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Article ; Online: Ectopic Expression of

Luengwilai, Kietsuda / Yu, Jingwei / Jiménez, Randi C / Thitisaksakul, Maysaya / Vega, Andrea / Dong, Shaoyun / Beckles, Diane M

International journal of molecular sciences

2022 Volume 23, Issue 19

Abstract: A large collection of transgenic tomato lines, each ectopically expressing a different Arabidopsis thaliana transcription factor, was screened for variants with alterations in leaf starch. Such lines may be affected in carbon partitioning, and in ... ...

Abstract	A large collection of transgenic tomato lines, each ectopically expressing a different Arabidopsis thaliana transcription factor, was screened for variants with alterations in leaf starch. Such lines may be affected in carbon partitioning, and in allocation to the sinks. We focused on ‘L4080’, which harbored an A. thaliana zDof (DNA-binding one zinc finger) isoform 1.3 (AtzDof1.3) gene, and which had a 2−4-fold higher starch-to-sucrose ratio in source leaves over the diel (p < 0.05). Our aim was to determine whether there were associated effects on productivity. L4080 plants were altered in nitrogen (N) and carbon (C) metabolism. The N-to-C ratio was higher in six-week-old L4080, and when treated with 1/10 N, L4080 growth was less inhibited compared to the wild-type and this was accompanied by faster root elongation (p < 0.05). The six-week-old L4080 acquired 42% more dry matter at 720 ppm CO2, compared to ambient CO2 (p < 0.05), while the wild-type (WT) remained unchanged. GC-MS-TOF data showed that L4080 source leaves were enriched in amino acids compared to the WT, and at 49 DPA, fruit had 25% greater mass, higher sucrose, and increased yield (25%; p < 0.05) compared to the WT. An Affymetrix cDNA array analysis suggested that only 0.39% of the 9000 cDNAs were altered by 1.5-fold (p < 0.01) in L4080 source leaves. 14C-labeling of fruit disks identified potential differences in 14-DPA fruit metabolism suggesting that post-transcriptional regulation was important. We conclude that AtzDof1.3 and the germplasm derived therefrom, should be investigated for their ‘climate-change adaptive’ potential.
MeSH term(s)	Amino Acids/metabolism ; Arabidopsis/metabolism ; Carbon/metabolism ; Carbon Dioxide/metabolism ; DNA/metabolism ; Ectopic Gene Expression ; Gene Expression Regulation, Plant ; Solanum lycopersicum/metabolism ; Nitrogen/metabolism ; Plant Leaves/genetics ; Plant Leaves/metabolism ; Plants, Genetically Modified/genetics ; Plants, Genetically Modified/metabolism ; Starch/metabolism ; Sucrose/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Amino Acids ; Transcription Factors ; Carbon Dioxide (142M471B3J) ; Sucrose (57-50-1) ; Carbon (7440-44-0) ; Starch (9005-25-8) ; DNA (9007-49-2) ; Nitrogen (N762921K75)
Language	English
Publishing date	2022-09-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms231911229
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Article ; Online: Allosteric Modulation of the Faecalibacterium prausnitzii Hepatitis Delta Virus-like Ribozyme by Glucosamine 6-Phosphate: The Substrate of the Adjacent Gene Product.

Passalacqua, Luiz F M / Jimenez, Randi M / Fong, Jennifer Y / Lupták, Andrej

Biochemistry

2017 Volume 56, Issue 45, Page(s) 6006–6014

Abstract: Self-cleaving ribozymes were discovered 30 years ago and have been found throughout nature, from bacteria to animals, but little is known about their biological functions and regulation, particularly how cofactors and metabolites alter their activity. A ... ...

Abstract	Self-cleaving ribozymes were discovered 30 years ago and have been found throughout nature, from bacteria to animals, but little is known about their biological functions and regulation, particularly how cofactors and metabolites alter their activity. A hepatitis delta virus-like self-cleaving ribozyme maps upstream of a phosphoglucosamine mutase (glmM) open reading frame in the genome of the human gut bacterium Faecalibacterium prausnitzii. The presence of a ribozyme in the untranslated region of glmM suggests a regulation mechanism of gene expression. In the bacterial hexosamine biosynthesis pathway, the enzyme glmM catalyzes the isomerization of glucosamine 6-phosphate into glucosamine 1-phosphate. In this study, we investigated the effect of these metabolites on the co-transcriptional self-cleavage rate of the ribozyme. Our results suggest that glucosamine 6-phosphate, but not glucosamine 1-phosphate, is an allosteric ligand that increases the self-cleavage rate of drz-Fpra-1, providing the first known example of allosteric modulation of a self-cleaving ribozyme by the substrate of the adjacent gene product. Given that the ribozyme is activated by the glmM substrate, but not the product, this allosteric modulation may represent a potential feed-forward mechanism of gene expression regulation in bacteria.
Language	English
Publishing date	2017-11-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.7b00879
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Article ; Online: National Cancer Institute Smoking Cessation at Lung Examination Trials Brief Report: Baseline Characteristics and Comparison With the U.S. General Population of Lung Cancer Screening-Eligible Patients.

