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Score: 9.00 |
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| Title: Conformational changes in a plant ketol-acid reductoisomerase upon Mg ( 2+ ) and NADPH binding as revealed by two crystal structures .
| | Author: Leung EW Guddat LW | | Journal: J Mol Biol Citation: V : 389 P : 167-82 Year: 2009 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19362563 Accession (PMID): 19362563 | | Abstract: Ketol-acid reductoisomerase ( KARI ; EC 1 . 1 . 1 . 86 ) is an enzyme in the branched-chain amino acid biosynthesis pathway where it catalyzes the conversion of 2-acetolactate into ( 2R ) -2 , 3-dihydroxy-3-isovalerate or the conversion of 2-aceto-2-hydroxybutyrate into ( 2R , 3R ) -2 , 3-dihydroxy-3-methylvalerate .
KARI catalyzes two reactions-alkyl migration and reduction-and requires Mg ( 2+ ) and NADPH for activity .
To date , the only reported structures for a plant KARI are those of the spinach enzyme-Mn ( 2+ ) - ( phospho ) ADP ribose- ( 2R , 3R ) -2 , 3-dihydroxy-3-methylvalerate complex and the spinach KARI-Mg ( 2 ) ( + ) -NADPH-N-hydroxy-N-isopropyloxamate complex , where N-hydroxy-N-isopropyloxamate is a predicted transition-state analog .
These studies demonstrated that the enzyme consists of two domains , N-domain and C-domain , with the active site at the interface of these domains .
Here , we have determined the structures of the rice KARI-Mg ( 2+ ) and rice KARI-Mg ( 2 ) ( + ) -NADPH complexes to 1 . 55 A and 2 . 80 A resolutions , respectively .
In comparing the structures of all the complexes , several differences are observed .
Firstly , the N-domain is rotated up to 15 degrees relative to the C-domain , expanding the active site by up to 4 A Secondly , an alpha-helix in the C-domain that includes residues V510-T519 and forms part of the active site moves by approximately 3 . 9 A upon binding of NADPH .
Thirdly , the 15 C-terminal amino acid residues in the rice KARI-Mg ( 2+ ) complex are disordered .
In the rice KARI-Mg ( 2 ) ( + ) -NADPH complex and the spinach KARI structures , many of the 15 residues bind to NADPH and the N-domain and cover the active site .
Fourthly , the location of the metal ions within the active site can vary by up to 2 . 7 A The new structures allow us to propose that an induced-fit mechanism operates to ( i ) allow substrate to enter the active site , ( ii ) close over the active site during catalysis , and ( iii ) open the active site to facilitate product release .
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[ Sen. 3, subscore: 2.00 ]: To date , the only reported structures for a plant KARI are those of the spinach enzyme-Mn ( 2+ ) - ( phospho ) ADP ribose- ( 2R , 3R ) -2 , 3-dihydroxy-3-methylvalerate complex and the spinach KARI-Mg ( 2 ) ( + ) -NADPH-N-hydroxy-N-isopropyloxamate complex , where N-hydroxy-N-isopropyloxamate is a predicted transition-state analog .
[ Sen. 5, subscore: 2.00 ]: Here , we have determined the structures of the rice KARI-Mg ( 2+ ) and rice KARI-Mg ( 2 ) ( + ) -NADPH complexes to 1 . 55 A and 2 . 80 A resolutions , respectively .
[ Sen. 9, subscore: 2.00 ]: In the rice KARI-Mg ( 2 ) ( + ) -NADPH complex and the spinach KARI structures , many of the 15 residues bind to NADPH and the N-domain and cover the active site .
[ Sen. 1, subscore: 1.00 ]: Ketol-acid reductoisomerase ( KARI ; EC 1 . 1 . 1 . 86 ) is an enzyme in the branched-chain amino acid biosynthesis pathway where it catalyzes the conversion of 2-acetolactate into ( 2R ) -2 , 3-dihydroxy-3-isovalerate or the conversion of 2-aceto-2-hydroxybutyrate into ( 2R , 3R ) -2 , 3-dihydroxy-3-methylvalerate .
