Chloroplast genomes: diversity, evolution, and applications in genetic engineering

Daniell, Henry; Lin, Chun-Shin; Yu, Ming; Chang, Wen‐Yu

doi:10.1186/s13059-016-1004-2

Cited by 1,127 publications

(1,101 citation statements)

References 317 publications

Supporting

Mentioning

1,001

Contrasting

Unclassified

Order By: Relevance

“…Transcript abundance is attributed to the high copy number of transgenes and the strength of the psbA promoter. Among more than 150 transgenes expressed in chloroplasts, more than 75% utilized psbA regulatory sequences (Jin and Daniell, 2015;Daniell et al, 2016aDaniell et al, , 2016b. In addition, three ribosome-binding regions in the 5ʹ UTR of psbA recruit ribosomes and efficiently form the translational initiation complex (Zou et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

“…The 5ʹ UTR of psbA also showed the highest translation activity in vitro among 11 5ʹ UTRs investigated (Yukawa et al, 2007). Therefore, among 140 transgenes expressed in chloroplasts, more than 75% use the psbA regulatory sequences (Jin and Daniell, 2015;Daniell et al, 2016aDaniell et al, , 2016b. Most importantly, compatibility between the 5ʹ UTR of psbA and its coding region is important for efficient translation initiation (Nakamura et al, 2016).…”

Section: Codon Optimization Of Human/viral Transgenesmentioning

confidence: 99%

“…Among more than 115 transgenes expressed via the chloroplast genome, 84 use the psbA regulatory sequence (Jin and Daniell, 2015;Daniell et al, 2016aDaniell et al, , 2016b. A recent study (Nakamura et al, 2016) shows the absence of any detectable translation when codons for the tat coding sequence of HIV-1 were optimized using all 79 tobacco chloroplast mRNAs and regulated by the psbA 5ʹ UTR (Nakamura et al, 2016), but the same sequence was expressed well using the phage T7 GENE10 5ʹ UTR.…”

Section: Codon Optimization Significantly Enhances Translation In Chlmentioning

confidence: 99%

“…FVIII; greater than 200 kD) that would require not only the optimization of codons but also compatibility with regulatory sequences for optimal translation initiation, elongation, and greater understanding of tRNAs encoded by the chloroplast genome or imported from the cytosol. However, no systematic study has been done to utilize the extensive knowledge gathered by sequencing several hundred chloroplast genomes (Daniell et al, 2016a) to understand codon usage and the frequency of highly expressed chloroplast genes.…”

mentioning

confidence: 99%

See 3 more Smart Citations

Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation

et al. 2016

Self Cite

View full text Add to dashboard Cite

Codon optimization based on psbA genes from 133 plant species eliminated 105 (human clotting factor VIII heavy chain [FVIII HC]) and 59 (polio VIRAL CAPSID PROTEIN1 [VP1]) rare codons; replacement with only the most highly preferred codons decreased transgene expression (77-to 111-fold) when compared with the codon usage hierarchy of the psbA genes. Targeted proteomic quantification by parallel reaction monitoring analysis showed 4.9-to 7.1-fold or 22.5-to 28.1-fold increase in FVIII or VP1 codon-optimized genes when normalized with stable isotope-labeled standard peptides (or housekeeping protein peptides), but quantitation using western blots showed 6.3-to 8-fold or 91-to 125-fold increase of transgene expression from the same batch of materials, due to limitations in quantitative protein transfer, denaturation, solubility, or stability. Parallel reaction monitoring, to our knowledge validated here for the first time for in planta quantitation of biopharmaceuticals, is especially useful for insoluble or multimeric proteins required for oral drug delivery. Northern blots confirmed that the increase of codonoptimized protein synthesis is at the translational level rather than any impact on transcript abundance. Ribosome footprints did not increase proportionately with VP1 translation or even decreased after FVIII codon optimization but is useful in diagnosing additional rate-limiting steps. A major ribosome pause at CTC leucine codons in the native gene of FVIII HC was eliminated upon codon optimization. Ribosome stalls observed at clusters of serine codons in the codon-optimized VP1 gene provide an opportunity for further optimization. In addition to increasing our understanding of chloroplast translation, these new tools should help to advance this concept toward human clinical studies.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Codon Optimization Of Human/viral Transgenesmentioning

