DOCSLIB.ORG

The Role of Planktonic Flavobacteria in Processing Algal Organic Matter in Coastal East Antarctica Revealed Using

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Role of Planktonic Flavobacteria in Processing Algal Organic Matter in Coastal East Antarctica Revealed Using The role of planktonic Flavobacteria in processing algal organicFor matter Peer in coastal Review East Antarctica Only revealed using metagenomics and metaproteomics Journal: Environmental Microbiology and Environmental Microbiology Reports Manuscript ID: EMI-2012-0714.R1 Manuscript Type: EMI - Research article Journal: Environmental Microbiology Date Submitted by the Author: n/a Complete List of Authors: Cavicchioli, Ricardo ecophysiology, environmental genomics, functional diversity, Keywords: genomics/functional genomics/comparative genomics, bacteria, metagenomics/community genomics, microbial ecology, archaea Wiley-Blackwell and Society for Applied Microbiology Page 1 of 165 The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics For Peer Review Only Timothy J. Williams 1, David Wilkins 1, Emilie Long 1,2 , Flavia Evans 1, Mathew Z. DeMaere 1, Mark J. Raftery 3, and Ricardo Cavicchioli 1† 1 School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia. 2 UFR 927, Université Pierre et Marie Curie (UPMC) Paris VI, 4 place Jussieu 75532, Paris, France 3 Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, 2052, Australia. † To whom correspondence should be addressed. E-mail: [email protected] Running head: Metaproteomics of marine Antarctic Flavobacteria 1 Wiley-Blackwell and Society for Applied Microbiology Page 2 of 165 1 Summary 2 3 Heterotrophic marine bacteria play key roles in remineralizing organic matter 4 generated from primary production. However, far more is known about which 5 groups areFor dominant Peerthan about the Review cellular processes they Only perform in order to 6 become dominant. In the Southern Ocean, eukaryotic phytoplankton are the 7 dominant primary producers. In this study we used metagenomics and 8 metaproteomics to determine how the dominant bacterial and archaeal plankton 9 processed bloom material. We examined the microbial community composition in 10 fourteen metagenomes and found that the relative abundance of Flavobacteria 11 (dominated by Polaribacter ) was positively correlated with chlorophyll a 12 fluorescence, and the relative abundance of SAR11 was inversely correlated with 13 both fluorescence and Flavobacteria abundance. By performing metaproteomics on 14 the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, 15 East Antarctica) we defined how Flavobacteria attach to and degrade diverse 16 complex organic material, how they make labile compounds available to 17 Alphaproteobacteria (especially SAR11) and Gammaproteobacteria , and how these 18 heterotrophic Proteobacteria target and utilize these nutrients. The presence of 19 methylotrophic proteins for archaea and bacteria also indicated the importance of 20 metabolic specialists. Overall, the study provides functional data for the microbial 21 mechanisms of nutrient cycling at the surface of the coastal Southern Ocean. 22 2 Wiley-Blackwell and Society for Applied Microbiology Page 3 of 165 23 Introduction 24 25 Bacterioplankton populations in the world’s oceans are typically dominated by three 26 bacterial clades: Alphaproteobacteria , Gammaproteobacteria , and Bacteroidetes 27 (Glöckner Foret al. , 1999; Peer Kirchman, 2002; Review Kirchman et al. , 2003; Only O’Sullivan et al. , 2004; 28 Abell and Bowman, 2005a). They also dominate Southern Ocean bacterioplankton 29 populations in the austral summer (Abell and Bowman, 2005a,b; Murray and Grzymski, 30 2007; Jamieson et al. , 2012; Grzymski et al., 2012). 31 Flavobacteria , the major clade of Bacteroidetes in the marine environment, are 32 heterotrophs that target complex organic matter, and specialize in the degradation of 33 biopolymers (Pinhassi et al. , 1999; Cottrell and Kirchman. 