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1. Efficient transposition of Tn4556 by alterations in inverted repeats using a delivery vector carrying a counter-selectable marker for Streptomyces

Author:
Sota, Masahiro; Sakoda, Akiko; Ikeda, Haruo
Source:
Journal of industrial microbiology & biotechnology 2019 v.46 no.3-4 pp. 477-482
ISSN:
1367-5435
Subject:
open reading frames,   etc   ; Streptomyces; methyltransferases; sequence analysis; transposons;     Show all 5 Subjects
Abstract:
... A 6625-base pair transposon, Tn4556, was initially isolated from a Streptomyces strain and a sequence analysis was performed; however, its annotation data remain incomplete. At least three positions were identified as frameshift and base-exchange errors by resequencing. The revised sequence revealed that Tn4556 contains four open reading frames that encode transposase, methyltransferase, isoprenyl ...
DOI:
10.1007/s10295-018-2101-x

2. Mining for Small Translated ORFs

Author:
Chugunova, Anastasia; Navalayeu, Tsimafei; Dontsova, Olga; Sergiev, Petr
Source:
Journal of proteome research 2018 v.17 no.1 pp. 1-11
ISSN:
1535-3907
Subject:
open reading frames,   etc   ; genome; peptides; probability; proteome;     Show all 5 Subjects
Abstract:
... Peptides encoded by short open reading frames (sORFs) are usually defined as peptides ≤100 aa long. Usually sORFs were ignored by automatic genome annotation programs due to the high probability of false discovery. However, improved computational tools along with a high-throughput RIBO-seq approach identified a myriad of translated sORFs. Their importance becomes evident as we are gaining experime ...
DOI:
10.1021/acs.jproteome.7b00707

3. Complete genome sequence of Kurlavirus, a novel member of the family Marseilleviridae isolated in Mumbai, India

Author:
Chatterjee, Anirvan; Kondabagil, Kiran
Source:
Archives of virology 2017 v.162 no.10 pp. 3243-3245
ISSN:
0304-8608
Subject:
open reading frames,   etc   ; genes; India;     Show all 3 Subjects
Abstract:
... The complete genome sequence of Kurlavirus, a new member of the family Marseilleviridae is reported. The Kurlavirus genome was found to encode a remarkable complement of genes homologous to those of other members of the family Marseilleviridae. Interestingly, the Kurlavirus genome contains 71 fewer ORFs than that of Marseillevirus, even though their genome sizes are comparable. ...
DOI:
10.1007/s00705-017-3469-z

4. Correction to: RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs

Author:
Murat, Pierre; Marsico, Giovanni; Herdy, Barbara; Ghanbarian, Avazeh T.; Portella, Guillem; Balasubramanian, Shankar
Source:
Genome biology 2019 v.20 no.1 pp. 11
ISSN:
1474-760X
Subject:
open reading frames,   etc   ; humans; messenger RNA; nucleic acid conformation; translation (genetics);     Show all 5 Subjects
Abstract:
... Following publication of the original article [1], the authors reported the following error in the name of the fourth author. ...
DOI:
10.1186/s13059-019-1623-5

5. A myelocytomatosis transcription factor from Hevea brasiliensis positively regulates the expression of the small rubber particle protein gene

Author:
Guo, Dong; Li, Hui-Liang; Wang, Ying; Zhu, Jia-Hong; Peng, Shi-Qing
Source:
Industrial crops and products 2019 v.133 pp. 90-97
ISSN:
0926-6690
Subject:
open reading frames,   etc   ; Hevea brasiliensis; amino acids; bark; biosynthesis; flowers; genes; latex; leaves; rubber; transcription factors;     Show all 11 Subjects
Abstract:
... Small rubber particle protein (SRPP) is a major rubber particle-associated protein in latex from rubber tree (Hevea brasiliensis Muell. Arg.), and it implicated in the natural rubber biosynthesis. However, the regulatory mechanism of H. brasiliensis SRPP gene (HbSRPP) is incompletely understood. In this study, a myelocytomatosis (MYC) transcription factor (designated as HbMYC2b) regulating the HbS ...
DOI:
10.1016/j.indcrop.2019.01.052

6. Construction and validation of the Tn5-PLtetO-1-msfGFP transposon as a tool to probe protein expression and localization

Author:
Passaris, Ioannis; Tadesse, Wubishet M.; Gayán, Elisa; Aertsen, Abram
Source:
Journal of microbiological methods 2019 v.161 pp. 56-62
ISSN:
0167-7012
Subject:
open reading frames,   etc   ; antibiotic resistance; fluorescence microscopy; prokaryotic cells; protein synthesis; proteins; transposons;     Show all 7 Subjects
Abstract:
... In this study we report the design, construction and validation of a novel transposon aimed to systematically screen for protein localization and expression patterns in prokaryotes using fluorescence microscopy. Upon random insertion in an open reading frame in the proper frame and orientation, the transposon creates an N-terminal fluorescent protein fusion to the msfGFP reporter. Moreover, in ord ...
DOI:
10.1016/j.mimet.2019.04.012

