scholarly journals A proteomic analysis of peanut seed at different stages of underground development to understand the changes of seed proteins

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243132
Author(s):  
Haifen Li ◽  
Xuanqiang Liang ◽  
Baojin Zhou ◽  
Xiaoping Chen ◽  
Yanbin Hong ◽  
...  
Keyword(s):  
Amino Acid ◽  
Profile Analysis ◽  
Time Of Flight ◽  
Seed Proteins ◽  
Hierarchical Cluster ◽  
Amino Acid Sequences ◽  
Pcr Analysis ◽  
Functional Categories ◽  
Flight Mass Spectrometry ◽  
A Genome

In order to obtain more valuable insights into the protein dynamics and accumulation of allergens in seeds during underground development, we performed a proteomic study on developing peanut seeds at seven different stages. A total of 264 proteins with altered abundance and contained at least one unique peptide was detected by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS). All identified proteins were classified into five functional categories as level 1 and 20 secondary functional categories as level 2. Among them, 88 identified proteins (IPs) were related to carbohydrate/ amino acid/ lipid transport and metabolism, indicating that carbohydrate/amino acid/ lipid metabolism played a key role in the underground development of peanut seeds. Hierarchical cluster analysis showed that all IPs could be classified into eight cluster groups according to the abundance profiles, suggesting that the modulatory patterns of these identified proteins were complicated during seed development. The largest group contained 41 IPs, the expression of which decreased at R 2 and reached a maximum at R3 but gradually decreased from R4. A total of 14 IPs were identified as allergen-like proteins by BLAST with A genome (Arachis duranensis) or B genome (Arachis ipaensis) translated allergen sequences. Abundance profile analysis of 14 identified allergens showed that the expression of all allergen proteins was low or undetectable by 2-DE at the early stages (R1 to R4), and began to accumulate from the R5 stage and gradually increased. Network analysis showed that most of the significant proteins were involved in active metabolic pathways in early development. Real time RT-PCR analysis revealed that transcriptional regulation was approximately consistent with expression at the protein level for 8 selected identified proteins. In addition, some amino acid sequences that may be associated with new allergens were also discussed.

Biochemical data bearing on the origin of the B genome in the polyploid wheats

Genome ◽  
1990 ◽  
Vol 33 (3) ◽  
pp. 360-368 ◽  
Author(s):  
K. Kerby ◽  
J. Kuspira ◽  
B. L. Jones ◽  
G. L. Lookhart
Keyword(s):  
Amino Acid ◽  
B Chromosome ◽  
Amino Acid Sequences ◽  
Chromosome 1 ◽  
Aegilops Speltoides ◽  
B Genome ◽  
Aegilops Longissima ◽  
Aegilops Sharonensis ◽  
A Genome ◽  
Genome Donors

For many years each of the species Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Aegilops speltoides, and Triticum urartu has been implicated as the donor of the B genome in the polyploid wheats. Biochemical and cytological data have revealed that T. urartu possesses a genome similar to that of T. monococcum, and therefore it may be the source of the A genome in T. turgidum and T. aestivum. This revelation therefore excludes T. urartu from the list of putative B-genome donors. To determine which of the remaining species is the source of the B chromosome set, the amino acid sequences of their purothionins were compared with that of the α1 purothionin coded for by the Pur-1B gene on chromosome 1 in the B genome of T. turgidum and T. aestivum. The residue sequences of this protein from Ae. bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides differed by 1, 6, 1, 1, and 2 amino acid substitutions, respectively, from the α1 protein. These results suggest that either Ae. bicornis, Ae. searsii, or Ae. sharonensis was the most likely donor of the B genome. If the B genome in the polyploid wheats is monophyletic in origin, the collective findings of this and other investigations indicate that Ae. searsii is the most likely donor. The possibility that the B genome in the polyploid wheats could have a polyphyletic origin is also discussed.Key words: polyploid wheats, putative B-genome donors, purothionins, monophyletic, polyphyletic.

scholarly journals Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution

2020 ◽  
Author(s):  
Ilias Georgakopoulos-Soares ◽  
Ofer Yizhar Barnea ◽  
Ioannis Mouratidis ◽  
Martin Hemberg ◽  
Nadav Ahituv
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Significant Proportion ◽  
Scoring Function ◽  
Amino Acid Sequences ◽  
Dna Fingerprints ◽  
Functional Categories ◽  
Coding Sequences ◽  
A Genome ◽  
Genomic Characterization

