Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Innovatieproject Hondsbossche Duinen
Ouwerkerk, Sonja ; Bodde, W. ; Smit, Marije ; Verheijen, Anne ; Leenders, Jakolien ; Wegman, Carolien ; Lagendijk, Georgette ; Scholl, Michaela ; Kuiters, A.T. ; Smits, N.A.C. ; Vries, Daisy de; Huiskes, H.P.J. ; Kramer, Henk ; Valk, Bert van der; IJff, Stéphanie - \ 2018
Ecoshape - 101 p.
Innovatieve kustversterking in de Hondsbossche Duinen
Ouwerkerk, S.J. ; Leenders, J. ; Bodde, W. ; Lagendijk, Georgette ; IJff, S. - \ 2018
Land + Water (2018)9. - ISSN 0926-8456 - p. 30 - 31.
Functional analysis of the HD-Zip transcription factor genes Oshox12 and Oshox14 in rice
Shao, Jingxia ; Haider, Imran ; Xiong, Lizhong ; Zhu, Xiaoyi ; Hussain, Rana Muhammad Fraz ; Övernäs, Elin ; Meijer, Annemarie H. ; Zhang, Gaisheng ; Wang, Mei ; Bouwmeester, Harro J. ; Ouwerkerk, Pieter B.F. - \ 2018
PLoS ONE 13 (2018)7. - ISSN 1932-6203

The homeodomain-leucine zipper (HD-Zip) transcription factor family plays vital roles in plant development and morphogenesis as well as responses to biotic and abiotic stresses. In barley, a recessive mutation in Vrs1 (HvHox1) changes two-rowed barley to six-rowed barley, which improves yield considerably. The Vrs1 gene encodes an HD-Zip subfamily I transcription factor. Phylogenetic analysis has shown that the rice HD-Zip I genes Oshox12 and Oshox14 are the closest homologues of Vrs1. Here, we show that Oshox12 and Oshox14 are ubiquitously expressed with higher levels in developing panicles. Trans-activation assays in yeast and rice protoplasts demonstrated that Oshox12 and Oshox14 can bind to a specific DNA sequence, AH1 (CAAT(A/T)ATTG), and activate reporter gene expression. Overexpression of Oshox12 and Oshox14 in rice resulted in reduced panicle length and a dwarf phenotype. In addition, Oshox14 overexpression lines showed a deficiency in panicle exsertion. Our findings suggest that Oshox12 and Oshox14 may be involved in the regulation of panicle development. This study provides a significant advancement in understanding the functions of HD-Zip transcription factors in rice.

Akkermansia muciniphila induces gut microbiota remodelling and controls islet autoimmunity in NOD mice
Hänninen, Arno ; Toivonen, Raine ; Pöysti, Sakari ; Belzer, Clara ; Plovier, Hubert ; Ouwerkerk, Janneke P. ; Emani, Rohini ; Cani, Patrice D. ; Vos, Willem M. de - \ 2018
Gut 67 (2018)8. - ISSN 0017-5749 - p. 1445 - 1453.
autoimmunity - bacterial interactions - diabetes mellitus - gut immunology - probiotics

Objective Intestinal microbiota is implicated in the pathogenesis of autoimmune type 1 diabetes in humans and in non-obese diabetic (NOD) mice, but evidence on its causality and on the role of individual microbiota members is limited. We investigated if different diabetes incidence in two NOD colonies was due to microbiota differences and aimed to identify individual microbiota members with potential significance. Design We profiled intestinal microbiota between two NOD mouse colonies showing high or low diabetes incidence by 16S ribosomal RNA gene sequencing and colonised the high-incidence colony with the microbiota of the low-incidence colony. Based on unaltered incidence, we identified a few taxa which were not effectively transferred and thereafter, transferred experimentally one of these to test its potential significance. Results Although the high-incidence colony adopted most microbial taxa present in the low-incidence colony, diabetes incidence remained unaltered. Among the few taxa which were not transferred, Akkermansia muciniphila was identified. As A. muciniphila abundancy is inversely correlated to the risk of developing type 1 diabetes-related autoantibodies, we transferred A. muciniphila experimentally to the high-incidence colony. A. muciniphila transfer promoted mucus production and increased expression of antimicrobial peptide Reg3γ, outcompeted Ruminococcus torques from the microbiota, lowered serum endotoxin levels and islet toll-like receptor expression, promoted regulatory immunity and delayed diabetes development. Conclusion Transfer of the whole microbiota may not reduce diabetes incidence despite a major change in gut microbiota, but single symbionts such as A. muciniphila with beneficial metabolic and immune signalling effects may reduce diabetes incidence when administered as a probiotic.