2000; Kirchman, 2002; Abell 34 and Bowman, 2005a,b; González et al. , 2008; Teeling et al. , 2012). Flavobacteria target 35 high molecular weight compounds and tend to be abundant during phytoplankton blooms 36 (DeLong et al., 1993; Glöckner et al. , 1999; Pinhassi, 2004; West et al. , 2008; Teeling et 37 al. , 2012). Increased Flavobacteria abundance has been linked to enhanced primary 38 production (Brown and Bowman, 2001; Kirchman, 2002; Horner-Devine et al. , 2003; 39 Abell and Bowman, 2005a; Murray and Grzymski, 2007), consistent with their role as 40 major mineralizers of organic matter (Cottrell and Kirchman, 2000). Flavobacteria are 41 especially important as the “first responders” to phytoplankton blooms, and by breaking 42 down complex organic matter by direct attachment and exoenzymatic attack of algal cells 43 and algal-derived detrital particles (Kirchman, 2002; Gómez-Pereira et al. , 2012; Teeling 44 et al. , 2012). Consistent with this, Flavobacteria tend to be abundant in the Southern 3 Wiley-Blackwell and Society for Applied Microbiology Page 4 of 165 45 Ocean where the waters are enriched in nutrients and phytoplankton (Abell and Bowman 46 2005a), particularly in summer (Grzymski et al., 2012; Williams et al., 2012). 47 Marine Alphaproteobacteria populations are dominated by the SAR11 and 48 Roseobacter clades, which favor labile substrates, including byproducts from the growth 49 of algae andFor Flavobacteria Peer (Mou et al.Review, 2008; Teeling et al. , 2012).Only Members of the 50 SAR11 clade are obligately planktonic, scavenge low concentrations of nutrients from 51 seawater (Morris et al. , 2002; Giovannoni et al. , 2005), and are most abundant where 52 phytoplankton biomass and primary production are low (Morris et al. , 2002; Sowell et 53 al. , 2009). Members of the Roseobacter clade of the Rhodobacterales are metabolically 54 diverse, targeting a wider range of substrates than SAR11 (Wagner-Döbler and Biebl, 55 2006; Moran et al. , 2007), and are often found in close association with phytoplankton 56 (Pinhassi et al. , 2004; West et al. , 2008). SAR116 is a clade of Alphaproteobacteria that 57 has also been detected in a range of marine environments, and has been regarded as a 58 metabolic generalist (Oh et al. , 2010). Gammaproteobacteria also comprise a major 59 component of marine bacterioplankton, and are represented by phylogenetically diverse 60 clades. Marine members of Oceanospirillales and Alteromonadales include heterotrophs 61 with broad substrate preferences, with cold-adapted genera such as Colwellia , 62 Pseudoalteromonas , Marinobacter and Psychromonas recorded in Southern Ocean 63 seawater and sea-ice off Antarctica (Bowman et al. , 1997; Piquet et al. , 2011). The 64 Oligotrophic Marine Gammaproteobacteria (OMG) group are physiologically diverse 65 marine heterotrophs that have been shown to be obligately oligotrophic when grown in 66 culture (Cho and Giovannoni, 2004). 4 Wiley-Blackwell and Society for Applied Microbiology Page 5 of 165 67 In addition to these groups, Antarctic surface waters include putative 68 chemolithoautotrophs, notably sulfur-oxidizing Gammaproteobacteria and ammonia- 69 oxidizing Marine Group I Crenarchaeota (MGI), as major components of the 70 picoplankton (Murray and Grzymski, 2007; Gzymski et al. , 2012; Williams et al. , 2012). 71 Bacteria ofFor the gammaproteobacterial Peer Reviewsulfur oxidizer EOSA-1 Only (GSO-EOSA-1) complex 72 have been reported in global mesopelagic waters (Swan et al., 2011) and oxygen 73 minimum zones (Walsh et al., 2009; Canfield et al., 2010), and their ecological role in 74 surface waters is yet to be determined (Grzymski et al. , 2012; Williams et al. , 2012). 75 MGI (also called Thaumarchaeota ) appear to play an important role performing ‘dark’ 76 chemolithotrophic carbon fixation and nitrification in the bulk ocean (Konneke et al. , 77 2005; Wuchter et al., 2006; Berg et al. , 2007), as well as in Antarctic surface waters in 78 winter (Grzymski et al. , 2012; Williams et al. , 2012). 79 In the North Sea, specific populations of Alphaproteobacteria , 80 Gammaproteobacteria and Bacteroidetes have been shown to successively exploit 81 organic matter in response to diatom blooms (Teeling et al. , 2012). During the decline in 82 chlorophyll a levels that followed a bloom (marked by a rapid increase in chlorophyll a 83 levels from essentially zero to ~25 µg L -1), the relative abundances of specific 84 Flavobacteria (Ulvibacter spp., Formosa spp., and Polaribacter spp.) and 85 Gammaproteobacteria (Reinekea spp. and SAR92 clade) were found to peak, while 86 specific groups of Alphaproteobacteria (SAR11 and Roseobacter clade) remained 87 comparatively constant (Teeling et al. , 2012). 