[ Sen. 2, subscore: 1.00 ]: KARI catalyzes two reactions-alkyl migration and reduction-and requires Mg ( 2+ ) and NADPH for activity .
[ Sen. 8, subscore: 1.00 ]: Thirdly , the 15 C-terminal amino acid residues in the rice KARI-Mg ( 2+ ) complex are disordered .
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Score: 7.00 |
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| Title: Karyotypic Variation within Clonal Lineages of the Rice Blast Fungus , Magnaporthe grisea .
| | Author: Talbot NJ Salch YP Ma M Hamer JE .
| | Journal: Citation: V : 59 ( 2 ) P : 585-593 Year: 1993 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16348876 Accession (PMID): 16348876 | | Abstract: We have analyzed the karyotype of the rice blast fungus , Magnaporthe grisea , by using pulsed-filed gel electrophoresis .
We tested whether the electrophoretic karyotype of an isolate was related to its pathotype , as determined by infection assays , or its genetic lineage , as determined by DNA fingerprinting .
Highly reproducible electrophoretic karyotypes were obtained for a collection of US and Chinese isolates representing a diverse collection of pathotypes and genetic lineages .
Chromosomes ranged in size from 3 to 10 Mb .
Although chromosome number was largely invariant , chromosome length polymorphisms were frequent .
Minichromosomes were also found , although their presence was not ubiquitous .
They ranged in number from 1 to 3 and in size from 470 kb to 2 . 2 Mb .
Karyotypes were sufficiently variable as to obscure the obvious relatedness of isolates on the basis of pathogenicity assays or genetic lineage analysis by DNA fingerprinting .
We documented that the electrophoretic karyotype of an isolate can change after prolonged serial transfer in culture and that this change did not alter the isolates pathotype .
The mechanisms bringing about karyotype variability involve deletions , translocations , and more complex rearrangements .
We conclude that karyotypic variability in the rice blast fungus is a reflection of the lack of sexuality in wild populations which leads to the maintenance of neutral genomic rearrangements in clones of the fungus .
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[ Sen. 1, subscore: 1.00 ]: We have analyzed the karyotype of the rice blast fungus , Magnaporthe grisea , by using pulsed-filed gel electrophoresis .
[ Sen. 2, subscore: 1.00 ]: We tested whether the electrophoretic karyotype of an isolate was related to its pathotype , as determined by infection assays , or its genetic lineage , as determined by DNA fingerprinting .
[ Sen. 3, subscore: 1.00 ]: Highly reproducible electrophoretic karyotypes were obtained for a collection of US and Chinese isolates representing a diverse collection of pathotypes and genetic lineages .
[ Sen. 8, subscore: 1.00 ]: Karyotypes were sufficiently variable as to obscure the obvious relatedness of isolates on the basis of pathogenicity assays or genetic lineage analysis by DNA fingerprinting .
[ Sen. 9, subscore: 1.00 ]: We documented that the electrophoretic karyotype of an isolate can change after prolonged serial transfer in culture and that this change did not alter the isolates pathotype .
[ Sen. 10, subscore: 1.00 ]: The mechanisms bringing about karyotype variability involve deletions , translocations , and more complex rearrangements .
[ Sen. 11, subscore: 1.00 ]: We conclude that karyotypic variability in the rice blast fungus is a reflection of the lack of sexuality in wild populations which leads to the maintenance of neutral genomic rearrangements in clones of the fungus .
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Score: 7.00 |
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| Title: Specialisation within the DWARF14 protein family confers distinct responses to karrikins and strigolactones in Arabidopsis .
| | Author: Waters MT Nelson DC Scaffidi A Flematti GR Sun YK Dixon KW Smith SM | | Journal: Development Citation: V : 139 P : 1285-95 Year: 2012 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub22357928 Accession (PMID): 22357928 | | Abstract: Karrikins are butenolides derived from burnt vegetation that stimulate seed germination and enhance seedling responses to light .
Strigolactones are endogenous butenolide hormones that regulate shoot and root architecture , and stimulate the branching of arbuscular mycorrhizal fungi .