Preparation and preservation of viable Akkermansia muciniphila cells for therapeutic interventions
Ouwerkerk, J.P. ; Aalvink, S. ; Belzer, C. ; Vos, Willem de - \ 2017
Beneficial Microbes 8 (2017)2. - ISSN 1876-2883 - p. 163 - 169.
Delivery - Laboratory scale production - Stability - Therapeutic microbe - Viability

The anaerobic gut bacterium Akkermansia muciniphila is a well-characterised member of the mucosal microbiota and has shown to be a gut symbiont in human. A. muciniphila has been negatively associated with obesity and its associated metabolic disorders in various human cohorts while treatment with A. muciniphila cells reversed highfat diet-induced obesity and its associated metabolic disorders in mouse models. Therefore, administration of A. muciniphila has been suggested as a possible new therapeutic treatment for these omnipresent diseases. Here we describe a potentially scalable workflow for the preparation and preservation of high numbers of viable cells of A. muciniphila obtained from 1 l laboratory scale growth under strict anaerobic conditions for therapeutic interventions. This resulted in viable A. muciniphila cells with high yields and very high stability, with up to 97.9±4.5% survival for a time period of 1 year at -80 °C in glycerol-amended medium. Moreover, various quality assessment and control procedures were developed to ensure the use of viable cells of A. muciniphila. Several microscopic, culturing, and molecular approaches were applied to monitor the presence, abundance and recovery of A. muciniphila before, during, and after its administration to high-fat treated mice. We show that viable A. muciniphila cells can be recovered from caecal and colon content (up to 1×1010 cells/g), testifying for the efficiency of the described workflow.

Complete genome sequence of Akkermansia glycaniphila strain PytT, a mucin-degrading specialist of the reticulated python gut
Ouwerkerk, Janneke P. ; Koehorst, Jasper J. ; Schaap, Peter J. ; Ritari, Jarmo ; Paulin, Lars ; Belzer, Clara ; Vos, Willem M. de - \ 2017
Genome Announcements 5 (2017)1. - ISSN 2169-8287

Akkermansia glycaniphila is a novel Akkermansia species that was isolated from the intestine of the reticulated python and shares the capacity to degrade mucin with the human strain Akkermansia muciniphila MucT. Here, we report the complete genome sequence of strain PytT of 3,074,121 bp. The genomic analysis reveals genes for mucin degradation and aerobic respiration

Complete genome sequence of the Akkermansia glycaniphila strain PytT a mucin-degrading specialist of the reticulated python gut
Ouwerkerk, J.P. ; Koehorst, J.J. ; Schaap, P.J. ; Ritari, Jarmo ; Paulin, Lars ; Belzer, C. ; Vos, W.M. de - \ 2016
PRJEB15121 - Akkermansia glycaniphila - LT629973
Complete genome sequence of the Akkermansia glycaniphila strain PytT a mucin-degrading specialist of the reticulated python gut
The role of vegetation in Building with Nature pilot sandy foreshore Houtribdijk
Lange, H.J. de; Huiskes, H.P.J. ; Groot, G.A. de; Penning, E. ; Steetzel, H.J. ; Fiselier, J. ; Ouwerkerk, S. ; Thiel de Vries, J.S.M. van - \ 2016
- 1 p.
The natural situation of foreshores in shallow lakes with a gradual slope, sometimes a sandy beach and a well-developed riparian zone (submerged macrophytes and helophytes) is quite rare in the Netherlands. Still, the various ecosystem services that natural foreshores offer, e.g. attenuation of incoming wave action and habitat for fauna, gives inspiration to innovative solutions. Especially the wave attenuation service has received attention as a viable alternative to conventional dike reinforcement. To increase our understanding of a constructed foreshore, we applied 70.000 m3 of sand along a 400 m long stretch of the Houtribdijk (Markermeer) during the summer of 2014, creating a foreshore with a gradual slope (1:30). The pilot was divided into four sections, two of which have an additional top layer of a sand-clay mixture to promote vegetation development. Each section was partially planted with selected wetland species, related to the possibilities and limitations to construct the desired abiotic environment. The vegetation is expected to deliver two ecosystem services related to flood protection: roots will prevent erosion of the sand, and aboveground biomass will dissipate wave energy. One of the chosen species is Common reed (Phragmites australis). To further enhance our understanding of the success of reed, we study the genetic diversity of Common reed in the Netherlands to identify if specific genotypes or phenotypes can be associated with its success at a given habitat. We present the first results of this genetic analysis and give advice on how this species can be promoted in newly constructed foreshores.
Establishing vegetated foreshores to increase dike safety along lake shores
Penning, E. ; Steetzel, H.J. ; Santen, R. van; Lange, H.J. de; Ouwerkerk, S. ; Vuik, V. ; Fiselier, J. ; Thiel de Vries, J.S.M. van - \ 2016
Vegetated foreshores in front of existing dikes can contribute to the overall reduction of wave loads on the dike. In order to test this concept in large shallow lakes a field pilot was constructed along the Houtribdijk in Lake Markermeer (the Netherlands) in 2014 to gain experience with construction, stability, maintenance and governance aspects. A large scale monitoring programme was set up to follow the hydrodynamic forcing, morphological changes and vegetation development on the pilot. The pilot is located on an exposed south-westerly direction, and experiences substantial wave impact. As a result the desired vegetation on the land-water interface has not been able to establish, but a rather dynamic sandy beach is currently the main feature along the waterline of the site. Higher up the slope planted reeds, and a mixture of willows has well established itself in the first growing season. The exposed position of the location makes that hardly any natural pioneer vegetation has settled, only in small sheltered areas some annuals were able to germinate and maintain themselves.
Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces
Ouwerkerk, Janneke P. ; Aalvink, Steven ; Belzer, Clara ; Vos, Willem M. de - \ 2016
International Journal of Systematic and Evolutionary Microbiology 66 (2016)11. - ISSN 1466-5026 - p. 4614 - 4620.
Anaerobic - Faeces - Gastrointestinal - Most probable number - Mucin-degrader - Python