confidence: 99%

Section: Codon Optimization Significantly Enhances Translation In Chlmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…Образование первичных углеводов происходит в хлоропластах в процессе фото-синтеза. Хотя фотосинтез признается ключевой функцией пластид, они играют также важную роль в других аспек-тах физиологии и развития растений, включая синтез аминокислот, нуклеотидов, жирных кислот, фитогормо-нов, витаминов и множества метаболитов (Daniell et al, 2016).…”

unclassified

Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa

Филюшин¹,

Mazur²,

Щенникова³

et al. 2018

Vestn. VOGiS

View full text Add to dashboard Cite

Sequencing and comparative characterization of plant plastid genomes, or plastomes, is an important tool for modern phylogenetic and taxonomic studies, as well as for understanding the plastome evolution. The genusAlliumL. (family Amaryllidaceae) incorporates more than 900 species, includes economically significant vegetable crops such as garlicA. sativum, onionA. cepa, leekA. porrum, etc. In this work, the plastome of garlicA. sativumhas been completely sequenced. TheA. sativumplastome is 153172 bp in size. It consists of a large unique (LSC, 82035 bp) and small unique (SSC, 18015 bp) copies, separated by inverted repeats (IRa and IRb) of 26561 bp each. In the garlic plastome, 134 genes have been annotated: 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 6 pseudogenes. Comparative analysis ofA. sativumandA. cepaplastomes reveals differences in the sizes of structural elements and spacers at the inverted repeat boundaries. The total numbers of genes inA. sativumandA. cepaare the same, but the gene composition is different: therpl22gene is functional inA. sativum, being a pseudogene inA. cepa; conversely, therps16gene is a pseudogene inA. sativumand a protein-coding gene inA. cepa. In theA. sativumandA. cepaplastomes, 32 SSR sequences have been identified. More than half of them are dinucleotides, and the remaining are tetra-, penta-, and hexanucleotides at the same time, trinucleotides were absent. The compared plastomes differ in the numbers of certain SSRs, and some are present in only one of the species.

show abstract

Complete chloroplast genomes of Achnatherum inebrians and comparative analyses with related species from Poaceae

Wei

Chen

et al. 2021

FEBS Open Bio

View full text Add to dashboard Cite

This paper reports the complete chloroplast genome of Achnatherum inebrians, a poisonous herb that is widely distributed in the rangelands of Northern China. The genome is 137,714 bp in total, and consists of a large single-copy (LSC, 81,758 bp) and small single-copy (SSC, 12,682 bp) region separated by a pair of inverted repeats (IRs, 21,637 bp). The genome contains 130 genes, including 84 protein-coding genes, 38 tRNA genes and 8 ribosomal RNA genes, and the GC content is 36.17%. We subsequently performed comparative analysis of complete genomes from A.inebrians and other Poaceae related species from GenBank. Thirty-eight simple sequence repeats (SSRs) were identified, further demonstrating rapid evolution in Poaceae. Finally, the phylogenetic trees of 37 species of Poaceae and two species of Amaranthaceae were constructed by using Maximum likelihood (ML) and Bayesian Inference (BI) methods, based on the genes of the complete chloroplast genome. We identified hotspots which can be used as molecular markers and barcodes for phylogenetic analysis as well as for species identification. Phylogenetic analysis indicated that A. inebrians is a member of the genus Stipa rather than Achnatherum.

show abstract

Chloroplast genomes: diversity, evolution, and applications in genetic engineering

Cited by 1,127 publications

References 317 publications

Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation

Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation

Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa

Complete chloroplast genomes of Achnatherum inebrians and comparative analyses with related species from Poaceae

Contact Info

Product

Resources

About