7. Genome characterization and temporal evolution analysis of a non-epidemic norovirus variant GII.8

Author:
Xue, Liang; Cai, Weicheng; Gao, Junshan; Zhang, Le; Wu, Haoming; Pang, Rui; Li, Ying; Wang, Juan; Zhang, Jumei; Wu, Shi; Ye, Qinghua; Lei, Tao; Wu, Qingping
Source:
Infection, genetics, and evolution 2019 v.70 pp. 15-23
ISSN:
1567-1348
Subject:
open reading frames,   etc   ; Norovirus; amino acids; capsid; enzymes; epitopes; gastroenteritis; genome; genotype; mutation; oligodeoxyribonucleotides; proteins; China;     Show all 13 Subjects
Abstract:
... Noroviruses are the primary cause of non-bacterial acute gastroenteritis worldwide, and GII.8 belongs to a non-epidemic genotype with a limited understanding currently. In this study, we assembled the first GII.8 norovirus genome from China and clarified the temporal evolutionary process of this non-epidemic variant. Using the “4+1+1” application strategy with newly designed primer sets, the genom ...
DOI:
10.1016/j.meegid.2019.02.010

8. An integrated approach for identification of exon locations using recursive Gauss Newton tuned adaptive Kaiser window

Author:
Das, Lopamudra; Nanda, Sarita; Das, J.K.
Source:
Genomics 2019 v.111 no.3 pp. 284-296
ISSN:
0888-7543
Subject:
open reading frames,   etc   ; DNA; algorithms; bioinformatics; covariance; exons; prediction; processing technology;     Show all 8 Subjects
Abstract:
... Identification of exon location in a DNA sequence has been considered as the most demanding and challenging research topic in the field of Bioinformatics. This work proposes a robust approach combining the Trigonometric mapping with Adaptive tuned Kaiser Windowing approach for locating the protein coding regions (EXONS) in a genetic sequence. For better convergence as well as improved accurateness ...
DOI:
10.1016/j.ygeno.2018.10.008

9. High diversity and rapid spatial turnover of integron gene cassettes in soil

Author:
Ghaly, Timothy M.; Geoghegan, Jemma L.; Alroy, John; Gillings, Michael R.
Source:
Environmental microbiology 2019 v.21 no.5 pp. 1567-1574
ISSN:
1462-2912
Subject:
open reading frames,   etc   ; antibiotic resistance; bacteria; ecology; genes; metagenomics; proteins; soil; Antarctica; Australia;     Show all 10 Subjects
Abstract:
... Integrons are genetic elements that promote rapid adaptation in bacteria by capturing exogenous, mobile gene cassettes. Recently, a subset of gene cassettes has facilitated the global spread of antibiotic resistance. However, outside clinical settings, very little is known about their diversity and spatial ecology. To address this question, we sequenced integron gene cassettes from soils sampled a ...
DOI:
10.1111/1462-2920.14551

10. Preparation of malto-oligosaccharides with specific degree of polymerization by a novel cyclodextrinase from Palaeococcus pacificus

Author:
Ji, Hangyan; Bai, Yuxiang; Li, XiaoXiao; Wang, Jinpeng; Xu, Xueming; Jin, Zhengyu
Source:
Carbohydrate polymers 2019 v.210 pp. 64-72
ISSN:
0144-8617
Subject:
open reading frames,   etc   ; amylose; beta-cyclodextrin; enzymes; genomics; hydrolysis; pH; polymerization; pullulan; substrate specificity; temperature;     Show all 11 Subjects
Abstract:
... An open reading frame from Palaeococcus pacificus was discovered by genomic analysis. The recombinant PpCD was proved as novel extremely thermal-stable cyclodextrinase with potential on production of malto-oligosaccharides with specific degree of polymerization. This enzyme has extremely high substrate specificity toward cyclodextrins, while the rates of hydrolysis toward macromolecular or linear ...
DOI:
10.1016/j.carbpol.2019.01.041

11. A helicase links upstream ORFs and RNA structure

Author:
Jankowsky, Eckhard; Guenther, Ulf-Peter
Source:
Current genetics 2019 v.65 no.2 pp. 453-456
ISSN:
0172-8083
Subject:
open reading frames,   etc   ; codons; enzymes; messenger RNA; protein synthesis; translation (genetics);     Show all 6 Subjects
Abstract:
... Upstream open reading frames (uORFs) in 5′ UTRs of eukaryotic mRNAs are increasingly recognized as important elements that regulate cellular protein synthesis. Since uORFs can start from non-AUG codons, an enormous number of potential uORF initiation sites exists in 5′UTRs. However, only a subset of these sites is used and it has been unclear how actual start sites are selected. Studies of the DEA ...
DOI:
10.1007/s00294-018-0911-z