A Gram-stain-negative, non-motile, strictly anaerobic, oval-shaped, non-spore-forming bacterium (strain PytT) was isolated from reticulated python faeces. Strain PytT was capable of using mucin as sole carbon, energy and nitrogen source. Cells could grow singly, in pairs, and were also found to aggregate. Scanning electron microscopy revealed the presence of filamentous structures connecting individual bacterial cells. Strain PytT could grow on a limited number of single sugars, including N-acetylglucosamine, N-acetylgalactosamine, glucose, lactose and galactose, but only when a plentiful protein source was provided. Phylogenetic analysis based on 16S rRNA gene sequencing showed strain PytT to belong to the Verrucomicrobiae class I, family Akkermansiaceae, genus Akkermansia, with Akkermansia muciniphila MucT as the closest relative (94.4% sequence similarity). DNA–DNA hybridization revealed low relatedness of 28.3% with A. muciniphila MucT. The G+C content of DNA from strain PytT was 58.2 mol%. The average nucleotide identity (ANI) of the genome of strain PytT compared to the genome of strain MucT was 79.7 %. Chemotaxonomic data supported the affiliation of strain PytT to the genus Akkermansia. Based on phenotypic, phylogenetic and genetic characteristics, strain PytT represents a novel species of the genus Akkermansia, for which the name Akkermansia glycaniphila sp. nov. is proposed. The type strain is PytT (=DSM 100705T=CIP 110913T).

