scholarly journals The Genome of the Alga-Associated Marine Flavobacterium Formosa agariphila KMM 3901TReveals a Broad Potential for Degradation of Algal Polysaccharides

2013 ◽  
Vol 79 (21) ◽  
pp. 6813-6822 ◽  
Author(s):  
Alexander J. Mann ◽  
Richard L. Hahnke ◽  
Sixing Huang ◽  
Johannes Werner ◽  
Peng Xing ◽  
...  
Keyword(s):  
Building Blocks ◽  
Glycoside Hydrolases ◽  
Acid Fermentation ◽  
Content Type ◽  
Mixed Acid ◽  
Marine Habitats ◽  
Wide Range ◽  
Algal Polysaccharides ◽  
Polysaccharide Utilization Loci ◽  
Growth Experiments

ABSTRACTIn recent years, representatives of theBacteroideteshave been increasingly recognized as specialists for the degradation of macromolecules.Formosaconstitutes aBacteroidetesgenus within the classFlavobacteria, and the members of this genus have been found in marine habitats with high levels of organic matter, such as in association with algae, invertebrates, and fecal pellets. Here we report on the generation and analysis of the genome of the type strain ofFormosa agariphila(KMM 3901T), an isolate from the green algaAcrosiphonia sonderi.F. agariphilais a facultative anaerobe with the capacity for mixed acid fermentation and denitrification. Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced specialization for the degradation of proteins, polysaccharides, and glycoproteins. Sixty-five of the glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci, where they are clustered with TonB-dependent receptors, SusD-like proteins, sensors/transcription factors, transporters, and often sulfatases. These loci play a pivotal role in bacteroidetal polysaccharide biodegradation and in the case ofF. agariphilarevealed the capacity to degrade a wide range of algal polysaccharides from green, red, and brown algae and thus a strong specialization of toward an alga-associated lifestyle. This was corroborated by growth experiments, which confirmed usage particularly of those monosaccharides that constitute the building blocks of abundant algal polysaccharides, as well as distinct algal polysaccharides, such as laminarins, xylans, and κ-carrageenans.

scholarly journals Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci

2016 ◽  
Vol 82 (10) ◽  
pp. 2975-2987 ◽  
Author(s):  
Cong Sun ◽  
Ge-yi Fu ◽  
Chong-ya Zhang ◽  
Jing Hu ◽  
Lin Xu ◽  
...  
Keyword(s):  
Brown Seaweed ◽  
Laminaria Japonica ◽  
Glycoside Hydrolases ◽  
Content Type ◽  
Polysaccharide Lyases ◽  
Good Potential ◽  
Alginate Lyases ◽  
Genotypic Characteristics ◽  
Algal Polysaccharides ◽  
Polysaccharide Utilization Loci

ABSTRACTThe members of the phylumBacteroidetesare recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research onBacteroidetesin the human gut, research on polysaccharide degradation by marineBacteroidetesis still rare. The genusAlgibacterbelongs to theFlavobacteriaceaefamily of theBacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (Laminaria japonica). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genusAlgibacterwith the proposed nameAlgibacter alginolyticasp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the classFlavobacteria. Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22Tcan completely degrade alginate. This work reveals that strain HZ22Thas good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22Tare worth further research.

A logic model of the implementation of a regional workforce strategy in positive behavioural support

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Steve Noone ◽  
Alison Branch ◽  
Melissa Sherring
Keyword(s):  
Large Scale ◽  
Social Care ◽  
Building Blocks ◽  
Logic Model ◽  
Competency Framework ◽  
Health Staff ◽  
Content Type ◽  
Behavioural Support ◽  
Health And Social Care ◽  
Wide Range

Purpose Positive behavioural support (PBS) as a framework for delivering quality services is recognised in important policy documents (CQC, 2020; NICE, 2018), yet there is an absence in the literature on how this could be implemented on a large scale. The purpose of this paper is to describe a recent implementation of a workforce strategy to develop PBS across social care and health staff and family carers, within the footprint of a large integrated care system. Design/methodology/approach A logic model describes how an initial scoping exercise led to the production of a regional workforce strategy based on the PBS Competence Framework (2015). It shows how the creation of a regional steering group was able to coordinate important developmental stages and integrate multiple agencies into a single strategy to implement teaching and education in PBS. It describes the number of people who received teaching and education in PBS and the regional impact of the project in promoting cultural change within services. Findings This paper demonstrates a proof of concept that it is possible to translate the PBS Competency Framework (2015) into accredited courses. Initial scoping work highlighted the ineffectiveness of traditional training in PBS. Using blended learning and competency-based supervision and assessment, it was possible to create a new way to promote large-scale service developments in PBS supported by the governance of a new organisational structure. This also included family training delivered by family trainers. This builds on the ideas by Denne et al. (2020) that many of the necessary building blocks of implementation already exist within a system. Social implications A co-ordinated teaching and education strategy in PBS may help a wide range of carers to become more effective in supporting the people they care for. Originality/value This is the first attempt to describe the implementation of a framework for PBS within a defined geographical location. It describes the collaboration of health and social care planners and a local university to create a suite of courses built around the PBS coalition competency framework.