Thus , karrikins and strigolactones are structurally similar but physiologically distinct plant growth regulators .
In Arabidopsis thaliana , responses to both classes of butenolides require the F-box protein MAX2 , but it remains unclear how discrete responses to karrikins and strigolactones are achieved .
In rice , the DWARF14 protein is required for strigolactone-dependent inhibition of shoot branching .
Here , we show that the Arabidopsis DWARF14 orthologue , AtD14 , is also necessary for normal strigolactone responses in seedlings and adult plants .
However , the AtD14 paralogue KARRIKIN INSENSITIVE 2 ( KAI2 ) is specifically required for responses to karrikins , and not to strigolactones .
Phylogenetic analysis indicates that KAI2 is ancestral and that AtD14 functional specialisation has evolved subsequently .
Atd14 and kai2 mutants exhibit distinct subsets of max2 phenotypes , and expression patterns of AtD14 and KAI2 are consistent with the capacity to respond to either strigolactones or karrikins at different stages of plant development .
We propose that AtD14 and KAI2 define a class of proteins that permit the separate regulation of karrikin and strigolactone signalling by MAX2 .
Our results support the existence of an endogenous , butenolide-based signalling mechanism that is distinct from the strigolactone pathway , providing a molecular basis for the adaptive response of plants to smoke .
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[ Sen. 7, subscore: 2.00 ]: However , the AtD14 paralogue KARRIKIN INSENSITIVE 2 ( KAI2 ) is specifically required for responses to karrikins , and not to strigolactones .
[ Sen. 1, subscore: 1.00 ]: Karrikins are butenolides derived from burnt vegetation that stimulate seed germination and enhance seedling responses to light .
[ Sen. 3, subscore: 1.00 ]: Thus , karrikins and strigolactones are structurally similar but physiologically distinct plant growth regulators .
[ Sen. 4, subscore: 1.00 ]: In Arabidopsis thaliana , responses to both classes of butenolides require the F-box protein MAX2 , but it remains unclear how discrete responses to karrikins and strigolactones are achieved .
[ Sen. 9, subscore: 1.00 ]: Atd14 and kai2 mutants exhibit distinct subsets of max2 phenotypes , and expression patterns of AtD14 and KAI2 are consistent with the capacity to respond to either strigolactones or karrikins at different stages of plant development .
[ Sen. 10, subscore: 1.00 ]: We propose that AtD14 and KAI2 define a class of proteins that permit the separate regulation of karrikin and strigolactone signalling by MAX2 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 5.00 |
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| Title: Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma .
| | Author: Komatsu M Shimamoto K Kyozuka J | | Journal: Plant Cell Citation: V : 15 ( 8 ) P : 1934-44 Year: 2003 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12897263 Accession (PMID): 12897263 | | Abstract: Here , we report the identification of Karma , a LINE-type retrotransposon of plants for which continuous retrotransposition was observed in consecutive generations .
The transcription of Karma is activated in cultured cells of rice upon DNA hypomethylation .
However , transcription is insufficient for retrotransposition , because no increase in the copy number was observed in cultured cells or in the first generation of plants regenerated from them .
Despite that finding , copy number increase was detected in the next generation of regenerated plants as well as in later generations , suggesting that the post-transcriptional regulation of Karma retrotransposition is development dependent .
Our results indicate that two different mechanisms , one transcriptional and the other developmental , control the mobilization of KARMA : In addition , unlike other known active plant retrotransposons , Karma is not subject to de novo methylation , and retrotransposition persists through several generations . | Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: Our results indicate that two different mechanisms , one transcriptional and the other developmental , control the mobilization of KARMA : In addition , unlike other known active plant retrotransposons , Karma is not subject to de novo methylation , and retrotransposition persists through several generations .
[ Sen. 1, subscore: 1.00 ]: Here , we report the identification of Karma , a LINE-type retrotransposon of plants for which continuous retrotransposition was observed in consecutive generations .