Erratum: Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
Henderson, Gemma ; Cox, Faith ; Ganesh, Siva ; Jonker, Arjan ; Young, Wayne ; Abecia, Leticia ; Angarita, Erika ; Aravena, Paula ; Nora Arenas, Graciela ; Ariza, Claudia ; Attwood, Graeme T. ; Mauricio Avila, Jose ; Avila-stagno, Jorge ; Bannink, André ; Barahona, Rolando ; Batistotti, Mariano ; Bertelsen, Mads F. ; Brown-Kav, Aya ; Carvajal, Andres M. ; Cersosimo, Laura ; Vieira Chaves, Alexandre ; Church, John ; Clipson, Nicholas ; Cobos-peralta, Mario A. ; Cookson, Adrian L. ; Cravero, Silvio ; Cristobal Carballo, Omar ; Crosley, Katie ; Cruz, Gustavo ; Cerón Cucchi, María ; Barra, Rodrigo de la; Menezes, Alexandre B. de; Detmann, Edenio ; Dieho, Kasper ; Dijkstra, Jan ; Reis, William L.S. Dos; Dugan, Mike E.R. ; Hadi Ebrahimi, Seyed ; Eythórsdóttir, Emma ; Nde Fon, Fabian ; Fraga, Martín ; Franco, Francisco ; Friedeman, Chris ; Fukuma, Naoki ; Gagić, Dragana ; Gangnat, Isabelle ; Javier Grilli, Diego ; Guan, Le Luo ; Heidarian Miri, Vahideh ; Hernandez-Sanabria, Emma ; Gomez, Alma Ximena Ibarra ; Isah, Olubukola A. ; Ishaq, Suzanne ; Jami, Elie ; Jelincic, Juan ; Kantanen, Juha ; Kelly, William J. ; Kim, Seon-Ho ; Klieve, Athol ; Kobayashi, Yasuo ; Koike, Satoshi ; Kopecny, Jan ; Nygaard Kristensen, Torsten ; Julie Krizsan, Sophie ; Lachance, Hannah ; Lachman, Medora ; Lamberson, William R. ; Lambie, Suzanne ; Lassen, Jan ; Leahy, Sinead C. ; Lee, Sang-Suk ; Leiber, Florian ; Lewis, Eva ; Lin, Bo ; Lira, Raúl ; Lund, Peter ; Macipe, Edgar ; Mamuad, Lovelia L. ; Cuquetto Mantovani, Hilário ; Marcoppido, Gisela Ariana ; Márquez, Cristian ; Martin, Cécile ; Martinez, Gonzalo ; Eugenia Martinez, Maria ; Lucía Mayorga, Olga ; McAllister, Tim A. ; McSweeney, Chris ; Mestre, Lorena ; Minnee, Elena ; Mitsumori, Makoto ; Mizrahi, Itzhak ; Molina, Isabel ; Muenger, Andreas ; Muñoz, Camila ; Murovec, Bostjan ; Newbold, John ; Nsereko, Victor ; O’donovan, Michael ; Okunade, Sunday ; O’neill, Brendan ; Ospina, Sonia ; Ouwerkerk, Diane ; Parra, Diana ; Pereira, Luiz Gustavo Ribeiro ; Pinares-patiño, Cesar ; Pope, Phil B. ; Poulsen, Morten ; Rodehutscord, Markus ; Rodriguez, Tatiana ; Saito, Kunihiko ; Sales, Francisco ; Sauer, Catherine ; Shingfield, Kevin ; Shoji, Noriaki ; Simunek, Jiri ; Stojanović-Radić, Zorica ; Stres, Blaz ; Sun, Xuezhao ; Swartz, Jeffery ; Liang Tan, Zhi ; Tapio, Ilma ; Taxis, Tasia M. ; Tomkins, Nigel ; Ungerfeld, Emilio ; Valizadeh, Reza ; Adrichem, Peter van; Hamme, Jonathan van; Hoven, Woulter van; Waghorn, Garry ; Wallace, John R. ; Wang, Min ; Waters, Sinéad M. ; Keogh, Kate ; Witzig, Maren ; Wright, Andre-Denis G. ; Yamano, Hidehisa ; Yan, Tianhai ; Yáñez-ruiz, David R. ; Yeoman, Carl J. ; Zambrano, Ricardo ; Zeitz, Johanna ; Zhou, Mi ; Wei Zhou, Hua ; Xia Zou, Cai ; Zunino, Pablo ; Janssen, Peter H. - \ 2016
Scientific Reports 6 (2016). - ISSN 2045-2322 - 2 p.
Adaptation of Akkermansia muciniphila to the oxic-anoxic interface of the mucus layer
Ouwerkerk, Janneke P. ; Ark, Kees C.H. van der; Davids, Mark ; Claassens, Nico J. ; Finestra, Teresa Robert ; Vos, Willem M. de; Belzer, Clara - \ 2016
Applied and Environmental Microbiology 82 (2016)23. - ISSN 0099-2240 - p. 6983 - 6993.

Akkermansia muciniphila colonizes the mucus layer of the gastrointestinal tract, where the organism can be exposed to the oxygen that diffuses from epithelial cells. To understand how A. muciniphila is able to survive and grow at this oxic-anoxic interface, its oxygen tolerance and response and reduction capacities were studied. A. muciniphila was found to be oxygen tolerant. On top of this, under aerated conditions, A. muciniphila showed significant oxygen reduction capacities and its growth rate and yield were increased compared to those seen under strict anaerobic conditions. Transcriptome analysis revealed an initial oxygen stress response upon exposure to oxygen. Thereafter, genes related to respiration were expressed, including those coding for the cytochrome bd complex, which can function as a terminal oxidase. The functionality of A. muciniphila cytochrome bd genes was proven by successfully complementing cytochrome-deficient Escherichia coli strain ECOM4. We conclude that A. muciniphila can use oxygen when it is present at nanomolar concentrations.

Akkermansia species : phylogeny, physiology and comparative genomics
Ouwerkerk, J.P. - \ 2016
Wageningen University. Promotor(en): Willem de Vos, co-promotor(en): Clara Belzer. - Wageningen : Wageningen University - ISBN 9789462577411 - 178
akkermansia - akkermansia muciniphila - gastrointestinal microbiota - phylogeny - physiology - genomics - dna sequencing - nucleotide sequences - transcriptomes - antibiotic resistance - genome annotation - akkermansia - akkermansia muciniphila - microbiota van het spijsverteringskanaal - fylogenie - fysiologie - genomica - dna-sequencing - nucleotidenvolgordes - transcriptomen - antibioticaresistentie - genoomannotatie

The gastrointestinal tract is lined with a mucus layer, which is colonized by a distinct mucosal microbial population. The anaerobic gut bacterium Akkermansia muciniphila is a well-described member of the mucosal microbiota and has been shown to be a human gut symbiont. In the mucus layer this gut symbiont is likely exposed to the oxygen that diffuses from mucosal epithelial cells. We showed that A. muciniphila has an active detoxification system to cope with reactive oxygen species and can use oxygen for respiration at nanomolar oxygen concentrations, with cytochrome bd as terminal oxidase.