88 The Southern Ocean is dominated by eukaryotic phytoplankton (rather than 89 Cyanobacteria ), and consists mainly of diatoms, dinoflagellates, and haptophytes (Wright 5 Wiley-Blackwell and Society for Applied Microbiology Page 6 of 165 90 et al. , 2010). Antarctic surface blooms occur as a result of release of nutrients 91 (particularly iron) upwelled over winter or through other nutrient incursions (Boyd and 92 Ellwood, 2010). For much of the Southern Ocean, surface concentrations of <0.3 – 0.4 µg 93 L-1 are typical, while higher chlorophyll concentrations (>1 µg L -1) are associated with 94 the major SouthernFor Ocean Peer fronts, ice edgeReview blooms during sea-ice Only retreat in summer, and 95 coastal/shelf waters (Moore and Abbott, 2000). However to date, metagenome- or 96 metaproteome-based studies of the bacterial and archaeal communities associated with 97 high chlorophyll
Load more

Recommended publications
  • Table of Contents
    Table of contents SUMMARY IX ZUSAMMENFASSUNG XI 1. INTRODUCTION 1 1.1 The immune system 1 1.1.1 Function 1 1.1.2 Overview 1 1.1.3 Function of MHC molecules 1 1.1.4 The Major Histocompatibility Complex (MHC) Genes 2 1.1.5 Structure of MHC molecules 2 1.2 Antigen presentation 5 1.2.1 Outline of the conventional MHC class I pathway 5 1.3 The components of the peptide loading complex 7 1.3.1 Transporter associated with antigen presentation (TAP) 7 1.3.2 Calreticulin and calnexin 9 1.3.4 ERp 57/ER60 10 1.3.5 Tapasin (Tpn) 11 1.4 (a) The proteasomes 12 1.4 (b) Cytosolic peptidase 15 1.5 Endoplasmic Reticulum Associated Peptidase/s 16 1.6 Protein sorting 17 1.6.2 Vesicular transport in the Golgi apparatus 20 1.6.3 Endocytic pathway 20 1.6.4 Endocytic proteases 24 1.6.4.1 Biosynthesis and transport of cathepsins 25 1.6.4.2 Activation of cathepsins 26 1.6.4.3 Inhibitors of endosomal proteases. 26 1.7 Antigen processing by alternative pathways 27 1.8 Aim of the thesis 30 i 2. MATERIALS AND METHODS 31 2.1 Materials 31 2.1.1 Bacterial strains 31 2.1.2 Plasmids 31 2.1.2.1 Construction of plasmids 31 2.1.3 Primer list 32 2.1.4 PCR conditions 33 2.1.5 Antibiotics 34 2.1.6 Chemicals 34 2.1.7 Media for bacterial cells 34 2.1.8 Protein Chemicals 35 2.1.9 Animal cell culture media 37 2.1.11 Antibodies 39 2.1.11 siRNA oligonucleotides.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 6,395,889 B1 Robison (45) Date of Patent: May 28, 2002
    USOO6395889B1 (12) United States Patent (10) Patent No.: US 6,395,889 B1 Robison (45) Date of Patent: May 28, 2002 (54) NUCLEIC ACID MOLECULES ENCODING WO WO-98/56804 A1 * 12/1998 ........... CO7H/21/02 HUMAN PROTEASE HOMOLOGS WO WO-99/0785.0 A1 * 2/1999 ... C12N/15/12 WO WO-99/37660 A1 * 7/1999 ........... CO7H/21/04 (75) Inventor: fish E. Robison, Wilmington, MA OTHER PUBLICATIONS Vazquez, F., et al., 1999, “METH-1, a human ortholog of (73) Assignee: Millennium Pharmaceuticals, Inc., ADAMTS-1, and METH-2 are members of a new family of Cambridge, MA (US) proteins with angio-inhibitory activity', The Journal of c: - 0 Biological Chemistry, vol. 274, No. 33, pp. 23349–23357.* (*) Notice: Subject to any disclaimer, the term of this Descriptors of Protease Classes in Prosite and Pfam Data patent is extended or adjusted under 35 bases. U.S.C. 154(b) by 0 days. * cited by examiner (21) Appl. No.: 09/392, 184 Primary Examiner Ponnathapu Achutamurthy (22) Filed: Sep. 9, 1999 ASSistant Examiner William W. Moore (51) Int. Cl." C12N 15/57; C12N 15/12; (74) Attorney, Agent, or Firm-Alston & Bird LLP C12N 9/64; C12N 15/79 (57) ABSTRACT (52) U.S. Cl. .................... 536/23.2; 536/23.5; 435/69.1; 435/252.3; 435/320.1 The invention relates to polynucleotides encoding newly (58) Field of Search ............................... 536,232,235. identified protease homologs. The invention also relates to 435/6, 226, 69.1, 252.3 the proteases. The invention further relates to methods using s s s/ - - -us the protease polypeptides and polynucleotides as a target for (56) References Cited diagnosis and treatment in protease-mediated disorders.
