Comparisons within the Rice GA 2-Oxidase Gene Family Revealed Three Dominant Paralogs and a Functional Attenuated Gene that Led to the Identification of Four Amino Acid Variants Associated with GA Deactivation Capability

Abstract Background GA 2-oxidases (GA2oxs) are involved in regulating GA homeostasis in plants by inactivating bioactive GAs through 2β-hydroxylation. Rice GA2oxs are encoded by a family of 10 genes; some of them have been characterized, but no comprehensive comparisons for all these genes have been conducted. Results Rice plants with nine functional GA2oxs were demonstrated in the present study, and these genes not only were differentially expressed but also revealed various capabilities for GA deactivation based on their height-reducing effects in transgenic plants. Compared to that of wild-type plants, the relative plant height (RPH) of transgenic plants was scored to estimate their reducing effects, and 8.3% to 59.5% RPH was observed. Phylogenetic analysis of class I GA2ox genes revealed two functionally distinct clades in the Poaceae. The OsGA2ox3, 4, and 8 genes belonging to clade A showed the most severe effect (8.3% to 8.7% RPH) on plant height reduction, whereas the OsGA2ox7 gene belonging to clade B showed the least severe effect (59.5% RPH). The clade A OsGA2ox3 gene contained two conserved C186/C194 amino acids that were crucial for enzymatic activity. In the present study, these amino acids were replaced with OsGA2ox7-conserved arginine (C186R) and proline (C194P), respectively, or simultaneously (C186R/C194P) to demonstrate their importance in planta. Another two amino acids, Q220 and Y274, conserved in OsGA2ox3 were substituted with glutamic acid (E) and phenylalanine (F), respectively, or simultaneously to show their significance in planta. In addition, through sequence divergence, RNA expression profile and GA deactivation capability analyses, we proposed that OsGA2ox1, OsGA2ox3 and OsGA2ox6 function as the predominant paralogs in each of their respective classes. Conclusions This study demonstrates rice has nine functional GA2oxs and the class I GA2ox genes are divided into two functionally distinct clades. Among them, the OsGA2ox7 of clade B is a functional attenuated gene and the OsGA2ox1, OsGA2ox3 and OsGA2ox6 are the three predominant paralogs in the family.

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Utilizing MIKC-type MADS-box protein SOC1 for yield potential enhancement in maize

Plant Cell Reports ◽

10.1007/s00299-021-02722-4 ◽

2021 ◽

Author(s):

Guo-qing Song ◽

Xue Han ◽

John T. Ryner ◽

Addie Thompson ◽

Kan Wang

Keyword(s):

Transgenic Plants ◽

Plant Height ◽

No Reduction ◽

Planting Density ◽

Yield Potential ◽

Grain Production ◽

Mads Box ◽

Young Leaves ◽

Mads Box Gene ◽

Transcriptome Comparison

Abstract Key message Overexpression of Zea mays SOC gene promotes flowering, reduces plant height, and leads to no reduction in grain production per plant, suggesting enhanced yield potential, at least, through increasing planting density. Abstract MIKC-type MADS-box gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) is an integrator conserved in the plant flowering pathway. In this study, the maize SOC1 (ZmSOC1) gene was cloned and overexpressed in transgenic maize Hi-II genotype. The T0 plants were backcrossed with nontransgenic inbred B73 to produce first generation backcross (BC1) seeds. Phenotyping of both transgenic and null segregant (NT) BC1 plants was conducted in three independent experiments. The BC1 transgenic plants showed new attributes such as increased vegetative growth, accelerated flowering time, reduced overall plant height, and increased grain weight. Second generation backcross (BC2) plants were evaluated in the field using two planting densities. Compared to BC2 NT plants, BC2 transgenic plants, were 12–18% shorter, flowered 5 days earlier, and showed no reduction in grain production per plant and an increase in fat, starch, and simple sugars in the grain. Transcriptome comparison in young leaves of 56-day-old BC1 plants revealed that the overexpressed ZmSOC1 resulted in 107 differentially expressed genes. The upregulated transcription factor DNA BINDING WITH ONE FINGER 5.4 (DOF5.4) was among the genes responsible for the reduced plant height. Modulating expression of SOC1 opens a new and effective approach to promote flowering and reduce plant height, which may have potential to enhance crop yield and improve grain quality.

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MdKNOX15, a class I knotted-like transcription factor of apple, controls flowering and plant height by regulating GA levels through promoting the MdGA2ox7 transcription

Environmental and Experimental Botany ◽

10.1016/j.envexpbot.2021.104411 ◽

2021 ◽

Vol 185 ◽

pp. 104411

Author(s):

Peng Jia ◽

Libo Xing ◽

Chenguang Zhang ◽

Hao Chen ◽

Youmei Li ◽

...