scholarly journals Analysis of the Proteome of Intracellular Shigella flexneri Reveals Pathways Important for Intracellular Growth

2013 ◽  
Vol 81 (12) ◽  
pp. 4635-4648 ◽  
Author(s):  
Rembert Pieper ◽  
C. R. Fisher ◽  
Moo-Jin Suh ◽  
S.-T. Huang ◽  
P. Parmar ◽  
...  
Keyword(s):  
Shigella Flexneri ◽  
Intracellular Bacteria ◽  
Intracellular Growth ◽  
Iron Starvation ◽  
Acid Fermentation ◽  
Nadph Regeneration ◽  
Content Type ◽  
Mixed Acid Fermentation ◽  
Mixed Acid

ABSTRACTGlobal proteomic analysis was performed withShigella flexneristrain 2457T in association with three distinct growth environments:S. flexnerigrowing in broth (in vitro),S. flexnerigrowing within epithelial cell cytoplasm (intracellular), andS. flexnerithat were cultured with, but did not invade, Henle cells (extracellular). Compared toin vitroand extracellular bacteria, intracellular bacteria had increased levels of proteins required for invasion and cell-to-cell spread, including Ipa, Mxi, and Ics proteins. Changes in metabolic pathways in response to the intracellular environment also were evident. There was an increase in glycogen biosynthesis enzymes, altered expression of sugar transporters, and a reduced amount of the carbon storage regulator CsrA. Mixed acid fermentation enzymes were highly expressed intracellularly, while tricarboxylic acid (TCA) cycle oxidoreductive enzymes and most electron transport chain proteins, except CydAB, were markedly decreased. This suggested that fermentation and the CydAB system primarily sustain energy generation intracellularly. Elevated levels of PntAB, which is responsible for NADPH regeneration, suggested a shortage of reducing factors for ATP synthesis. These metabolic changes likely reflect changes in available carbon sources, oxygen levels, and iron availability. Intracellular bacteria showed strong evidence of iron starvation. Iron acquisition systems (Iut, Sit, FhuA, and Feo) and the iron starvation, stress-associated Fe-S cluster assembly (Suf) protein were markedly increased in abundance. Mutational analysis confirmed that the mixed-acid fermentation pathway was required for wild-type intracellular growth and spread ofS. flexneri. Thus, iron stress and changes in carbon metabolism may be key factors in theS. flexneritransition from the extra- to the intracellular milieu.

scholarly journals Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell

2007 ◽  
Vol 57 (4) ◽  
pp. 701-707 ◽  
Author(s):  
Dawn E. Holmes ◽  
Kelly P. Nevin ◽  
Trevor L. Woodard ◽  
Aaron D. Peacock ◽  
Derek R. Lovley
Keyword(s):  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Amino Acid Sequences ◽  
Rrna Gene ◽  
Acid Fermentation ◽  
Mixed Acid ◽  
Phylogenetic Cluster ◽  
Wide Range ◽  
Novel Genus And Species

A Gram-negative, non-motile, filamentous, rod-shaped, non-spore-forming bacterium (strain F2T) was isolated from the surface of an electricity-harvesting electrode incubated in marine sediments. Strain F2T does not contain c-type cytochromes, flexirubin or carotenoids. It is a facultative anaerobe that can ferment sugars by using a mixed acid fermentation pathway and it can grow over a wide range of temperatures (4–42 °C). The DNA G+C (44.9 mol%) content and chemotaxonomic characteristics (major fatty acids, a-15 : 0 and 15 : 0) were consistent with those of species within the phylum Bacteroidetes. Phylogenetic analysis of the 16S rRNA nucleotide and elongation factor G amino acid sequences indicated that strain F2T represents a unique phylogenetic cluster within the phylum Bacteroidetes. On the basis of 16S rRNA gene sequence phylogeny, the closest relative available in pure culture, Alkaliflexus imshenetskii, is only 87.5 % similar to strain F2T. Results from physiological, biochemical and phylogenetic analyses showed that strain F2T should be classified as a novel genus and species within the phylum Bacteroidetes, for which the name Prolixibacter bellariivorans gen. nov., sp. nov. is proposed. The type strain is F2T (=ATCC BAA-1284T=JCM 13498T).