    [Show full text]
  • Structure of Human Aspartyl Aminopeptidase Complexed With
    Chaikuad et al. BMC Structural Biology 2012, 12:14 http://www.biomedcentral.com/1472-6807/12/14 RESEARCH ARTICLE Open Access Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family Apirat Chaikuad1, Ewa S Pilka1, Antonio De Riso2, Frank von Delft1, Kathryn L Kavanagh1, Catherine Vénien-Bryan2, Udo Oppermann1,3 and Wyatt W Yue1* Abstract Backround: Aspartyl aminopeptidase (DNPEP), with specificity towards an acidic amino acid at the N-terminus, is the only mammalian member among the poorly understood M18 peptidases. DNPEP has implicated roles in protein and peptide metabolism, as well as the renin-angiotensin system in blood pressure regulation. Despite previous enzyme and substrate characterization, structural details of DNPEP regarding ligand recognition and catalytic mechanism remain to be delineated. Results: The crystal structure of human DNPEP complexed with zinc and a substrate analogue aspartate-β- hydroxamate reveals a dodecameric machinery built by domain-swapped dimers, in agreement with electron microscopy data. A structural comparison with bacterial homologues identifies unifying catalytic features among the poorly understood M18 enzymes. The bound ligands in the active site also reveal the coordination mode of the binuclear zinc centre and a substrate specificity pocket for acidic amino acids. Conclusions: The DNPEP structure provides a molecular framework to understand its catalysis that is mediated by active site loop swapping, a mechanism likely adopted in other M18 and M42 metallopeptidases that form dodecameric complexes as a self-compartmentalization strategy. Small differences in the substrate binding pocket such as shape and positive charges, the latter conferred by a basic lysine residue, further provide the key to distinguishing substrate preference.
    [Show full text]
  • Transcriptomic Analysis of Staphylococcus Xylosus in Solid Dairy Matrix Reveals an Aerobic Lifestyle Adapted to Rind
    microorganisms Article Transcriptomic Analysis of Staphylococcus xylosus in Solid Dairy Matrix Reveals an Aerobic Lifestyle Adapted to Rind 1, 2 1, 3, 4 Sabine Leroy *, Sergine Even , Pierre Micheau y, Anne de La Foye y, Valérie Laroute , Yves Le Loir 2 and Régine Talon 1 1 Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France; [email protected] (P.M.); [email protected] (R.T.) 2 INRAE, Agrocampus Ouest, STLO, Rennes, France; [email protected] (S.E.); [email protected] (Y.L.L.) 3 INRAE, UMRH, Saint-Genès-Champanelle, France; [email protected] 4 TBI, Université de Toulouse, CNRS, INRAE, Toulouse, France; [email protected] * Correspondence: [email protected] Current address: Université Clermont Auvergne, INRAE, UNH, Clermont-Ferrand, France. y Received: 26 October 2020; Accepted: 14 November 2020; Published: 17 November 2020 Abstract: Staphylococcus xylosus is found in the microbiota of traditional cheeses, particularly in the rind of soft smeared cheeses. Despite its frequency, the molecular mechanisms allowing the growth and adaptation of S. xylosus in dairy products are still poorly understood. A transcriptomic approach was used to determine how the gene expression profile is modified during the fermentation step in a solid dairy matrix. S. xylosus developed an aerobic metabolism perfectly suited to the cheese rind. It overexpressed genes involved in the aerobic catabolism of two carbon sources in the dairy matrix, lactose and citrate. Interestingly, S. xylosus must cope with nutritional shortage such as amino acids, peptides, and nucleotides, consequently, an extensive up-regulation of genes involved in their biosynthesis was observed.