Until now, the type strain A. muciniphila MucT was the only cultured representative of this species. We isolated and characterized six new A. muciniphila strains from faecal samples of four different human subjects. These A. muciniphila strains showed minimal genomic and physiologic divergence while retaining their mucin degrading and utilisation capacities. Apart from the human gastrointestinal tract, we detected Akkermansia species in intestinal samples of numerous mammals. An additional ten new A. muciniphila strains were isolated from seven different mammalian species and showed high genomic and physiologic similarity to type strain A. muciniphila MucT. Apart from Akkermansia species, other Verrucomicrobia were identified within the gastrointestinal tract of non-human mammals. Furthermore, we obtained an Akkermansia isolate from the reticulated python, which had a similar mucin degrading capacity as the human strain A. muciniphila MucT but showed more efficient galactose utilization. On the basis of further phylogenetic, physiological, and genomic characterisations, strain PytT was found to represent a novel species within the genus Akkermansia, for which the name Akkermansia glycaniphilus sp. nov. is proposed.

Overall, A. muciniphila strains isolated from intestinal samples of human and other mammals show very limited genomic and physiologic divergence. This together with the widely-spread global presence of A. muciniphila and the dependence on mucin for optimal growth, points towards a conserved symbiosis. This conserved symbiosis might be indicative for the beneficial role of this organism in respect to the host metabolic health. This is in line with the observation that A. muciniphila has been negatively associated with obesity and its associated metabolic disorders.

In mice, treatment with viable A. muciniphila cells reversed high-fat diet-induced obesity. We described a scalable workflow for the preparation and preservation of high numbers of viable cells of A. muciniphila under strict anaerobic conditions for therapeutic interventions. Moreover, we developed various quality assessment and control procedures aimed to ensure the use of viable cells of A. muciniphila at any location in the world. These viable cells were used in a pilot study in humans in which no adverse events were observed. This is promising for future applications of A. muciniphila as a new therapeutic, leading towards the potential treatment of unhealthy states of the microbiota.

Natural foreshores as an alternative to traditional dike re-enforcements: a field pilot in the large shallow lake Markermeer, The Netherlands
Penning, W.E. ; Steetzel, H.J. ; Santen, R. van; Fiselier, J. ; Lange, H.J. de; Vuik, V. ; Ouwerkerk, S. ; Thiel de Vries, J.S.M. van - \ 2015
In: E-proceedings of the 36th IAHR World Congress. - 2015 : - 4 p.
nature development - flood control - dykes - riparian vegetation - coasts - hydrodynamics - natuurontwikkeling - hoogwaterbeheersing - dijken - oevervegetatie - kusten - hydrodynamica
Natural foreshores are shallow zones and beaches with a gradual slope and a (near-)natural vegetation that can be used
as an additional protection against flooding by reducing the wave attack on existing dikes, or can even completely
replace an existing dike system. In order to test the applicability of this concept a 500 m long pilot section of a sandy
foreshore was constructed along an already existing dike in the large shallow lake Markermeer, the Netherlands. The
pilot was equipped with permanent monitoring equipment for hydrodynamics and meteorological conditions and monthly
surveys of the morphology of the pilot section. These measurements will be carried out for the coming four years. This
paper presents the first results after the construction and the first winter season with the pilot in place.
OsJAR1 is required for JA-regulated floret opening and anther dehiscence in rice
Xiao, Y. ; Charnikhova, T. ; Mulder, P.P.J. ; Heijmans, J. ; Hoogenboom, A. ; Agalou, A. ; Michel, C. ; Morel, J.B. ; Dreni, L. ; Kater, M.M. ; Bouwmeester, H.J. ; Wang, B. ; Zhu, Z. ; Ouwerkerk, P.B.F. - \ 2014
Plant Molecular Biology 86 (2014)1-2. - ISSN 0167-4412 - p. 19 - 33.
jasmonic acid biosynthesis - male-sterile mutant - l-isoleucine - methyl jasmonate - gene encodes - arabidopsis - enzyme - proteins - tomato - (+)-7-iso-jasmonoyl-l-isoleucine
Jasmonates are important phytohormones regulating reproductive development. We used two recessive rice Tos17 alleles of OsJAR1, osjar1-2 and osjar1-3, to study the biological function of jasmonates in rice anthesis. The florets of both osjar1 alleles stayed open during anthesis because the lodicules, which control flower opening in rice, were not withering on time. Furthermore, dehiscence of the anthers filled with viable pollen, was impaired, resulting in lower fertility. In situ hybridization and promoter GUS transgenic analysis confirmed OsJAR1 expression in these floral tissues. Flower opening induced by exogenous applied methyl jasmonate was impaired in osjar1 plants and was restored in a complementation experiment with transgenics expressing a wild type copy of OsJAR1 controlled by a rice actin promoter. Biochemical analysis showed that OsJAR1 encoded an enzyme conjugating jasmonic acid (JA) to at least Ile, Leu, Met, Phe, Trp and Val and both osjar1 alleles had substantial reduction in content of JA-Ile, JA-Leu and JA-Val in florets. We conclude that OsJAR1 is a JA-amino acid synthetase that is required for optimal flower opening and closing and anther dehiscence in rice
Molecular regulation of drought tolerance in rice
Haider, I. - \ 2014
Wageningen University. Promotor(en): Harro Bouwmeester, co-promotor(en): Carolien Ruyter-Spira; P.B.F. Ouwerkerk. - Wageningen : Wageningen University - ISBN 9789461738431 - 183
oryza - oryza sativa - oryza glaberrima - plantenfysiologie - droogte - droogteresistentie - stress - moleculaire biologie - plantengroeiregulatoren - oryza - oryza sativa - oryza glaberrima - plant physiology - drought - drought resistance - stress - molecular biology - plant growth regulators