scholarly journals Improvement of FK506 Production in Streptomyces tsukubaensis by Genetic Enhancement of the Supply of Unusual Polyketide Extender Units via Utilization of Two Distinct Site-Specific Recombination Systems

2012 ◽  
Vol 78 (15) ◽  
pp. 5093-5103 ◽  
Author(s):  
Dandan Chen ◽  
Qi Zhang ◽  
Qinglin Zhang ◽  
Peilin Cen ◽  
Zhinan Xu ◽  
...  
Keyword(s):  
Genetic Manipulation ◽  
Acyl Carrier Protein ◽  
Building Blocks ◽  
Transcriptional Analysis ◽  
Genetic Enhancement ◽  
Side Chain ◽  
Original Strain ◽  
Content Type ◽  
Streptomyces Tsukubaensis ◽  
Wide Range

ABSTRACTFK506 is a potent immunosuppressant that has a wide range of clinical applications. Its 23-member macrocyclic scaffold, mainly with a polyketide origin, features two methoxy groups at C-13 and C-15 and one allyl side chain at C-21, due to the region-specific incorporation of two unusual extender units derived from methoxymalonyl-acyl carrier protein (ACP) and allylmalonyl-coenzyme A (CoA), respectively. Whether their intracellular formations can be a bottleneck for FK506 production remains elusive. In this study, we report the improvement of FK506 yield in the producing strainStreptomyces tsukubaensisby the duplication of two sets of pathway-specific genes individually encoding the biosyntheses of these two extender units, thereby providing a promising approach to generate high-FK506-producing strains via genetic manipulation. Taking advantage of the fact thatS. tsukubaensisis amenable to two actinophage (ΦC31 and VWB) integrase-mediated recombination systems, we genetically enhanced the biosyntheses of methoxymalonyl-ACP and allylmalonyl-CoA, as indicated by transcriptional analysis. Together with the optimization of glucose supplementation, the maximal FK506 titer eventually increased by approximately 150% in comparison with that of the original strain. The strategy of engineering the biosynthesis of unusual extender units described here may be applicable to improving the production of other polyketide or nonribosomal peptide natural products that contain pathway-specific building blocks.

scholarly journals Genomic Features of a Bumble Bee Symbiont Reflect Its Host Environment

2014 ◽  
Vol 80 (13) ◽  
pp. 3793-3803 ◽  
Author(s):  
Vincent G. Martinson ◽  
Tanja Magoc ◽  
Hauke Koch ◽  
Steven L. Salzberg ◽  
Nancy A. Moran
Keyword(s):  
Nadh Dehydrogenase ◽  
Tca Cycle ◽  
Nitrate Respiration ◽  
Bumble Bee ◽  
Metabolic Reconstruction ◽  
Low Oxygen ◽  
Acid Fermentation ◽  
Content Type ◽  
Mixed Acid ◽  
Complex Interactions

ABSTRACTHere, we report the genome of one gammaproteobacterial member of the gut microbiota, for which we propose the name “CandidatusSchmidhempelia bombi,” that was inadvertently sequenced alongside the genome of its host, the bumble bee,Bombus impatiens. This symbiont is a member of the recently described bacterial orderOrbales, which has been collected from the guts of diverse insect species; however, “Ca. Schmidhempelia” has been identified exclusively with bumble bees. Metabolic reconstruction reveals that “Ca. Schmidhempelia” lacks many genes for a functioning NADH dehydrogenase I, all genes for the high-oxygen cytochromeo, and most genes in the tricarboxylic acid (TCA) cycle. “Ca. Schmidhempelia” has retained NADH dehydrogenase II, the low-oxygen specific cytochromebd, anaerobic nitrate respiration, mixed-acid fermentation pathways, and citrate fermentation, which may be important for survival in low-oxygen or anaerobic environments found in the bee hindgut. Additionally, a type 6 secretion system, a Flp pilus, and many antibiotic/multidrug transporters suggest complex interactions with its host and other gut commensals or pathogens. This genome has signatures of reduction (2.0 megabase pairs) and rearrangement, as previously observed for genomes of host-associated bacteria. A survey of wild and laboratoryB. impatiensrevealed that “Ca. Schmidhempelia” is present in 90% of individuals and, therefore, may provide benefits to its host.