Meza, Rafael / Jeon, Jihyoun / Jimenez-Mendoza, Evelyn / Mok, Yoonseo / Cao, Pianpian / Foley, Kristie L / Chiles, Caroline / Ostroff, Jamie S / Cinciripini, Paul M / Minnix, Jennifer / Rigotti, Nancy A / Haas, Jennifer S / Taylor, Kathryn / Williams, Randi M / Toll, Benjamin A / Joseph, Anne M

JTO clinical and research reports

2022 Volume 3, Issue 7, Page(s) 100352

Abstract: Introduction: The National Cancer Institute Smoking Cessation at Lung Examination (SCALE) Collaboration includes eight clinical trials testing smoking cessation interventions delivered with lung cancer screening (LCS). This investigation compared pooled ...

Abstract	Introduction: The National Cancer Institute Smoking Cessation at Lung Examination (SCALE) Collaboration includes eight clinical trials testing smoking cessation interventions delivered with lung cancer screening (LCS). This investigation compared pooled participant baseline demographic and smoking characteristics of seven SCALE trials to LCS-eligible smokers in three U.S. nationally representative surveys. Methods: Baseline variables (age, sex, race, ethnicity, education, income, cigarettes per day, and time to the first cigarette) from 3614 smokers enrolled in SCALE trials as of September 2020 were compared with pooled data from the Tobacco Use Supplement-Current Population Survey (2018-2019), National Health Interview Survey (2017-2018), and Population Assessment of Tobacco and Health (wave 4, 2016-2017) using the U.S. Preventive Services Task Force 2013 (N = 4803) and 2021 (N = 8604) LCS eligibility criteria. Results: SCALE participants have similar average age as the U.S. LCS-eligible smokers using the 2013 criteria but are 2.8 years older using the 2021 criteria ( Conclusions: SCALE participants smoke slightly less than the LCS-eligible smokers in the general population, perhaps related to socioeconomic status or race. Other demographic variables reveal small but statistically significant differences, likely of limited clinical relevance with respect to tobacco treatment outcomes. SCALE trial results should be applicable to LCS-eligible smokers from the U.S. population.
Language	English
Publishing date	2022-06-03
Publishing country	United States
Document type	Journal Article
ISSN	2666-3643
ISSN (online)	2666-3643
DOI	10.1016/j.jtocrr.2022.100352
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Article ; Online: Structure-based search and in vitro analysis of self-cleaving ribozymes.

Jimenez, Randi M / Lupták, Andrej

Methods in molecular biology (Clifton, N.J.)

2012 Volume 848, Page(s) 131–143

Abstract: Detecting functional RNAs is increasingly accomplished through structure-based searches for patterns of conserved secondary structure. With large amounts of new sequencing data becoming available, there is a greater demand for efficient methods of ... ...

Abstract	Detecting functional RNAs is increasingly accomplished through structure-based searches for patterns of conserved secondary structure. With large amounts of new sequencing data becoming available, there is a greater demand for efficient methods of identifying new RNAs. Here we present a method of identifying self-cleaving ribozymes and characterizing the in vitro activity.
MeSH term(s)	Computational Biology/methods ; Oligoribonucleotides/chemistry ; Oligoribonucleotides/genetics ; Oligoribonucleotides/metabolism ; RNA, Catalytic/chemistry ; RNA, Catalytic/genetics ; RNA, Catalytic/metabolism ; Software ; Transcription, Genetic ; User-Computer Interface
Chemical Substances	Oligoribonucleotides ; RNA, Catalytic
Language	English
Publishing date	2012
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-61779-545-9_9
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Article: Chemistry and Biology of Self-Cleaving Ribozymes.

Jimenez, Randi M / Polanco, Julio A / Lupták, Andrej

Trends in biochemical sciences

2015 Volume 40, Issue 11, Page(s) 648–661

Abstract: Self-cleaving ribozymes were discovered 30 years ago, but their biological distribution and catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a distinct structure, with unique active sites accelerating the same ... ...