12. Alternative Translation Initiation at a UUG Codon Gives Rise to Two Functional Variants of the Mitochondrial Protein Kgd4

Author:
Heublein, Manfred; Ndi, Mama; Vazquez-Calvo, Carmela; Vögtle, F.-Nora; Ott, Martin
Source:
Journal of molecular biology 2019 v.431 no.7 pp. 1460-1467
ISSN:
0022-2836
Subject:
open reading frames,   etc   ; alpha-ketoglutaric acid; alternative splicing; biogenesis; enzymes; messenger RNA; mitochondria; translation (genetics); yeasts;     Show all 9 Subjects
Abstract:
... Kgd4 is a novel subunit of the mitochondrial α-ketoglutarate dehydrogenase complex (KGDH). In yeast, the protein is present in two forms of unknown origin, as there is only one open reading frame and no alternative splicing. Here, we show that the two forms of Kgd4 derive from one mRNA that is translated by employing two alternative start sites. The standard, annotated AUG codon gives rise to the ...
DOI:
10.1016/j.jmb.2019.02.023

13. Characterization of a Regulator pgsR on Endogenous Plasmid p2Sip and Its Complementation for Poly(γ-glutamic acid) Accumulation in Bacillus amyloliquefaciens

Author:
Qiu, Yibin; Zhu, Yifan; Zhang, Yatao; Sha, Yuanyuan; Xu, Zongqi; Li, Sha; Feng, Xiaohai; Xu, Hong
Source:
Journal of agricultural and food chemistry 2019 v.67 no.13 pp. 3711-3722
ISSN:
1520-5118
Subject:
open reading frames,   etc   ; Bacillus amyloliquefaciens; enzymes; genes; genomics; glutamic acid; loci; plasmids; polyglutamic acid; secretion;     Show all 10 Subjects
Abstract:
... Bacillus amyloliquefaciens NX-2S154 is a promising poly(γ-glutamic acid) (γ-PGA) producing strain discovered in previous studies. However, the wild-type strain contains an unknown endogenous plasmid, p2Sip, which causes low transformation efficiency and instability of exogenous plasmids. In our study, p2Sip is 5622 bp with 41% G+C content and contains four putative open reading frames (ORFs), incl ...
DOI:
10.1021/acs.jafc.9b00332

14. An endogenous adeno-associated virus element in elephants

Author:
Kobayashi, Yuki; Shimazu, Tsukika; Murata, Koichi; Itou, Takuya; Suzuki, Yoshiyuki
Source:
Virus research 2019 v.262 pp. 10-14
ISSN:
0168-1702
Subject:
open reading frames,   etc   ; Dependoparvovirus; Elephas maximus; amino acid sequences; gene expression; genes; liver; mammals; messenger RNA;     Show all 9 Subjects
Abstract:
... An endogenous viral element derived from adeno-associated virus containing a nearly intact open reading frame (ORF) of the rep gene (enAAV-rep) has been identified in the genomes of various mammals including degu and African elephant. Particularly, in degu, mRNA expression of enAAV-rep has been observed specifically in the liver. Here we newly identified enAAV-rep in Asian elephant and rock hyrax, ...
DOI:
10.1016/j.virusres.2018.04.015

15. Complete genome sequence of a novel bacteriophage, PBKP05, infecting Klebsiella pneumoniae

Author:
Oh, Hyun Keun; Cha, Kyoungeun; Hwang, Yoon Jung; Cho, Jaehak; Jo, Yunyeol; Myung, Heejoon
Source:
Archives of virology 2019 v.164 no.3 pp. 885-888
ISSN:
0304-8608
Subject:
open reading frames,   etc   ; DNA; Klebsiella pneumoniae; bacteriophages; genome; multiple drug resistance; phage therapy;     Show all 7 Subjects
Abstract:
... An increasing number of Klebsiella pneumoniae isolates have been found to be multi-drug resistant. A novel bacteriophage, PBKP05, which infects K. pneumoniae, was isolated and characterized. It has a linear double-stranded DNA genome of 30,240 base pairs in length. Its G+C content is 53%, and 47 putative open reading frames are functionally annotated. This phage can be a candidate material for pha ...
DOI:
10.1007/s00705-018-04121-9

16. Complete nucleotide sequence analysis of a novel Bacillus subtilis-infecting phage, BSP38, possibly belonging to a new genus in the subfamily Spounavirinae