scholarly journals Functional Analyses of Multiple Lichenin-Degrading Enzymes from the Rumen Bacterium Ruminococcus albus 8

2011 ◽  
Vol 77 (21) ◽  
pp. 7541-7550 ◽  
Author(s):  
Michael Iakiviak ◽  
Roderick I. Mackie ◽  
Isaac K. O. Cann
Keyword(s):  
Plant Cell Wall ◽  
Bioinformatic Analysis ◽  
Major Product ◽  
Glycoside Hydrolases ◽  
Rumen Bacterium ◽  
Cell Wall Polysaccharides ◽  
Ruminococcus Albus ◽  
Content Type ◽  
Wide Range ◽  
Functional Analyses

ABSTRACTRuminococcus albus8 is a fibrolytic ruminal bacterium capable of utilization of various plant cell wall polysaccharides. A bioinformatic analysis of a partial genome sequence ofR. albusrevealed several putative enzymes likely to hydrolyze glucans, including lichenin, a mixed-linkage polysaccharide of glucose linked together in β-1,3 and β-1,4 glycosidic bonds. In the present study, we demonstrate the capacity of four glycoside hydrolases (GHs), derived fromR. albus, to hydrolyze lichenin. Two of the genes encoded GH family 5 enzymes (Ra0453 and Ra2830), one gene encoded a GH family 16 enzyme (Ra0505), and the last gene encoded a GH family 3 enzyme (Ra1595). Each gene was expressed inEscherichia coli, and the recombinant protein was purified to near homogeneity. Upon screening on a wide range of substrates, Ra0453, Ra2830, and Ra0505 displayed different hydrolytic properties, as they released unique product profiles. The Ra1595 protein, predicted to function as a β-glucosidase, preferred cleavage of a nonreducing end glucose when linked by a β-1,3 glycosidic bond to the next glucose residue. The major product of Ra0505 hydrolysis of lichenin was predicted to be a glucotriose that was degraded only by Ra0453 to glucose and cellobiose. Most importantly, the four enzymes functioned synergistically to hydrolyze lichenin to glucose, cellobiose, and cellotriose. This lichenin-degrading enzyme mix should be of utility as an additive to feeds administered to monogastric animals, especially those high in fiber.

scholarly journals The Pentose Moiety of Adenosine and Inosine Is an Important Energy Source for the Fermented-Meat Starter Culture Lactobacillus sakei CTC 494

2011 ◽  
Vol 77 (18) ◽  
pp. 6539-6550 ◽  
Author(s):  
T. Rimaux ◽  
G. Vrancken ◽  
B. Vuylsteke ◽  
L. De Vuyst ◽  
F. Leroy
Keyword(s):  
Starter Culture ◽  
Energy Sources ◽  
Lactobacillus Sakei ◽  
Acid Fermentation ◽  
Content Type ◽  
Mixed Acid ◽  
Arginine Catabolism ◽  
Adenosine Deaminase Activity ◽  
End Products ◽  
Ph Range

ABSTRACTThe genome sequence ofLactobacillus sakei23K has revealed that the speciesL. sakeiharbors several genes involved in the catabolism of energy sources other than glucose in meat, such as glycerol, arginine, and nucleosides. In this study, a screening of 15L. sakeistrains revealed that arginine, inosine, and adenosine could be used as energy sources by all strains. However, no glycerol catabolism occurred in any of theL. sakeistrains tested. A detailed kinetic analysis of inosine and adenosine catabolism in the presence of arginine byL. sakeiCTC 494, a fermented-meat starter culture, was performed. It showed that nucleoside catabolism occurred as a mixed-acid fermentation in a pH range (pH 5.0 to 6.5) relevant for sausage fermentation. This resulted in the production of a mixture of acetic acid, formic acid, and ethanol from ribose, while the nucleobase (hypoxanthine and adenine in the case of fermentations with inosine and adenosine, respectively) was excreted into the medium stoichiometrically. This indicates that adenosine deaminase activity did not take place. The ratios of the different fermentation end products did not vary with environmental pH, except for the fermentation with inosine at pH 5.0, where lactic acid was produced too. In all cases, no other carbon-containing metabolites were found; carbon dioxide was derived only from arginine catabolism. Arginine was cometabolized in all cases and resulted in the production of both citrulline and ornithine. Based on these results, a pathway for inosine and adenosine catabolism inL. sakeiCTC 494 was presented, whereby both nucleosides are directly converted into their nucleobase and ribose, the latter entering the heterolactate pathway. The present study revealed that the pentose moiety (ribose) of the nucleosides inosine and adenosine is an effective fermentable substrate forL. sakei. Thus, the ability to use these energy sources offers a competitive advantage for this species in a meat environment.

