Comparative whole-genome and proteomics analyses of the next seed bank and the original master seed bank of MucoRice-CTB 51A line, a rice-based oral cholera vaccine

Abstract Background We have previously developed a rice-based oral vaccine against cholera diarrhea, MucoRice-CTB. Using Agrobacterium-mediated co-transformation, we produced the selection marker–free MucoRice-CTB line 51A, which has three copies of the cholera toxin B subunit (CTB) gene and two copies of an RNAi cassette inserted into the rice genome. We determined the sequence and location of the transgenes on rice chromosomes 3 and 12. The expression of alpha-amylase/trypsin inhibitor, a major allergen protein in rice, is lower in this line than in wild-type rice. Line 51A was self-pollinated for five generations to fix the transgenes, and the seeds of the sixth generation produced by T5 plants were defined as the master seed bank (MSB). T6 plants were grown from part of the MSB seeds and were self-pollinated to produce T7 seeds (next seed bank; NSB). NSB was examined and its whole genome and proteome were compared with those of MSB. Results We re-sequenced the transgenes of NSB and MSB and confirmed the positions of the three CTB genes inserted into chromosomes 3 and 12. The DNA sequences of the transgenes were identical between NSB and MSB. Using whole-genome sequencing, we compared the genome sequences of three NSB with three MSB samples, and evaluated the effects of SNPs and genomic structural variants by clustering. No functionally important mutations (SNPs, translocations, deletions, or inversions of genic regions on chromosomes) between NSB and MSB samples were detected. Analysis of salt-soluble proteins from NSB and MSB samples by shot-gun MS/MS detected no considerable differences in protein abundance. No difference in the expression pattern of storage proteins and CTB in mature seeds of NSB and MSB was detected by immuno-fluorescence microscopy. Conclusions All analyses revealed no considerable differences between NSB and MSB samples. Therefore, NSB can be used to replace MSB in the near future.

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RNAi-mediated suppression of endogenous storage proteins leads to a change in localization of overexpressed cholera toxin B-subunit and the allergen protein RAG2 in rice seeds

Plant Cell Reports ◽

10.1007/s00299-013-1513-3 ◽

2013 ◽

Vol 33 (1) ◽

pp. 75-87 ◽

Cited By ~ 16

Author(s):

Shiho Kurokawa ◽

Masaharu Kuroda ◽

Mio Mejima ◽

Rika Nakamura ◽

Yuko Takahashi ◽

...

Keyword(s):

Cholera Toxin ◽

Storage Proteins ◽

Cholera Toxin B Subunit ◽

Toxin B ◽

Cholera Toxin B ◽

B Subunit ◽

Allergen Protein ◽

Rice Seeds

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Comparative whole-genome analyses of selection marker–free rice-based cholera toxin B-subunit vaccine lines and wild-type lines

BMC Genomics ◽

10.1186/s12864-015-1285-y ◽

2015 ◽

Vol 16 (1) ◽

pp. 48 ◽

Cited By ~ 11

Author(s):

Koji Kashima ◽

Mio Mejima ◽

Shiho Kurokawa ◽

Masaharu Kuroda ◽

Hiroshi Kiyono ◽

...

Keyword(s):

Subunit Vaccine ◽

Selection Marker ◽

Cholera Toxin B Subunit ◽

Whole Genome ◽

Wild Type ◽

Toxin B ◽

Cholera Toxin B ◽

B Subunit ◽

Marker Free ◽

Genome Analyses

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Clusters of interspersed repeated DNA sequences in the rice genome (Oryza)

Genome ◽

10.1139/g93-124 ◽

1993 ◽

Vol 36 (5) ◽

pp. 944-953 ◽

Cited By ~ 6

Author(s):

Xinping Zhao ◽

Gary Kochert

Keyword(s):