Abiotic stresses are the primary cause of crop failure worldwide, reducing average yields by more than 50%. Among the various forms of abiotic stress, drought is the most limiting factor for rice productivity. Drought affects about 20% of the total rice cultivation area in Asia. Understanding the various aspects of drought stress, the response and resistance mechanisms in relation to plant growth is therefore of fundamental importance to improve sustainable agriculture.

Drought tolerance is usually controlled by complex gene networks and engineering of a single gene is unlikely to improve this trait. However, altering the expression of Transcription Factors (TFs) may be a tool for improvement of drought tolerance since they have been shown to activate the expression of multiple genes in a coordinated manner and they are therefore attractive and promising targets for application in molecular breeding or genetic engineering. In addition, studies on TFs will improve our understanding of the physiological and molecular mechanisms of drought tolerance. The overall objective of the work presented in this thesis was to get more detailed insight in the molecular regulation of drought tolerance in rice, with a particular focus on the role of TFs of the homeobox class and two groups of plant hormones, abscisic acid and strigolactones.

In Chapter 2, I described the isolation and characterisation of the rice Oshox22 gene which is an homeobox gene of the HD-Zip I family. I showed that the expression of Oshox22 is strongly induced by salt stress, abscisic acid (ABA) and polyethylene glycol (PEG) treatment, and weakly by cold stress. Trans-activation assays in yeast and transient expression analyses in rice protoplasts demonstrated that Oshox22 is able to bind to the CAAT(G/C)ATTG element and acts as a transcriptional activator that requires both the HD and Zip domains. Rice plants homozygous for a T-DNA insertion in the promoter region of Oshox22 showedreduced Oshox22 expression and ABA content, decreased sensitivity to ABA, and enhanced tolerance to drought and salt stress in the seedling stage. In contrast, transgenic rice over-expressing Oshox22 showed increased sensitivity to ABA, increased ABA content, and decreased drought and salt tolerances. These results support the conclusion that Oshox22 acts as a negative regulator in stress response. Since reporter gene studies in yeast and rice cells suggested that Oshox22 acts as a transcriptional activator, its function as a negative regulator in stress responses might be explained via activation of other repressors.

As Oshox22 is highly expressed in developing panicles and grains, in Chapter 4 I investigated the role of Oshox22 in controlling grain length (GL) in rice. We found a stable quantitative trait locus (QTL) for GL on this position in four mapping populations. Sequence analysis of Oshox22 in rice cultivars Bala, Azucena and Nipponbare revealed an extra A base in the Azucena promoter, which is a long grain type rice. Using a PCR-based insertion/deletion (InDel) CAPS maker assay in rice populations and collections, I found an association between the A InDel in the Oshox22 promoter with GL. Furthermore, expression of Oshox22 under the control of a promoterwith the A InDelin Zhonghua 11 (which does not have the A InDel) resulted in a significant increase in GL in Zhongua 11. Scanning electron microscopy revealed that the enhanced GL was caused by an increased cell length in the inner epidermal cells of the lemma. In addition, the data show that there is a tendency for lower expression of Oshox22 when GL increases which would suggest that Oshox22 functions as a repressor of GL.These findings suggest that natural variation in the Oshox22 promoter can be exploited in breeding programmes to modify GL using molecular marker-assisted selection. However, the exact mechanism of regulation of GL by Oshox22 is still not clear. Since Oshox22 is a homeobox gene, it will exert its function via regulation of downstream target genes which we do not know yet. Therefore, more research is needed to elucidate the genetic and biochemical pathways to understand the molecular mechanisms underlying rice GL development and to determine if there are interactions with other known regulators of GL.