scholarly journals High Yields of 2,3-Butanediol and Mannitol in Lactococcus lactis through Engineering of NAD+Cofactor Recycling

2011 ◽  
Vol 77 (19) ◽  
pp. 6826-6835 ◽  
Author(s):  
Paula Gaspar ◽  
Ana Rute Neves ◽  
Michael J. Gasson ◽  
Claire A. Shearman ◽  
Helena Santos
Keyword(s):  
Lactate Dehydrogenase ◽  
Lactococcus Lactis ◽  
Growth Parameters ◽  
Genetic Redundancy ◽  
Acid Fermentation ◽  
Content Type ◽  
Mixed Acid ◽  
Reverse Transcription Pcr ◽  
Theoretical Yield ◽  
Maximal Yield

ABSTRACTManipulation of NADH-dependent steps, and particularly disruption of thelas-located lactate dehydrogenase (ldh) gene inLactococcus lactis, is common to engineering strategies envisaging the accumulation of reduced end products other than lactate. Reverse transcription-PCR experiments revealed that three out of the four genes assigned to lactate dehydrogenase in the genome ofL. lactis, i.e., theldh,ldhB, andldhXgenes, were expressed in the parental strain MG1363. Given that genetic redundancy is often a major cause of metabolic instability in engineered strains, we set out to develop a genetically stable lactococcal host tuned for the production of reduced compounds. Therefore, theldhBandldhXgenes were sequentially deleted inL. lactisFI10089, a strain with a deletion of theldhgene. The single, double, and triple mutants, FI10089, FI10089ΔldhB, and FI10089ΔldhBΔldhX, showed similar growth profiles and displayed mixed-acid fermentation, ethanol being the main reduced end product. Hence, the alcohol dehydrogenase-encoding gene, theadhEgene, was inactivated in FI10089, but the resulting strain reverted to homolactic fermentation due to induction of theldhBgene. The three lactate dehydrogenase-deficient mutants were selected as a background for the production of mannitol and 2,3-butanediol. Pathways for the biosynthesis of these compounds were overexpressed under the control of a nisin promoter, and the constructs were analyzed with respect to growth parameters and product yields under anaerobiosis. Glucose was efficiently channeled to mannitol (maximal yield, 42%) or to 2,3-butanediol (maximal yield, 67%). The theoretical yield for 2,3-butanediol was achieved. We show that FI10089ΔldhBis a valuable basis for engineering strategies aiming at the production of reduced compounds.

scholarly journals Discovery and Characterization of a 5-Hydroxymethylfurfural Oxidase from Methylovorus sp. Strain MP688

2013 ◽  
Vol 80 (3) ◽  
pp. 1082-1090 ◽  
Author(s):  
Willem P. Dijkman ◽  
Marco W. Fraaije
Keyword(s):  
Building Blocks ◽  
Degradation Pathway ◽  
Enzyme Characterization ◽  
Bacterial Degradation ◽  
Primary Alcohols ◽  
Content Type ◽  
Wide Range ◽  
Furandicarboxylic Acid ◽  
Ph Range

ABSTRACTIn the search for useful and renewable chemical building blocks, 5-hydroxymethylfurfural (HMF) has emerged as a very promising candidate, as it can be prepared from sugars. HMF can be oxidized to 2,5-furandicarboxylic acid (FDCA), which is used as a substitute for petroleum-based terephthalate in polymer production. On the basis of a recently identified bacterial degradation pathway for HMF, candidate genes responsible for selective HMF oxidation have been identified. Heterologous expression of a protein fromMethylovorussp. strain MP688 inEscherichia coliand subsequent enzyme characterization showed that the respective gene indeed encodes an efficient HMF oxidase (HMFO). HMFO is a flavin adenine dinucleotide-containing oxidase and belongs to the glucose-methanol-choline-type flavoprotein oxidase family. Intriguingly, the activity of HMFO is not restricted to HMF, as it is active with a wide range of aromatic primary alcohols and aldehydes. The enzyme was shown to be relatively thermostable and active over a broad pH range. This makes HMFO a promising oxidative biocatalyst that can be used for the production of FDCA from HMF, a reaction involving both alcohol and aldehyde oxidations.

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