AbstractNullomers and nullpeptides are short DNA or amino acid sequences that are absent from a genome or proteome, respectively. One potential cause for their absence could be that they have a detrimental impact on an organism. Here, we identified all possible nullomers and nullpeptides in the genomes and proteomes of over thirty species and show that a significant proportion of these sequences are under negative selection. We assign nullomers to different functional categories (coding sequences, exons, introns, 5’UTR, 3’UTR and promoters) and show that nullomers from coding sequences and promoters are most likely to be selected against. Utilizing variants in the human population, we annotate variant-associated nullomers, highlighting their potential use as DNA ‘fingerprints’. Phylogenetic analyses of nullomers and nullpeptides across evolution shows that they could be used to build phylogenetic trees. Our work provides a catalog of genomic and proteome derived absent k-mers, together with a novel scoring function to determine their potential functional importance. In addition, it shows how these unique sequences could be used as DNA ‘fingerprints’ or for phylogenetic analyses.

scholarly journals Isolation and Characterization of Genes Responsible for Naphthalene Degradation from Thermophilic Naphthalene Degrader, Geobacillus sp. JF8

2019 ◽  
Vol 8 (1) ◽  
pp. 44 ◽  
Author(s):  
Daisuke Miyazawa ◽  
Le Thi Ha Thanh ◽  
Akio Tani ◽  
Masaki Shintani ◽  
Nguyen Hoang Loc ◽  
...  
Keyword(s):  
Amino Acid ◽  
Thermophilic Bacterium ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Pcr Analysis ◽  
Naphthalene Degradation ◽  
Isolation And Characterization ◽  
Dihydrodiol Dehydrogenase ◽  
Reading Frames

Geobacillus sp. JF8 is a thermophilic biphenyl and naphthalene degrader. To identify the naphthalene degradation genes, cis-naphthalene dihydrodiol dehydrogenase was purified from naphthalene-grown cells, and its N-terminal amino acid sequence was determined. Using a DNA probe encoding the N-terminal region of the dehydrogenase, a 10-kb DNA fragment was isolated. Upstream of nahB, a gene for dehydrogenase, there were two open reading frames which were designated as nahAc and nahAd, respectively. The products of nahAc and nahAd were predicted to be alpha and beta subunit of ring-hydroxylating dioxygenases, respectively. Phylogenetic analysis of amino acid sequences of NahB indicated that it did not belong to the cis-dihydrodiol dehydrogenase group that includes those of classical naphthalene degradation pathways. Downstream of nahB, four open reading frames were found, and their products were predicted as meta-cleavage product hydrolase, monooxygenase, dehydrogenase, and gentisate 1,2-dioxygenase, respectively. A reverse transcriptase-PCR analysis showed that transcription of nahAcAd was induced by naphthalene. These findings indicate that we successfully identified genes involved in the upper pathway of naphthalene degradation from a thermophilic bacterium.

Biochemical data bearing on the relationship between the genome of Triticum urartu and the A and B genomes of the polyploid wheats

Genome ◽  
1988 ◽  
Vol 30 (4) ◽  
pp. 576-581 ◽  
Author(s):  
K. Kerby ◽  
J. Kuspira ◽  
B. L. Jones
Keyword(s):  
Amino Acid ◽  
Triticum Turgidum ◽  
Amino Acid Sequences ◽  
Triticum Monococcum ◽  
Triticum Urartu ◽  
B Genome ◽  
Genome Donor ◽  
A Genome ◽  
The Relationship ◽  
Donor Species

To determine whether the Triticum urartu genome is more closely related to the A or B genome of the polyploid wheats, the amino acid sequence of its purothionin was compared to the amino acid sequences of the purothionins in Triticum monococcum, Triticum turgidum, and Triticum aestivum. The residue sequence of the purothionin from T. urartu differs by five and six amino acid substitutions respectively from the α1 and α2 forms coded for by genes in the B and D genomes, and is identical to the β form specified by a gene in the A genome. Therefore, the T. urartu purothionin is either coded by a gene in the A genome or a chromosome set highly homologous to it. The results demonstrate that at least a portion of the T. urartu and T. monococcum genomes is homologous and probably identical. A variety of other studies have also shown that T. urartu is very closely related to T. monococcum and, in all likelihood, also possesses the A genome. Therefore, it could be argued that either T. urartu and T. monococcum are the same species or that T. urartu rather than T. monococcum is the source of the A genome in T. turgidum and T. aestivum. Except for Johnson's results, our data and that of others suggest a revised origin of polyploid wheats. Specifically, the list of six putative B genome donor species is reduced to five, all members of the Sitopsis section of the genus Aegilops.Key words: Triticum monococcum, Triticum urartu, polyploid wheats, genomes A and B, purothionins.

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