The strigolactones are a relatively new class of plant hormones and a possible role in drought tolerance is unknown. In Chapter 4 of this thesis, I reviewed the various roles that strigolactones (SLs) play both in the rhizosphere and as endogenous plant hormone. In addition, the current knowledge on the SL biosynthetic and downstream signalling pathways and the interactions of SLs with other plant hormones, such as ABA, is described.

It has been reported that there seems to be a functional link between ABA and SLs but the mechanism of that link remained unknown. In Chapter 5, I studied the intimate relationship between ABA and SL biosynthesis through the further characterisation of β-carotene isomerase D27 in rice. The results show that the ABA content was increased in SL-deficient and -insensitive dwarf (d) rice mutants, d10, d17 and d3 compared with wild type, while it was reduced in d27. In addition, this difference was significantly enhanced by exposure to drought. Interestingly, as a consequence of their enhanced ABA levels, d10, d17 and d3 plants displayed an increased tolerance to drought compared with wild-type plants, while the ABA deficient d27 plants were more drought sensitive. Transient over-expression of OsD27 in Nicotiana benthamianaenhanced both ABA and SL production. However, constitutive over-expression of OsD27 in rice plants showed no significant changes in ABA and SL levelsunder normal conditions. Still, OsD27 over-expression did result in higher SL levels, compared with wild-type plants, under phosphate starvation. This suggests that likewise, OsD27over-expression may only result in increased ABA levels during drought stress conditions. I concluded that the OsD27 gene is involved in SL as well as ABA biosynthesis, and that, depending on the environmental conditions, the expression of the more downstream SL and ABA specific biosynthetic genes determines which of the two and how much is being produced.

In Chapter 6, I discussed the main findings of this thesis and presented the future perspective of how the knowledge generated in this thesis can contribute to the improvement of drought tolerance and GL in rice.