Abstract	Self-cleaving ribozymes were discovered 30 years ago, but their biological distribution and catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a distinct structure, with unique active sites accelerating the same transesterification reaction across the families. Biochemical studies show that general acid-base catalysis is the most common mechanism of self-cleavage, but metal ions and metabolites can be used as cofactors. Ribozymes have been discovered in highly diverse genomic contexts throughout nature, from viroids to vertebrates. Their biological roles include self-scission during rolling-circle replication of RNA genomes, co-transcriptional processing of retrotransposons, and metabolite-dependent gene expression regulation in bacteria. Other examples, including highly conserved mammalian ribozymes, suggest that many new biological roles are yet to be discovered.
MeSH term(s)	Animals ; Hydrolysis ; RNA, Catalytic/metabolism
Chemical Substances	RNA, Catalytic
Language	English
Publishing date	2015-11
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	194216-5
ISSN	1362-4326 ; 0968-0004 ; 0376-5067
ISSN (online)	1362-4326
ISSN	0968-0004 ; 0376-5067
DOI	10.1016/j.tibs.2015.09.001
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Article ; Online: Synthesis and polymerase activity of a fluorescent cytidine TNA triphosphate analogue.

Mei, Hui / Shi, Changhua / Jimenez, Randi M / Wang, Yajun / Kardouh, Miramar / Chaput, John C

Nucleic acids research

2017 Volume 45, Issue 10, Page(s) 5629–5638

Abstract: Threose nucleic acid (TNA) is an artificial genetic polymer capable of undergoing Darwinian evolution to produce aptamers with affinity to specific targets. This property, coupled with a backbone structure that is refractory to nuclease digestion, makes ... ...

Abstract	Threose nucleic acid (TNA) is an artificial genetic polymer capable of undergoing Darwinian evolution to produce aptamers with affinity to specific targets. This property, coupled with a backbone structure that is refractory to nuclease digestion, makes TNA an attractive biopolymer system for diagnostic and therapeutic applications. Expanding the chemical diversity of TNA beyond the natural bases would enable the development of functional TNA molecules with enhanced physiochemical properties. Here, we describe the synthesis and polymerase activity of a fluorescent cytidine TNA triphosphate analogue (1,3-diaza-2-oxo-phenothiazine, tCfTP) that maintains Watson-Crick base pairing with guanine. Polymerase-mediated primer-extension assays reveal that tCfTP is efficiently added to the growing end of a TNA primer. Detailed kinetic assays indicate that tCfTP and tCTP have comparable rates for the first nucleotide incorporation step (kobs1). However, addition of the second nucleotide (kobs2) is 700-fold faster for tCfTP than tCTP due the increased effects of base stacking. Last, we found that TNA replication using tCfTP in place of tCTP exhibits 98.4% overall fidelity for the combined process of TNA transcription and reverse transcription. Together, these results expand the chemical diversity of enzymatically generated TNA molecules to include a hydrophobic base analogue with strong fluorescent properties that is compatible with in vitro selection.
MeSH term(s)	Base Pairing ; Biomimetic Materials/chemistry ; Fluorescence ; Guanine/chemistry ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Nucleic Acids/chemistry ; Nucleic Acids/genetics ; Phenothiazines/chemistry ; Polyphosphates/chemistry ; Tetroses/chemistry ; Time Factors ; Transcription, Genetic
Chemical Substances	1,3-diaza-2-oxophenothiazin-3-ylacetic acid ; Nucleic Acids ; Phenothiazines ; Polyphosphates ; Tetroses ; Guanine (5Z93L87A1R) ; triphosphoric acid (NU43IAG5BC) ; erythrose (X3EI0WE8Q4)
Language	English
Publishing date	2017-06-02
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkx368
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Article: Allosteric Modulation of the Faecalibacterium prausnitzii Hepatitis Delta Virus-like Ribozyme by Glucosamine 6-Phosphate: The Substrate of the Adjacent Gene Product

Passalacqua, Luiz F. M / Andrej Lupták / Jennifer Y. Fong / Randi M. Jimenez

Biochemistry. 2017 Nov. 14, v. 56, no. 45

2017

Abstract	Self-cleaving ribozymes were discovered 30 years ago and have been found throughout nature, from bacteria to animals, but little is known about their biological functions and regulation, particularly how cofactors and metabolites alter their activity. A hepatitis delta virus-like self-cleaving ribozyme maps upstream of a phosphoglucosamine mutase (glmM) open reading frame in the genome of the human gut bacterium Faecalibacterium prausnitzii. The presence of a ribozyme in the untranslated region of glmM suggests a regulation mechanism of gene expression. In the bacterial hexosamine biosynthesis pathway, the enzyme glmM catalyzes the isomerization of glucosamine 6-phosphate into glucosamine 1-phosphate. In this study, we investigated the effect of these metabolites on the co-transcriptional self-cleavage rate of the ribozyme. Our results suggest that glucosamine 6-phosphate, but not glucosamine 1-phosphate, is an allosteric ligand that increases the self-cleavage rate of drz-Fpra-1, providing the first known example of allosteric modulation of a self-cleaving ribozyme by the substrate of the adjacent gene product. Given that the ribozyme is activated by the glmM substrate, but not the product, this allosteric modulation may represent a potential feed-forward mechanism of gene expression regulation in bacteria.
Keywords	bacteria ; biosynthesis ; hepatitis ; humans ; intestinal microorganisms ; isomerization ; ligands ; metabolites ; open reading frames ; ribozymes
Language	English
Dates of publication	2017-1114
Size	p. 6006-6014.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.7b00879
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Article ; Online: Synthesis and Evolution of a Threose Nucleic Acid Aptamer Bearing 7-Deaza-7-Substituted Guanosine Residues.