    [Show full text]
  • Supplementary Materials
    Supplementary Materials Figure S1. Differentially abundant spots between the mid-log phase cells grown on xylan or xylose. Red and blue circles denote spots with increased and decreased abundance respectively in the xylan growth condition. The identities of the circled spots are summarized in Table 3. Figure S2. Differentially abundant spots between the stationary phase cells grown on xylan or xylose. Red and blue circles denote spots with increased and decreased abundance respectively in the xylan growth condition. The identities of the circled spots are summarized in Table 4. S2 Table S1. Summary of the non-polysaccharide degrading proteins identified in the B. proteoclasticus cytosol by 2DE/MALDI-TOF. Protein Locus Location Score pI kDa Pep. Cov. Amino Acid Biosynthesis Acetylornithine aminotransferase, ArgD Bpr_I1809 C 1.7 × 10−4 5.1 43.9 11 34% Aspartate/tyrosine/aromatic aminotransferase Bpr_I2631 C 3.0 × 10−14 4.7 43.8 15 46% Aspartate-semialdehyde dehydrogenase, Asd Bpr_I1664 C 7.6 × 10−18 5.5 40.1 17 50% Branched-chain amino acid aminotransferase, IlvE Bpr_I1650 C 2.4 × 10−12 5.2 39.2 13 32% Cysteine synthase, CysK Bpr_I1089 C 1.9 × 10−13 5.0 32.3 18 72% Diaminopimelate dehydrogenase Bpr_I0298 C 9.6 × 10−16 5.6 35.8 16 49% Dihydrodipicolinate reductase, DapB Bpr_I2453 C 2.7 × 10−6 4.9 27.0 9 46% Glu/Leu/Phe/Val dehydrogenase Bpr_I2129 C 1.2 × 10−30 5.4 48.6 31 64% Imidazole glycerol phosphate synthase Bpr_I1240 C 8.0 × 10−3 4.7 22.5 8 44% glutamine amidotransferase subunit Ketol-acid reductoisomerase, IlvC Bpr_I1657 C 3.8 × 10−16
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,603,824 B2 Ramseier Et Al
    USOO8603824B2 (12) United States Patent (10) Patent No.: US 8,603,824 B2 Ramseier et al. (45) Date of Patent: Dec. 10, 2013 (54) PROCESS FOR IMPROVED PROTEIN 5,399,684 A 3, 1995 Davie et al. EXPRESSION BY STRAIN ENGINEERING 5,418, 155 A 5/1995 Cormier et al. 5,441,934 A 8/1995 Krapcho et al. (75) Inventors: Thomas M. Ramseier, Poway, CA 5,508,192 A * 4/1996 Georgiou et al. .......... 435/252.3 (US); Hongfan Jin, San Diego, CA 5,527,883 A 6/1996 Thompson et al. (US); Charles H. Squires, Poway, CA 5,558,862 A 9, 1996 Corbinet al. 5,559,015 A 9/1996 Capage et al. (US) 5,571,694 A 11/1996 Makoff et al. (73) Assignee: Pfenex, Inc., San Diego, CA (US) 5,595,898 A 1/1997 Robinson et al. 5,610,044 A 3, 1997 Lam et al. (*) Notice: Subject to any disclaimer, the term of this 5,621,074 A 4/1997 Bjorn et al. patent is extended or adjusted under 35 5,622,846 A 4/1997 Kiener et al. 5,641,671 A 6/1997 Bos et al. U.S.C. 154(b) by 471 days. 5,641,870 A 6/1997 Rinderknecht et al. 5,643,774 A 7/1997 Ligon et al. (21) Appl. No.: 11/189,375 5,662,898 A 9/1997 Ligon et al. (22) Filed: Jul. 26, 2005 5,677,127 A 10/1997 Hogan et al. 5,683,888 A 1 1/1997 Campbell (65) Prior Publication Data 5,686,282 A 11/1997 Lam et al.
