complexes, total extracts pre-purified cellular compartments, i.e. organelles. Most commonly, chromatographic methods (41Liu X. Yang W.C. Gao Q Regnier Toward interacting networks.J. Chromatography. 1178: 24-32Crossref (34) 42Kirkwood Ahmad Larance Lamond A.I. isoform variation size-fractionation-based quantitative proteomics.Mol. Proteomics. 2013; 12: 3851-3873Abstract (99) 43Wan Borgeson Phanse Tu Drew Clark Xiong Kagan O. Kwan Bezginov Chessman Pal Cromar Papoulas Ni Boutz Stoilova Havugimana Guo Malty R.H. Sarov Greenblatt Babu Derry W.B. Tillier E.R. Wallingford J.B. Parkinson Marcotte E.M. Emili Panorama ancient metazoan macromolecular complexes.Nature. 525: 339-344Crossref (317) plants, adopted chloroplasts (44Olinares P.D.B. Ponnala van Wijk Megadalton chloroplast stroma thaliana exclusion chromatography, spectrometry, hierarchical clustering.Mol. 9: 1594-1615Abstract (151) (45Aryal U.K. McBride Kihara Xie Hall M.C. Szymanski D.B. global complexes.Plant 3867-3882Crossref PubMe
Язык: Английский
Процитировано
41
Frontiers in Microbiology, Год журнала: 2023, Номер 14
Опубликована: Март 22, 2023
The genomic, environmental, and evolutionary interruptions caused the changes in bacterial growth, which were stringently associated with gene expression. growth expression remained unclear response to these that occurred combinative. As a pilot study, whether how was affected by individual dual of genome reduction, environmental stress, adaptive evolution investigated. Growth assay showed presence stressors, i.e., threonine chloramphenicol, significantly decreased rate wild-type Escherichia coli , whereas not reduced genome. It indicated canceling effect due interruption genomic changes. Experimental released improving fitness. Intriguingly, transcriptome architecture maintained homeostatic chromosomal periodicity regardless interruptions. Negative epistasis reorganization commonly observed interruptions, might contribute effect. supported numbers differentially expressed genes (DEGs) enriched regulons functions. Gene network analysis newly constructed 11 modules, one out correlated rate. Enrichment DEGs modules successfully categorized them into three types, conserved, responsive, epistatic. Taken together, homeostasis essential being alive, it be attributed negative functional differentiation modules. present study directly connected fitness provided global view microorganisms responded for survival from wild nature.
Язык: Английский
Процитировано
12
Scientific Reports, Год журнала: 2023, Номер 13(1)
Опубликована: Авг. 29, 2023
Abstract Survival of the live attenuated Bacillus Calmette-Guérin (BCG) vaccine amidst harsh host environments is key for BCG effectiveness as it allows continuous immune response induction and protection against tuberculosis. Mycobacterial DNA binding protein 1 (MDP1), a nucleoid associated protein, essential in BCG. However, there limited knowledge on extent MDP1 gene regulation how this influences survival. Here, we demonstrate that conditional knockdown (cKD) grows slower than vector control vitro , dies faster upon exposure to antibiotics (bedaquiline) oxidative stress (H 2 O menadione). MDP1-cKD also exhibited low infectivity survival THP-1 macrophages mice indicating possible susceptibility mediated stress. Consequently, vivo resulted reduced cytokine (IFN-gamma TNF-alpha) production by splenocytes. Temporal transcriptome profiling showed more upregulated (81–240) downregulated (5–175) genes suppression. Pathway analysis suppression biosynthetic pathways coincide with growth. Notable was deferential expression involved ( sigI ), maintenance integrity mutT1 REDOX balance WhiB3 interactions PE/PE_PGRS ). Thus, study shows MDP1’s importance highlights MDP1-dependent suggesting its role growth adaptation.
Язык: Английский
Процитировано
12
Nature Microbiology, Год журнала: 2023, Номер 8(10), С. 1834 - 1845
Опубликована: Сен. 14, 2023
Abstract Translational control is an essential process for the cell to adapt varying physiological or environmental conditions. To survive adverse conditions such as low nutrient levels, translation can be shut down almost entirely by inhibiting ribosomal function. Here we investigated eukaryotic hibernating ribosomes from microsporidian parasite Spraguea lophii in situ a combination of electron cryo-tomography and single-particle cryo-microscopy. We show that spores contain are locked dimeric (100S) state, which formed unique dimerization mechanism involving beak region. The within dimer fully assembled, suggesting they ready activated once host invaded. This study provides structural evidence acting hibernation microsporidia, therefore demonstrates eukaryotes utilize this translational control.
Язык: Английский
Процитировано
11