scholarly journals Phloem Loading of Sorbitol in Apple (Malus domestica Borkh.): Cloning and Sequence Analysis of Potential H+/Sorbitol Symporters from a Mature Leaf cDNA Library

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 756B-756
Author(s):  
Edwin J. Reidel* ◽  
Brian G. Ayre ◽  
E. Robert Turgeon ◽  
Lailiang Cheng
Keyword(s):  
Cdna Library ◽  
Malus Domestica ◽  
Phloem Loading ◽  
Open Reading Frames ◽  
Sugar Transporter ◽  
Sugar Transporters ◽  
Apple Leaves ◽  
Complete Sequencing ◽  
Membrane Bound ◽  
Reading Frames

Sorbitol (d-glucitol) is the major end product of photosynthesis in apple (Malus domestica Borkh.), as well as the predominant phloem-translocated carbohydrate. The mechanism by which sorbitol is phloem-loaded for transport to heterotrophic sink tissues is unknown. We hypothesized that a plasma membrane-bound H+/sorbitol symporter mediates apoplastic phloem-loading of sorbitol. To discover genes potentially encoding sorbitol transporters, a cDNA library was constructed from mature `Gala' apple leaves. A homologous probe was synthesized via PCR with primers were designed against the cherry fruit sorbitol transporter, PcSot1, and using library lysate as template. From an initial plating of approximately 5 × 105 clones, twelve positives were identified after three rounds of hybridization screening. Following single-pass, 5' end sequencing, the clones were sorted into four contiguous sequences. One clone was chosen from each contig for complete sequencing. The four clones, provisionally named MdSOT1-4 (Malus domesitca Sorbitol Transporter), potentially encode full-length cDNAs for sorbitol transporters: Translated-BLAST searching (blastx) revealed that the open reading frames encode the complete Pfam sugar transporter domain, and the most significant alignments are with sequences encoding known- and putative polyol and sugar transporters.

scholarly journals The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli

2004 ◽  
Vol 17 (8) ◽  
pp. 827-836 ◽  
Author(s):  
Claudia B. Monteiro-Vitorello ◽  
Luis E. A. Camargo ◽  
Marie A. Van Sluys ◽  
João P. Kitajima ◽  
Daniela Truffi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gc Content ◽  
Open Reading Frames ◽  
Circular Chromosome ◽  
Free Sugars ◽  
Sugar Transporters ◽  
Living Organisms ◽  
Bacterial Plant Pathogen ◽  
Single Circular Chromosome ◽  
Reading Frames

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

scholarly journals Membrane-Bound, 2-Keto-d-Gluconate-Yielding d-Gluconate Dehydrogenase from “Gluconobacter dioxyacetonicus” IFO 3271: Molecular Properties and Gene Disruption

2007 ◽  
Vol 73 (20) ◽  
pp. 6551-6556 ◽  
Author(s):  
Hirohide Toyama ◽  
Naoko Furuya ◽  
Ittipon Saichana ◽  
Yoshitaka Ano ◽  
Osao Adachi ◽  
...  
Keyword(s):  
Double Mutant ◽  
Culture Medium ◽  
Wild Type Strain ◽  
Reductase Activity ◽  
Pcr Primers ◽  
Open Reading Frames ◽  
Pcr Product ◽  
Mutant Strains ◽  
Membrane Bound ◽  
Reading Frames

ABSTRACT Most Gluconobacter species produce and accumulate 2-keto-d-gluconate (2KGA) and 5KGA simultaneously from d-glucose via GA in culture medium. 2KGA is produced by membrane-bound flavin adenine dinucleotide-containing GA 2-dehydrogenase (FAD-GADH). FAD-GADH was purified from “Gluconobacter dioxyacetonicus” IFO 3271, and N-terminal sequences of the three subunits were analyzed. PCR primers were designed from the N-terminal sequences, and part of the FAD-GADH genes was cloned as a PCR product. Using this PCR product, gene fragments containing whole FAD-GADH genes were obtained, and finally the nucleotide sequence of 9,696 bp was determined. The cloned sequence had three open reading frames (ORFs), gndS, gndL, and gndC, corresponding to small, large, and cytochrome c subunits of FAD-GADH, respectively. Seven other ORFs were also found, one of which showed identity to glucono-δ-lactonase, which might be involved directly in 2KGA production. Three mutant strains defective in either gndL or sldA (the gene responsible for 5KGA production) or both were constructed. Ferricyanide-reductase activity with GA in the membrane fraction of the gndL-defective strain decreased by about 60% of that of the wild-type strain, while in the sldA-defective strain, activity with GA did not decrease and activities with glycerol, d-arabitol, and d-sorbitol disappeared. Unexpectedly, the strain defective in both gndL and sldA (double mutant) still showed activity with GA. Moreover, 2KGA production was still observed in gndL and double mutant strains. 5KGA production was not observed at all in sldA and double mutant strains. Thus, it seems that “G. dioxyacetonicus” IFO 3271 has another membrane-bound enzyme that reacts with GA, producing 2KGA.