Keyword(s):

Transcription Factor ◽

Plant Height ◽

Class I

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H-2M3a violates the paradigm for major histocompatibility complex class I peptide binding.

Journal of Experimental Medicine ◽

10.1084/jem.181.5.1817 ◽

1995 ◽

Vol 181 (5) ◽

pp. 1817-1825 ◽

Cited By ~ 22

Author(s):

J M Vyas ◽

J R Rodgers ◽

R R Rich

Keyword(s):

Amino Acids ◽

Mhc Class I ◽

Temperature Shift ◽

Class I ◽

Major Histocompatibility ◽

Histocompatibility Complex ◽

Compensatory Adaptation ◽

Chemotactic Peptides ◽

The Stability ◽

Formyl Peptides

The major histocompatibility (MHC) class I-b molecule H-2M3a binds and presents N-formylated peptides to cytotoxic T lymphocytes. This requirement potentially places severe constraints on the number of peptides that M3a can present to the immune system. Consistent with this idea, the M3a-Ld MHC class I chimera is expressed at very low levels on the cell surface, but can be induced significantly by the addition of specific peptides at 27 degrees C. Using this assay, we show that M3a binds many very short N-formyl peptides, including N-formyl chemotactic peptides and canonical octapeptides. This observation is in sharp contrast to the paradigmatic size range of peptides of 8-10 amino acids binding to most class I-a molecules and the class I-b molecule Qa-2. Stabilization by fMLF-benzyl amide could be detected at peptide concentrations as low as 100 nM. While N-formyl peptides as short as two amino acids in length stabilized expression of M3a-Ld, increasing the length of these peptides added to the stability of peptide-MHC complexes as determined by 27-37 degrees C temperature shift experiments. We propose that relaxation of the length rule may represent a compensatory adaptation to maximize the number of peptides that can be presented by H-2M3a.

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Legume seed flavonoids and nitrogenous metabolites as signals and protectants in early seedling development

Functional Plant Biology ◽

10.1071/fp03042 ◽

2003 ◽

Vol 30 (7) ◽

pp. 729 ◽

Cited By ~ 55

Author(s):

Patrick A. Ndakidemi ◽

Felix D. Dakora

Keyword(s):

Amino Acids ◽

Crop Yields ◽

Insect Pests ◽

Arbuscular Mycorrhizal ◽

Am Fungi ◽

Effective Control ◽

Plant Seeds ◽

Plant Pest ◽

The Family ◽

Early Seedling

Flavonoids and nitrogenous metabolites such as alkaloids, terpenoids, peptides and amino acids are major components of plant seeds. Conjugated forms of these compounds are soluble in water, and therefore, are easily released as chemical signals following imbibition. Once in the soil, these metabolites are first in line to serve as eco-sensing signals for suitable rhizobia and arbuscular mycorrhizal (AM) fungal partners required for the establishment of symbiotic mutualisms. They may also serve as defence molecules against pathogens and insect pests, as well as playing a role in the control of parasitic members of the family Scrophulariaceae, especially Striga, a major plant pest of cereal crops in Africa. Seed metabolites such as flavonoids, alkaloids, terpenoids, peptides and amino acids define seedling growth and, ultimately, crop yields. Thus, an improvement in our understanding of seed chemistry would permit manipulation of these molecules for effective control of pathogens, insect pests, Striga and destructive weeds, as well as for enhanced acquisition of N and P via symbioses with soil rhizobia and AM fungi.

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The Complete Nucleotide Sequence and Biotype Variability of Papaya leaf distortion mosaic virus

Phytopathology ◽

10.1094/phyto-95-0128 ◽

2005 ◽

Vol 95 (2) ◽

pp. 128-135 ◽

Cited By ~ 20

Author(s):

Tetsuo Maoka ◽

Tatsuji Hataya

Keyword(s):