O80 Akkermansia muciniphila communique avec l’épithélium intestinal pour contrôler le développement de l’obésité et du diabète de type 2
Everard, A. ; Belzer, C. ; Geurts, L. ; Ouwerkerk, J.P. ; Druart, C. ; Bindels, L.B. ; Guiot, Y. ; Derrien, M.M.N. ; Muccioli, G.G. ; Delzenne, N.M. ; Vos, W.M. de; Cani, P.D. - \ 2013
Diabetes & Metabolism 39 (2013)S1. - ISSN 1262-3636
Introduction Le microbiote intestinal est impliqué dans le développement de l’obésité, de l’insulino-résistance et du diabète de type 2. Nos travaux précédents ont mis en évidence qu’une bactérie découverte récemment et vivant dans le mucus intestinal, Akkermansia muciniphila, était diminuée (100 à 1 000 fois) dans des modèles nutritionnel ou génétique d’obésité et de diabète de type 2. Par contre sa présence dans le contenu caecal est normalisée lors d’un traitement à l’aide de prébiotiques. Cette modulation du microbiote intestinal est associée à une diminution de l’inflammation de bas grade et à une amélioration de la sensibilité à l’insuline et à la leptine. Cependant l’impact direct d’Akkermansia muciniphila sur le métabolisme n’a encore jamais été investigué. Matériels et méthodes Akkermansia muciniphila a été administrée quotidiennement par gavage oral chez des souris nourries avec un régime hyperlipidique pendant 4 semaines. Des marqueurs de l’homéostasie glucidique, du métabolisme lipidique et de la fonction barrière de l’intestin ont été investigués. Résultats Le traitement avec Akkermansia muciniphila améliore les marqueurs d’insulino-sensibilité et corrige l’hyperglycémie à jeun induite par le régime hyperlipidique. Ces effets bénéfiques sont notamment associés à une diminution de la néoglucogénèse hépatique (diminution de l’expression de l’ARNm de la glucose-6-phosphatase). L’administration d’Akkermansia muciniphila empêche la prise de masse grasse et le développement de l’inflammation du tissu adipeux sous régime hyperlipidique, sans affecter la quantité d’énergie ingérée. Akkermansia muciniphila restaure la fonction barrière de l’intestin (disparition de l’endotoxémie métabolique, restauration de la couche de mucus, modification de la production de peptides antimicrobiens). Conclusion Ces résultats mettent en évidence de nouveaux mécanismes de régulation du métabolisme par le microbiote intestinal (Akkermansia. muciniphila) et permettent également de mettre en avant l’intérêt du développement d’un traitement utilisant Akkermansia muciniphila pour la prévention ou le traitement de l’obésité et du diabète de type 2
Crosstalk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
Everard, A. ; Belzer, C. ; Geurts, L. ; Ouwerkerk, J.P. ; Druart, C. ; Bindels, L.B. ; Guiot, Y. ; Derrien, M.M.N. ; Muccioli, G.G. ; Delzenne, N.M. ; Vos, W.M. de; Cani, P.D. - \ 2013
Proceedings of the National Academy of Sciences of the United States of America 110 (2013)22. - ISSN 0027-8424 - p. 9066 - 9071.
gut microbiota - body-weight - inflammation - mice - endotoxemia - homeostasis - disease - system - bifidobacteria - metabolism
Obesity and type 2 diabetes are characterized by altered gut microbiota, inflammation, and gut barrier disruption. Microbial composition and the mechanisms of interaction with the host that affect gut barrier function during obesity and type 2 diabetes have not been elucidated. We recently isolated Akkermansia muciniphila, which is a mucin-degrading bacterium that resides in the mucus layer. The presence of this bacterium inversely correlates with body weight in rodents and humans. However, the precise physiological roles played by this bacterium during obesity and metabolic disorders are unknown. This study demonstrated that the abundance of A. muciniphila decreased in obese and type 2 diabetic mice. We also observed that prebiotic feeding normalized A. muciniphila abundance, which correlated with an improved metabolic profile. In addition, we demonstrated that A. muciniphila treatment reversed high-fat diet-induced metabolic disorders, including fat-mass gain, metabolic endotoxemia, adipose tissue inflammation, and insulin resistance. A. muciniphila administration increased the intestinal levels of endocannabinoids that control inflammation, the gut barrier, and gut peptide secretion. Finally, we demonstrated that all these effects required viable A. muciniphila because treatment with heat-killed cells did not improve the metabolic profile or the mucus layer thickness. In summary, this study provides substantial insight into the intricate mechanisms of bacterial (i.e., A. muciniphila) regulation of the cross-talk between the host and gut microbiota. These results also provide a rationale for the development of a treatment that uses this human mucus colonizer for the prevention or treatment of obesity and its associated metabolic disorders
Glycobiome: Bacteria and mucus at the epithelial interface
Ouwerkerk, J.P. ; Vos, W.M. de; Belzer, C. - \ 2013
Best Practice & Research: Clinical Gastroenterology 27 (2013)1. - ISSN 1521-6918 - p. 25 - 38.
inflammatory-bowel-disease - mucosa-associated microbiota - human gut microbiota - abo blood-group - intestinal microbiota - human colon - in-vivo - akkermansia-muciniphila - spatial-organization - bacteroides-thetaiotaomicron
The human gastrointestinal tract is colonised with a dense and diverse microbial community, that is an important player in human health and physiology. Close to the epithelial cells the mucosal microbiota is separated from the host with a thin lining of host derived glycans, including the cell surface glycocalyx and the extracellular secreted mucus. The mucosa-associated microbial composition differs from the luminal content and could be particularly important for nutrient exchange, communication with the host, development of the immune system, and resistance against invading pathogens. The mucosa-associated microbiota has adapted to the glycan rich environment by the production of mucus-degrading enzymes and mucus-binding extracellular proteins, and include mucus-degrading specialists such as Akkermansia muciniphila and Bacteroides thetaiotaomicron. This review is focussed on the host-microbe interactions within the glycan landscape at the epithelial interface and considers the spatial organisation and composition of the mucosa-associated microbiota in health and disease
Function of the HD-Zip I gene Oshox22 in ABA-mediated drought and salt tolerances in rice
Zhang, S. ; Kohlen, W. ; Jiang, L. ; Bouwmeester, H.J. ; Meijer, A.H. ; Schluepmann, H. ; Liu, C.M. ; Ouwerkerk, P.B.F. - \ 2012
Plant Molecular Biology 80 (2012)6. - ISSN 0167-4412 - p. 571 - 585.
plant craterostigma-plantagineum - acid signal-transduction - length cdna microarray - high-salinity stresses - abscisic-acid - transcription factor - homeobox gene - water-deficit - arabidopsis-thaliana - dna-binding
Oshox22 belongs to the homeodomain-leucine zipper (HD-Zip) family I of transcription factors, most of which have unknown functions. Here we show that the expression of Oshox22 is strongly induced by salt stress, abscisic acid (ABA), and polyethylene glycol treatment (PEG), and weakly by cold stress. Trans-activation assays in yeast and transient expression analyses in rice protoplasts demonstrated that Oshox22 is able to bind the CAAT(G/C)ATTG element and acts as a transcriptional activator that requires both the HD and Zip domains. Rice plants homozygous for a T-DNA insertion in the promoter region of Oshox22 showed reduced Oshox22 expression and ABA content, decreased sensitivity to ABA, and enhanced tolerance to drought and salt stresses at the seedling stage. In contrast, transgenic rice over-expressing Oshox22 showed increased sensitivity to ABA, increased ABA content, and decreased drought and salt tolerances. Based on these results, we conclude that Oshox22 affects ABA biosynthesis and regulates drought and salt responses through ABA-mediated signal transduction pathways.
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