scholarly journals RiboNT: A Noise-Tolerant Predictor of Open Reading Frames from Ribosome-Protected Footprints

Life ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 701
Author(s):  
Bo Song ◽  
Mengyun Jiang ◽  
Lei Gao
Keyword(s):  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Model Organisms ◽  
Widespread Application ◽  
Optimized Protocol ◽  
Membrane Bound ◽  
Noise Tolerant ◽  
Diverse Plant Species ◽  
Small Orfs ◽  
Reading Frames

Ribo-seq, also known as ribosome profiling, refers to the sequencing of ribosome-protected mRNA fragments (RPFs). This technique has greatly advanced our understanding of translation and facilitated the identification of novel open reading frames (ORFs) within untranslated regions or non-coding sequences as well as the identification of non-canonical start codons. However, the widespread application of Ribo-seq has been hindered because obtaining periodic RPFs requires a highly optimized protocol, which may be difficult to achieve, particularly in non-model organisms. Furthermore, the periodic RPFs are too short (28 nt) for accurate mapping to polyploid genomes, but longer RPFs are usually produced with a compromise in periodicity. Here we present RiboNT, a noise-tolerant ORF predictor that can utilize RPFs with poor periodicity. It evaluates RPF periodicity and automatically weighs the support from RPFs and codon usage before combining their contributions to identify translated ORFs. The results demonstrate the utility of RiboNT for identifying both long and small ORFs using RPFs with either good or poor periodicity. We implemented the pipeline on a dataset of RPFs with poor periodicity derived from membrane-bound polysomes of Arabidopsis thaliana seedlings and identified several small ORFs (sORFs) evolutionarily conserved in diverse plant species. RiboNT should greatly broaden the application of Ribo-seq by minimizing the requirement of RPF quality and allowing the use of longer RPFs, which is critical for organisms with complex genomes because these RPFs can be more accurately mapped to the position from which they were derived.

Incorporation of iron-sulphur clusters in membrane-bound proteins

2001 ◽  
Vol 29 (4) ◽  
pp. 418-421 ◽  
Author(s):  
A. Seidler ◽  
K. Jaschkowitz ◽  
M. Wollenberg
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Synechocystis Pcc 6803 ◽  
Membrane Bound ◽  
Nif Proteins ◽  
Reading Frames ◽  
Pcc 6803

The completely sequenced genome of the cyano-bacterium Synechocystis PCC 6803 contains several open reading frames, of which the deduced amino acid sequences show similarities to proteins known to be involved in FeS cluster synthesis of nitrogenase (Nif proteins) and other FeS proteins (Isc proteins). In this article, the results of our studies on these proteins are summarized and discussed with respect to their relevance in FeS cluster incorporation in chloroplasts. In cyanobacteria, there appears to exist several pathways for FeS cluster synthesis.

Expression of open reading frames in silkworm pupal cDNA library

2007 ◽  
Vol 136 (3) ◽  
pp. 327-343 ◽  
Author(s):  
Yao-Zhou Zhang ◽  
Jian Chen ◽  
Zuo-Ming Nie ◽  
Zheng-Bing Lü ◽  
Dan Wang ◽  
...  
Keyword(s):  
Cdna Library ◽  
Open Reading Frames ◽  
Reading Frames

scholarly journals Genetic Locus Encoding Functions Involved in Biosynthesis and Outer Membrane Localization of Xanthomonadin in Xanthomonas oryzae pv. oryzae

2002 ◽  
Vol 184 (13) ◽  
pp. 3539-3548 ◽  
Author(s):  
Ajay Kumar Goel ◽  
Lakshmi Rajagopal ◽  
Narayana Nagesh ◽  
Ramesh V. Sonti
Keyword(s):  
Outer Membrane ◽  
Polyketide Synthase ◽  
Genetic Locus ◽  
Open Reading Frames ◽  
Xanthomonas Oryzae ◽  
Membrane Localization ◽  
Acyl Carrier Proteins ◽  
Membrane Bound ◽  
First Time ◽  
Reading Frames

ABSTRACT Xanthomonadins are membrane-bound, brominated, aryl-polyene pigments specific to the genus Xanthomonas. We have characterized a genetic locus (pig) from Xanthomonas oryzae pv. oryzae which contains four open reading frames (ORFs) that are essential for xanthomonadin production. Three of these ORFs are homologous to acyl carrier proteins, dehydratases, and acyl transferases, suggesting a type II polyketide synthase pathway for xanthomonadin biosynthesis. The fourth ORF has no homologue in the database. For the first time, we report that a putative cytoplasmic membrane protein encoded in the pig locus is required for outer membrane localization of xanthomonadin in X. oryzae pv. oryzae. We also report the identification of a novel 145-bp palindromic Xanthomonas repetitive intergenic consensus element that is present in two places in the pig locus. We estimate that more than 100 copies of this element might be present in the genome of X. oryzae pv. oryzae and other xanthomonads.

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