Amino Acids ◽

Nucleotide Sequence ◽

Mosaic Virus ◽

Complete Nucleotide Sequence ◽

Distinct Species ◽

Cleavage Sites ◽

Reading Frame ◽

The Family ◽

Evolutionary Event ◽

Leaf Distortion

The complete nucleotide sequence of the genome of Papaya leaf distortion mosaic virus (PLDMV) was determined. The viral RNA genome of strain LDM (leaf distortion mosaic) comprised 10,153 nucleotides, excluding the poly(A) tail, and contained one long open reading frame encoding a polyprotein of 3,269 amino acids (molecular weight 373,347). The polyprotein contained nine putative proteolytic cleavage sites and some motifs conserved in other potyviral polyproteins with 44 to 50% identities, indicating that PLDMV is a distinct species in the genus Potyvirus. Like the W biotype of Papaya ringspot virus (PRSV), the non-papaya-infecting biotype of PLDMV (PLDMV-C) was found in plants of the family Cucurbitaceae. The coat protein (CP) sequence of PLDMV-C in naturally infected-Trichosanthes bracteata was compared with those of three strains of the P biotype (PLDMV-P), LDM and two additional strains M (mosaic) and YM (yellow mosaic), which are biologically different from each other. The CP sequences of three strains of PLDMV-P share high identities of 95 to 97%, while they share lower identities of 88 to 89% with that of PLDMV-C. Significant changes in hydrophobicity and a deletion of two amino acids at the N-terminal region of the CP of PLDMV-C were observed. The finding of two biotypes of PLDMV implies the possibility that the papaya-infecting biotype evolved from the cucurbitaceae-infecting potyvirus, as has been previously suggested for PRSV. In addition, a similar evolutionary event acquiring infectivity to papaya may arise frequently in viruses in the family Cucurbitaceae.

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Identification of regulatory genes to improve nitrogen use efficiency

Canadian Journal of Plant Science ◽

10.4141/cjps2013-154 ◽

2014 ◽

Vol 94 (6) ◽

pp. 1009-1012 ◽

Cited By ~ 2

Author(s):

David R. Guevara ◽

Yong-Mei Bi ◽

Steven J. Rothstein

Keyword(s):

Amino Acids ◽

Transgenic Plants ◽

Nitrogen Use Efficiency ◽

Complex Traits ◽

Regulatory Genes ◽

Yield Potential ◽

Environmental Damage ◽

Nitrogen Use ◽

Rice Plants ◽

Use Efficiency

Guevara, D. R., Bi, Y.-M. and Rothstein, S. J. 2014. Identification of regulatory genes to improve nitrogen use efficiency. Can. J. Plant Sci. 94: 1009–1012. Crop production on soils containing sub-optimal levels of nitrogen (N) severely compromises yield potential. The development of crop varieties displaying high N use efficiency (NUE) is necessary in order to optimize N fertilizer use, and reduce the environmental damage caused by the current excessive application of N in agricultural areas. Genome-wide microarray analysis of rice plants grown under N-limiting environments was performed to identify NUE candidate genes. An early nodulin gene, OsENOD93-1, was strongly up-regulated during plant growth under low N. A constitutive Ubiquitin promoter was used to drive the expression of the OsENOD93-1 gene in transgenic plants to determine the importance of OsENOD93-1 for rice NUE. Transgenic rice plants over-expressing the OsENOD93-1 gene achieved ∼23% and 16% more yield and biomass, respectively, compared with wild-type plants when grown under N-limitation conditions. OsENOD93-1-OX transgenic plants accumulated a higher amount of total amino acids in the roots and xylem sap under N stress, suggesting that OsENOD93-1 plays a role in the transportation of amino acids. Taken together, we demonstrate that an effective way to identify NUE gene candidates involves both transcriptional profiling coupled with a transgenic validation approach to improve complex traits such as NUE in important crops.

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Savitreea pentosicarens gen. nov., sp. nov., a yeast species in the family Saccharomycetaceae isolated from a grease trap

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004457 ◽

2020 ◽

Vol 70 (11) ◽

pp. 5665-5670

Author(s):

Varunya Sakpuntoon ◽

Jirameth Angchuan ◽

Chanita Boonmak ◽

Pannida Khunnamwong ◽

Noémie Jacques ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Yeast Species ◽

Sequence Divergence ◽

Its Region ◽

Rrna Gene ◽

Nucleotide Substitutions ◽

D2 Domain ◽

The Family ◽

Lsu Rrna Gene ◽

Lsu Rrna

Two strains (DMKU-GTCP10-8 and CLIB 1740) representing a novel anamorphic yeast species were isolated from a grease sample collected from a grease trap in Thailand and from an unidentified fungus collected in French Guiana, respectively. On the basis of phylogenetic analysis based on the combined D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, Lachancea fermentati CBS 707T was the closely related species with 12.8 % sequence divergence (70 nucleotide substitutions and three gaps in 571 nucleotides) and 28.1 % sequence divergence (93 nucleotide substitutions and 90 gaps in 651 nucleotides) in the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. Phylogenetic analysis based on the concatenated sequences of the five genes including the small subunit rRNA gene, the D1/D2 domain of the LSU rRNA gene, the ITS region, translation elongation factor-1 alpha (TEF1) and RNA polymerase II subunit 2 (RPB2) genes confirmed that the two strains (DMKU-GTCP10-8 and CLIB 1740) were well-separated from other described yeast genera in Saccharomycetaceae. Hence, Savitreea pentosicarens gen. nov., sp. nov. is proposed to accommodate these two strains as members of the family Saccharomycetaceae. The holotype is S. pentosicarens DMKU-GTCP10-8T (ex-type strain TBRC 12159=PYCC 8490; MycoBank number 835044).