Mei, Hui / Liao, Jen-Yu / Jimenez, Randi M / Wang, Yajun / Bala, Saikat / McCloskey, Cailen / Switzer, Christopher / Chaput, John C

Journal of the American Chemical Society

2018 Volume 140, Issue 17, Page(s) 5706–5713

Abstract: In vitro selection experiments carried out on artificial genetic polymers require robust and faithful methods for copying genetic information back and forth between DNA and xeno-nucleic acids (XNA). Previously, we have shown that Kod-RI, an engineered ... ...

Abstract	In vitro selection experiments carried out on artificial genetic polymers require robust and faithful methods for copying genetic information back and forth between DNA and xeno-nucleic acids (XNA). Previously, we have shown that Kod-RI, an engineered polymerase developed to transcribe DNA templates into threose nucleic acid (TNA), can function with high fidelity in the absence of manganese ions. However, the transcriptional efficiency of this enzyme diminishes greatly when individual templates are replaced with libraries of DNA sequences, indicating that manganese ions are still required for in vitro selection. Unfortunately, the presence of manganese ions in the transcription mixture leads to the misincorporation of tGTP nucleotides opposite dG residues in the templating strand, which are detected as G-to-C transversions when the TNA is reverse transcribed back into DNA. Here we report the synthesis and fidelity of TNA replication using 7-deaza-7-modified guanosine base analogues in the DNA template and incoming TNA nucleoside triphosphate. Our findings reveal that tGTP misincorporation occurs via a Hoogsteen base pair in which the incoming tGTP residue adopts a syn conformation with respect to the sugar. Substitution of tGTP for 7-deaza-7-phenyl tGTP enabled the synthesis of TNA polymers with >99% overall fidelity. A TNA library containing the 7-deaza-7-phenyl guanine analogue was used to evolve a biologically stable TNA aptamer that binds to HIV reverse transcriptase with low nanomolar affinity.
Language	English
Publishing date	2018--02
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.7b13031
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Article ; Online: RNA motif search with data-driven element ordering.

Rampášek, Ladislav / Jimenez, Randi M / Lupták, Andrej / Vinař, Tomáš / Brejová, Broňa

BMC bioinformatics

2016 Volume 17, Issue 1, Page(s) 216

Abstract: Background: In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is ...

Abstract	Background: In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. Results: We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. Conclusions: We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .
MeSH term(s)	Algorithms ; Entropy ; Humans ; Nucleotide Motifs ; RNA/chemistry ; Sequence Analysis, RNA/methods
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2016-05-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-016-1074-x
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Article: Chemistry and Biology of Self-Cleaving Ribozymes

Jimenez, Randi M / Julio A. Polanco / Andrej LuptÃ¡k

Trends in biochemical sciences. 2015 Nov., v. 40

2015

Abstract	Self-cleaving ribozymes were discovered 30 years ago, but their biological distribution and catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a distinct structure, with unique active sites accelerating the same transesterification reaction across the families. Biochemical studies show that general acid-base catalysis is the most common mechanism of self-cleavage, but metal ions and metabolites can be used as cofactors. Ribozymes have been discovered in highly diverse genomic contexts throughout nature, from viroids to vertebrates. Their biological roles include self-scission during rolling-circle replication of RNA genomes, co-transcriptional processing of retrotransposons, and metabolite-dependent gene expression regulation in bacteria. Other examples, including highly conserved mammalian ribozymes, suggest that many new biological roles are yet to be discovered.
Keywords	RNA replication ; active sites ; bacteria ; catalytic activity ; gene expression regulation ; genome ; mammals ; metabolites ; metal ions ; retrotransposons ; transesterification ; viroids
Language	English
Dates of publication	2015-11
Size	p. 648-661.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	194220-7
ISSN	0968-0004 ; 0376-5067
ISSN	0968-0004 ; 0376-5067
DOI	10.1016/j.tibs.2015.09.001
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