    [Show full text]
  • Serine Proteases with Altered Sensitivity to Activity-Modulating
    (19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants.
    [Show full text]
  • Jejunal Mucosa Proteomics Unravel Metabolic Adaptive Processes to Mild Chronic Heat Stress in Dairy Cows Franziska Koch1, Dirk Albrecht2, Solvig Görs1 & Björn Kuhla1*
    www.nature.com/scientificreports OPEN Jejunal mucosa proteomics unravel metabolic adaptive processes to mild chronic heat stress in dairy cows Franziska Koch1, Dirk Albrecht2, Solvig Görs1 & Björn Kuhla1* Climate change afects the duration and intensity of heat waves during summer months and jeopardizes animal health and welfare. High ambient temperatures cause heat stress in dairy cows resulting in a reduction of milk yield, feed intake, and alterations in gut barrier function. The objectives of this study were to investigate the mucosal amino acid, glucose and lactate metabolism, as well as the proteomic response of the small intestine in heat stressed (HS) Holstein dairy cows. Cows of the HS group (n = 5) were exposed for 4 days to 28 °C (THI = 76) in a climate chamber. Percentage decrease in daily ad libitum intake of HS cows was calculated to provide isocaloric energy intake to pair-fed control cows kept at 15 °C (THI = 60) for 4 days. The metabolite, mRNA and proteomic analyses revealed that HS induced incorrect protein folding, cellular destabilization, increased proteolytic degradation and protein kinase inhibitor activity, reduced glycolysis, and activation of NF-κB signaling, uronate cycling, pentose phosphate pathway, fatty acid and amino acid catabolism, mitochondrial respiration, ATPase activity and the antioxidative defence system. Our results highlight adaptive metabolic and immune mechanisms attempting to maintain the biological function in the small intestine of heat-stressed dairy cows. By the end of the twenty-frst century, mean ambient temperatures are predicted to increase resulting in a greater climate warming in the Northern hemisphere1. Consequently, both humans and animals are exposed to heat waves during summer months at a higher frequency, intensity and duration afecting behavior, health and welfare2,3.
    [Show full text]
  • Supplemental Methods
    Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection.
    [Show full text]
  • Supplementary Information
    Supplementary Information Table S1. Pathway analysis of the 1246 dwf1-specific differentially expressed genes. Fold Change Fold Change Fold Change Gene ID Description (dwf1/WT) (XL-5/WT) (XL-6/WT) Carbohydrate Metabolism Glycolysis/Gluconeogenesis POPTR_0008s11770.1 Glucose-6-phosphate isomerase −1.7382 0.512146 0.168727 POPTR_0001s47210.1 Fructose-bisphosphate aldolase, class I 1.599591 0.044778 0.18237 POPTR_0011s05190.3 Probable phosphoglycerate mutase −2.11069 −0.34562 −0.9738 POPTR_0012s01140.1 Pyruvate kinase −1.25054 0.074697 −0.16016 POPTR_0016s12760.1 Pyruvate decarboxylase 2.664081 0.021062 0.371969 POPTR_0012s08010.1 Aldehyde dehydrogenase (NAD+) −1.41556 0.479957 −0.21366 POPTR_0014s13710.1 Acetyl-CoA synthetase −1.337 0.154552 −0.26532 POPTR_0017s11660.1 Aldose 1-epimerase 2.770518 0.016874 0.73016 POPTR_0010s11970.1 Phosphoglucomutase −1.25266 −0.35581 0.074064 POPTR_0012s14030.1 Phosphoglucomutase −1.15872 −0.68468 −0.93596 POPTR_0002s10850.1 Phosphoenolpyruvate carboxykinase (ATP) 1.489119 0.967284 0.821559 Citrate cycle (TCA cycle) 2-Oxoglutarate dehydrogenase E2 component POPTR_0014s15280.1 −1.63733 0.076435 0.170827 (dihydrolipoamide succinyltransferase) POPTR_0002s26120.1 Succinyl-CoA synthetase β subunit −1.29244 −0.38517 −0.3497 POPTR_0007s12750.1 Succinate dehydrogenase (ubiquinone) flavoprotein subunit −1.83751 0.519356 0.309149 POPTR_0002s10850.1 Phosphoenolpyruvate carboxykinase (ATP) 1.489119 0.967284 0.821559 Pentose phosphate pathway POPTR_0008s11770.1 Glucose-6-phosphate isomerase −1.7382 0.512146 0.168727 POPTR_0013s00660.1 Glucose-6-phosphate 1-dehydrogenase −1.26949 −0.18314 0.374822 POPTR_0015s00960.1 6-Phosphogluconolactonase 2.022223 0.168877 0.971431 POPTR_0010s11970.1 Phosphoglucomutase −1.25266 −0.35581 0.074064 POPTR_0012s14030.1 Phosphoglucomutase −1.15872 −0.68468 −0.93596 POPTR_0001s47210.1 Fructose-bisphosphate aldolase, class I 1.599591 0.044778 0.18237 S2 Table S1.