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Optimization of Agrobacterium-mediated transformation conditions of prospective genotypes of winter bread wheat by in planta method

Faktori eksperimental'noi evolucii organizmiv ◽

10.7124/feeo.v28.1377 ◽

2021 ◽

Vol 28 ◽

pp. 66-71

Author(s):

O. V. Dubrovna ◽

L. V. Slivka

Keyword(s):

Transgenic Plants ◽

Bread Wheat ◽

Optical Density ◽

Dna Transfer ◽

Plant Genome ◽

In Planta ◽

Agrobacterium Mediated Transformation ◽

The Third ◽

Winter Bread Wheat ◽

Inoculation Medium

Aim. Optimization of conditions for genetic transformation of new promising genotypes of winter bread wheat (T. aestivum L.) by in planta method. Methods. Agrobacterium-mediated transformation by in planta method using the strain AGL0 and vector construct pBi2E. Results. The influence of air temperature, optical density of cells of agrobacterial suspension, inoculation day and composition of inoculation medium on the frequency of obtaining transgenic plants of new winter wheat genotypes was studied. The dependence of the frequency obtaining of transgenic plants from environmental conditions, in particular temperature, has been established. It was found that the temperature regime of 20-22°C provided the largest number (4.8%) of wheat transformants, and when the temperature is reduced to 16-18°C there is a decrease in the efficiency of T-DNA transfer into the plant genome and the lowest frequency of transformation (0.7%). Conclusions. The largest number of transformants was obtained using a inoculation medium without sucrose, the optical density of cells of the agrobacterial suspension of 0.6 op.od. and inoculation on the third day after castration of ears. Keywords: T. aestivum, Agrobacterium-mediated transformation in planta, optimization of conditions.

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Arac/XylS family of transcriptional regulators

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.61.4.393-410.1997 ◽

1997 ◽

Vol 61 (4) ◽

pp. 393-410

Author(s):

M T Gallegos ◽

R Schleif ◽

A Bairoch ◽

K Hofmann ◽

J L Ramos

Keyword(s):

Amino Acids ◽

Dna Sequences ◽

Carbon Metabolism ◽

Binding Sites ◽

Alpha Helix ◽

Transcriptional Regulators ◽

Biochemical Data ◽

Dimerization Domain ◽

Multiple Alignments ◽

The Family

The ArC/XylS family of prokaryotic positive transcriptional regulators includes more than 100 proteins and polypeptides derived from open reading frames translated from DNA sequences. Members of this family are widely distributed and have been found in the gamma subgroup of the proteobacteria, low- and high-G + C-content gram-positive bacteria, and cyanobacteria. These proteins are defined by a profile that can be accessed from PROSITE PS01124. Members of the family are about 300 amino acids long and have three main regulatory functions in common: carbon metabolism, stress response, and pathogenesis. Multiple alignments of the proteins of the family define a conserved stretch of 99 amino acids usually located at the C-terminal region of the regulator and connected to a nonconserved region via a linker. The conserved stretch contains all the elements required to bind DNA target sequences and to activate transcription from cognate promoters. Secondary analysis of the conserved region suggests that it contains two potential alpha-helix-turn-alpha-helix DNA binding motifs. The first, and better-fitting motif is supported by biochemical data, whereas existing biochemical data neither support nor refute the proposal that the second region possesses this structure. The phylogenetic relationship suggests that members of the family have recruited the nonconserved domain(s) into a series of existing domains involved in DNA recognition and transcription stimulation and that this recruited domain governs the role that the regulator carries out. For some regulators, it has been demonstrated that the nonconserved region contains the dimerization domain. For the regulators involved in carbon metabolism, the effector binding determinants are also in this region. Most regulators belonging to the AraC/XylS family recognize multiple binding sites in the regulated promoters. One of the motifs usually overlaps or is adjacent to the -35 region of the cognate promoters. Footprinting assays have suggested that these regulators protect a stretch of up to 20 bp in the target promoters, and multiple alignments of binding sites for a number of regulators have shown that the proteins recognize short motifs within the protected region.

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