Dna Sequences ◽

Blot Hybridization ◽

Rice Genome ◽

Repeated Sequence ◽

Repeated Sequences ◽

Repeated Dna ◽

Rice Varieties ◽

Slot Blot Hybridization ◽

Repeated Dna Sequence ◽

Genus Oryza

We have characterized a repeated DNA sequence (RTL 122) from rice (Oryza sauva L.) with respect to its organization in the rice genome and its distribution among rice and other plants. The results indicate that the RTL 122 sequence is interspersed in the rice genome and limited to the genus Oryza. It is highly polymorphic and can be used to fingerprint rice varieties. A structure was observed in which several repeated sequences were clustered in DNA regions of 15–20 kb. We characterized three bacteriophage lambda clones that contained the RTL 122 sequence. Southern analysis using probes derived from restriction fragments of the three lambda clones indicated that all fragments except one are interspersed repeated sequences and belong to different repeated sequence families. Subsequent slot blot hybridization showed that most of them are only present within the genus Oryza. Some of the Oryza-specific, physically linked sequences show the same phylogenetic distribution, which suggests that these sequences might have evolved in a coordinate fashion. On the other hand, some of the repeated sequences have a different distribution even though they are physically adjacent in the genome. We speculate that such blocks of interspersed repeated sequences may serve as hotspots for rapid changes in the rice genome.Key words: rice, Oryza, repeated sequences, DNA fingerprinting, coordinated evolution.

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Whole-Genome Sequence of a Pantoea sp. Strain Isolated from an Olive (Olea europaea L.) Knot

Microbiology Resource Announcements ◽

10.1128/mra.00978-19 ◽

2019 ◽

Vol 8 (42) ◽

Cited By ~ 2

Author(s):

Gabriela Vuletin Selak ◽

Marina Raboteg ◽

Audrey Dubost ◽

Danis Abrouk ◽

Katja Žanić ◽

...

Keyword(s):

Genome Size ◽

Genome Sequence ◽

Dna Sequences ◽

Sequence Data ◽

Whole Genome Sequence ◽

Trna Genes ◽

Whole Genome ◽

Ribosomal Operon ◽

Adriatic Coast ◽

Olive Trees

Here, we present the total genome sequence of Pantoea sp. strain paga, a plant-associated bacterium isolated from knots present on olive trees grown on the Adriatic Coast. The genome size of Pantoea sp. paga is 5.08 Mb, with a G+C content of 54%. The genome contains 4,776 predicted coding DNA sequences (CDSs), including 70 tRNA genes and 1 ribosomal operon. Obtained genome sequence data will provide insight on the physiology, ecology, and evolution of Pantoea spp.

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Cloning and characterization of repetitive DNA sequences from genomes of Oryza minuta and Oryza australiensis

Genome ◽

10.1139/g91-123 ◽

1991 ◽

Vol 34 (5) ◽

pp. 790-798 ◽

Cited By ~ 10

Author(s):

H. Aswidinnoor ◽

R. J. Nelson ◽

J. F. Dallas ◽

C. L. McIntyre ◽

H. Leung ◽

...

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Genomic Dna ◽

Repetitive Sequences ◽

Rice Genome ◽

Repetitive Dna Sequences ◽

Cross Hybridization ◽

Oryza Minuta ◽

Wild Rice Species ◽

Oryza Australiensis

The value of genome-specific repetitive DNA sequences for use as molecular markers in studying genome differentiation was investigated. Five repetitive DNA sequences from wild species of rice were cloned. Four of the clones, pOm1, pOm4, pOmA536, and pOmPB10, were isolated from Oryza minuta accession 101141 (BBCC genomes), and one clone, pOa237, was isolated from Oryza australiensis accession 100882 (EE genome). Southern blot hybridization to different rice genomes showed strong hybridization of all five clones to O. minuta genomic DNA and no cross hybridization to genomic DNA from Oryza sativa (AA genome). The pOm1 and pOmA536 sequences showed cross hybridization only to all of the wild rice species containing the C genome. However, the pOm4, pOmPB10, and pOa237 sequences showed cross hybridization to O. australiensis genomic DNA in addition to showing hybridization to the O. minuta genomic DNA.Key words: rice, genome-specific repetitive sequences, Oryza.