    [Show full text]
  • A Novel Pseudomonas Geniculata AGE Family Epimerase/Isomerase and Its Application in D-Mannose Synthesis
    foods Article A Novel Pseudomonas geniculata AGE Family Epimerase/Isomerase and Its Application in d-Mannose Synthesis Zhanzhi Liu 1,2, Ying Li 1,2, Jing Wu 1,2 and Sheng Chen 1,2,* 1 State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; [email protected] (Z.L.); [email protected] (Y.L.); [email protected] (J.W.) 2 School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China * Correspondence: [email protected] Received: 29 September 2020; Accepted: 3 December 2020; Published: 6 December 2020 Abstract: d-mannose has exhibited excellent physiological properties in the food, pharmaceutical, and feed industries. Therefore, emerging attention has been applied to enzymatic production of d-mannose due to its advantage over chemical synthesis. The gene age of N-acetyl-d-glucosamine 2-epimerase family epimerase/isomerase (AGEase) derived from Pseudomonas geniculata was amplified, and the recombinant P. geniculata AGEase was characterized. The optimal temperature and pH of P. geniculata AGEase were 60 ◦C and 7.5, respectively. The Km, kcat, and kcat/Km of P. geniculata AGEase for d-mannose were 49.2 8.5 mM, 476.3 4.0 s 1, and 9.7 0.5 s 1 mM 1, respectively. ± ± − ± − · − The recombinant P. geniculata AGEase was classified into the YihS enzyme subfamily in the AGE enzyme family by analyzing its substrate specificity and active center of the three-dimensional (3D) structure. Further studies on the kinetics of different substrates showed that the P.
    [Show full text]
  • Computational and Systems Biology Themed Issue
    View Article Online / Journal Homepage / Table of Contents for this issue Molecular BioSystems This article was published as part of the Computational and Systems Biology themed issue Please take a look at the full table of contents to access the other papers in this issue. Open Access Article. Published on 13 October 2009. Downloaded 9/23/2021 6:41:00 PM. View Article Online PAPER www.rsc.org/molecularbiosystems | Molecular BioSystems Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteinswz Lakshminarayan M. Iyer,a Saraswathi Abhiman,a A. Maxwell Burroughsb and L. Aravind*a Received 28th August 2009, Accepted 28th August 2009 First published as an Advance Article on the web 13th October 2009 DOI: 10.1039/b917682a Recent studies have shown that the ubiquitin system had its origins in ancient cofactor/amino acid biosynthesis pathways. Preliminary studies also indicated that conjugation systems for other peptide tags on proteins, such as pupylation, have evolutionary links to cofactor/amino acid biosynthesis pathways. Following up on these observations, we systematically investigated the non-ribosomal amidoligases of the ATP-grasp, glutamine synthetase-like and acetyltransferase folds by classifying the known members and identifying novel versions. We then established their contextual connections using information from domain architectures and conserved gene neighborhoods. This showed remarkable, previously uncharacterized functional links between diverse peptide ligases, several peptidases of unrelated folds and enzymes involved in synthesis of modified amino acids. Using the network of contextual connections we were able to predict numerous novel pathways for peptide synthesis and modification, amine-utilization, secondary metabolite synthesis and potential peptide-tagging systems.
    [Show full text]