[ Sen. 2, subscore: 1.00 ]: The transcription of Karma is activated in cultured cells of rice upon DNA hypomethylation .
[ Sen. 4, subscore: 1.00 ]: Despite that finding , copy number increase was detected in the next generation of regenerated plants as well as in later generations , suggesting that the post-transcriptional regulation of Karma retrotransposition is development dependent .
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Score: 5.00 |
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| Title: Environmental abundance of Anopheles ( Diptera : Culicidae ) larval habitats on land cover change sites in Karima Village , Mwea Rice Scheme , Kenya .
| | Author: Jacob BG Muturi E Halbig P Mwangangi J Wanjogu RK Mpanga E Funes J Shililu J Githure J Regens JL Novak RJ .
| | Journal: Am .
J Trop . Med . Hyg . Citation: V : 76 ( 1 ) P : 73-80 Year: 2007 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub17255233 Accession (PMID): 17255233 | | Abstract: A study was carried out at Karima Village in the Mwea Rice Irrigation Scheme in Kenya to assess the impact of rice husbandry and associated land cover change for mosquito larval abundance .
A multi-temporal , land use land cover ( LULC ) classification dataset incorporating distributions of Anopheles arabiensis aquatic larval habitats was produced in ERDAS Imagine version 8 . 7 using combined images from IKONOS at 4m spatial resolution from 2005 and Landsat Thematic Mapper ( TM ) trade mark classification data at 30-meters spatial resolution from 1988 for Karima .
Of 207 larval habitats sampled , most were either canals ( 53 . 4% ) or paddies ( 45 . 9% ) , and only one habitat was classified as a seep ( 0 . 5% ) .
The proportion of habitats that were poorly drained was 55 . 1% compared with 44 . 9% for the habitats that were well drained .
An LULC base map was generated .
A grid incorporating each rice paddy was overlaid over the LULC maps stratifying each cell based on levels of irrigation .
Paddies/grid cells were classified as 1 ) well irrigated and 2 ) poorly irrigated .
Early stages of rice growth showed peak larval production during the early part of the cropping cycle ( rainy season ) .
Total LULC change for Karima over 16 years was 59 . 8% .
Of those areas in which change was detected , the LULC change for Karima was 4 . 30% for rice field to built environment , 8 . 74% for fallow to built environment , 7 . 19% for rice field to fallow , 19 . 03% built to fallow , 5 . 52% for fallow to rice field , and 8 . 35% for built environment to rice field .
Of 207 aquatic habitats in Karima , 54 . 1 ( n = 112 ) were located in LULC change sites and 45 . 9 ( n = 95 ) were located in LULC non-change sites .
Rice crop LULC maps derived from IKONOS and TM data in geographic information systems can be used to investigate the relationship between rice cultivation practices and higher anopheline larval habitat distribution .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: A study was carried out at Karima Village in the Mwea Rice Irrigation Scheme in Kenya to assess the impact of rice husbandry and associated land cover change for mosquito larval abundance .
[ Sen. 2, subscore: 1.00 ]: A multi-temporal , land use land cover ( LULC ) classification dataset incorporating distributions of Anopheles arabiensis aquatic larval habitats was produced in ERDAS Imagine version 8 . 7 using combined images from IKONOS at 4m spatial resolution from 2005 and Landsat Thematic Mapper ( TM ) trade mark classification data at 30-meters spatial resolution from 1988 for Karima .
[ Sen. 9, subscore: 1.00 ]: Total LULC change for Karima over 16 years was 59 . 8% .
[ Sen. 10, subscore: 1.00 ]: Of those areas in which change was detected , the LULC change for Karima was 4 . 30% for rice field to built environment , 8 . 74% for fallow to built environment , 7 . 19% for rice field to fallow , 19 . 03% built to fallow , 5 . 52% for fallow to rice field , and 8 . 35% for built environment to rice field .
[ Sen. 11, subscore: 1.00 ]: Of 207 aquatic habitats in Karima , 54 . 1 ( n = 112 ) were located in LULC change sites and 45 . 9 ( n = 95 ) were located in LULC non-change sites .
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