Author:
Ghosh, Kuntal; Kim, Kwang-Pyo
Source:
Archives of virology 2019 v.164 no.3 pp. 875-878
ISSN:
0304-8608
Subject:
open reading frames,   etc   ; Myoviridae; bacteriophages; genome; genomics; new genus; sequence analysis; sewage; transfer RNA;     Show all 9 Subjects
Abstract:
... Bacillus subtilis-infecting phage BSP38 was isolated from a sewage sample. Morphologically, BSP38 was found to be similar to members of the subfamily Spounavirinae, family Myoviridae. Its genome is 153,268 bp long with 41.8% G+C content and 254 putative open reading frames (ORFs) as well as six tRNAs. A distinguishing feature for this phage among the reported B. subtilis-infecting phages is the pr ...
DOI:
10.1007/s00705-018-4110-5

17. The genetic divergences of codon usage shed new lights on transmission of hepatitis E virus from swine to human

Author:
Zhou, Jian-hua; Li, Xue-rui; Lan, Xi; Han, Sheng-Yi; Wang, Yi-ning; Hu, Yonghao; Pan, Qiuwei
Source:
Infection, genetics, and evolution 2019 v.68 pp. 23-29
ISSN:
1567-1348
Subject:
open reading frames,   etc   ; Hepatitis E virus; genetic variation; genome; genotype; hosts; humans; pathogens; public health; swine;     Show all 10 Subjects
Abstract:
... Hepatitis E virus (HEV) is an important pathogen causing public health burden. Swine has been recognized as a main reservoir. Interestingly, genotype 1 HEV only infects human; whereas genotype 3 and 4 are zoonotic. However, there is a lack of in-depth understanding in respect to the transmission from swine to human. Codon usage patterns generally participate in viral survival and fitness towards i ...
DOI:
10.1016/j.meegid.2018.11.024

18. The shufflon of IncI1 plasmids is rearranged constantly during different growth conditions

Author:
Brouwer, Michael S.M.; Jurburg, Stephanie D.; Harders, Frank; Kant, Arie; Mevius, Dik J.; Roberts, Adam P.; Bossers, Alex
Source:
Plasmid 2019 v.102 pp. 51-55
ISSN:
0147-619X
Subject:
open reading frames,   etc   ; Escherichia coli; cefotaxime; developmental stages; fimbriae; nanopores; plasmids; proteins;     Show all 8 Subjects
Abstract:
... One of the factors that can affect conjugation of IncI1 plasmids, amongst others, is the genetic region known as the shufflon. This multiple inversion system modifies the pilus tip proteins used during conjugation, thus affecting the affinity for different recipient cells. Although recombination is known to occur in in vitro conditions, little is known about the regulation and the extent of recomb ...
DOI:
10.1016/j.plasmid.2019.03.003

19. Salicylate and phthalate pathways contributed differently on phenanthrene and pyrene degradations in Mycobacterium sp. WY10

Author:
Sun, Shanshan; Wang, Haizhen; Chen, Yuanzhi; Lou, Jun; Wu, Laosheng; Xu, Jianming
Source:
Journal of hazardous materials 2019 v.364 pp. 509-518
ISSN:
0304-3894
Subject:
open reading frames,   etc   ; Mycobacterium; bacteria; enzymes; genes; metabolism; metabolites; phenanthrenes; phthalates;     Show all 9 Subjects
Abstract:
... Mycobacterium sp. WY10 was a highly effective PAHs-degrading bacterium that can degrade phenanthrene (PHE, 100 mg L−1) completely within 60 h and 83% of pyrene (PYR, 50 mg L-1) in 72 h. In this study, ten and eleven metabolites, respectively, were identified in PHE and PYR degradation cultures, and a detailed PHE and PYR metabolism maps were constructed based on the metabolic results. The strain W ...
DOI:
10.1016/j.jhazmat.2018.10.064

20. Characterization of the mitochondrial genome of the MAX1 type of cytoplasmic male-sterile sunflower

Author:
Makarenko, Maksim S.; Usatov, Alexander V.; Tatarinova, Tatiana V.; Azarin, Kirill V.; Logacheva, Maria D.; Gavrilova, Vera A.; Horn, Renate
Source:
BMC plant biology 2019 v.19 no.Supplement 1 pp. 51
ISSN:
1471-2229
Subject:
open reading frames,   etc   ; Helianthus annuus; cytoplasmic male sterility; genes; mitochondria; mitochondrial DNA; mitochondrial genome; phenotype;     Show all 8 Subjects
Abstract:
... BACKGROUND: More than 70 cytoplasmic male sterility (CMS) types have been identified in Helianthus, but only for less than half of them, research of mitochondrial organization has been conducted. Moreover, complete mitochondrion sequences have only been published for two CMS sources – PET1 and PET2. It has been demonstrated that other sunflower CMS sources like MAX1, significantly differ from the ...
DOI:
10.1186/s12870-019-1637-x