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Draft Genome Sequence of a Hypermucoviscous Extended-Spectrum-β-Lactamase-Producing Klebsiella quasipneumoniae subsp. similipneumoniae Clinical Isolate

Genome Announcements ◽

10.1128/genomea.00475-16 ◽

2016 ◽

Vol 4 (4) ◽

Cited By ~ 12

Author(s):

U. Garza-Ramos ◽

J. Silva-Sánchez ◽

J. Catalán-Nájera ◽

H. Barrios ◽

N. Rodríguez-Medina ◽

...

Keyword(s):

Adult Patient ◽

Clinical Isolate ◽

Genome Sequencing ◽

Dna Sequences ◽

Urine Culture ◽

Draft Genome ◽

Trna Genes ◽

Whole Genome ◽

Genome Sequences ◽

Extended Spectrum

A clinical isolate of extended-spectrum-β-lactamase-producing Klebsiella quasipneumoniae subsp. similipneumoniae 06-219 with hypermucoviscosity phenotypes obtained from a urine culture of an adult patient was used for whole-genome sequencing. Here, we report the draft genome sequences of this strain, consisting of 53 contigs with an ~5.6-Mb genome size and an average G+C content of 57.36%. The annotation revealed 6,622 coding DNA sequences and 77 tRNA genes.

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Whole-Genome Analysis of Clinical Vibrio cholerae O1 in Kolkata, India, and Dhaka, Bangladesh, Reveals Two Lineages of Circulating Strains, Indicating Variation in Genomic Attributes

mBio ◽

10.1128/mbio.01227-20 ◽

2020 ◽

Vol 11 (6) ◽

Author(s):

Daichi Morita ◽

Masatomo Morita ◽

Munirul Alam ◽

Asish K. Mukhopadhyay ◽

Fatema-tuz Johura ◽

...

Keyword(s):

South Asia ◽

Cholera Toxin ◽

Vibrio Cholerae ◽

Sub Saharan Africa ◽

Cholera Toxin B Subunit ◽

Whole Genome ◽

Global Public Health ◽

Whole Genome Analysis ◽

Genetic Traits ◽

Content Type

ABSTRACT Vibrio cholerae serogroup O1 is responsible for epidemic and pandemic cholera and remains a global public health threat. This organism has been well established as a resident flora of the aquatic environment that alters its phenotypic and genotypic attributes for better adaptation to the environment. To reveal the diversity of clinical isolates of V. cholerae O1 in the Bay of Bengal, we performed whole-genome sequencing of isolates from Kolkata, India, and Dhaka, Bangladesh, collected between 2009 and 2016. Comparison with global isolates by phylogenetic analysis placed the current isolates in two Asian lineages, with lineages 1 and 2 predominant in Dhaka and Kolkata, respectively. Each lineage possessed different genetic traits in the cholera toxin B subunit gene, Vibrio seventh pandemic island II, integrative and conjugative element, and antibiotic-resistant genes. Thus, although recent global transmission of V. cholerae O1 from South Asia has been attributed only to isolates of lineage 2, another distinct lineage exists in Bengal. IMPORTANCE Cholera continues to be a global concern, as large epidemics have occurred recently in Haiti, Yemen, and countries of sub-Saharan Africa. A single lineage of Vibrio cholerae O1 has been considered to be introduced into these regions from South Asia and to cause the spread of cholera. Using genomic epidemiology, we showed that two distinct lineages exist in Bengal, one of which is linked to the global lineage. The other lineage was found only in Iran, Iraq, and countries in Asia and differed from the global lineage regarding cholera toxin variant and drug resistance profile. Therefore, the potential transmission of this lineage to other regions would likely cause worldwide cholera spread and may result in this lineage replacing the current global lineage.

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