scholarly journals Interspecies transfer of syntenic RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture

2022 ◽  
Author(s):  
Josh Strable ◽  
Erica Unger-Wallace ◽  
Alejandro Aragón-Raygoza ◽  
Sarah Briggs ◽  
Erik Vollbrecht
Keyword(s):  
Gene Transfer ◽  
Upstream Region ◽  
Coding Region ◽  
Inflorescence Architecture ◽  
Inflorescence Development ◽  
Temporal Regulation ◽  
Functional Conservation ◽  
Inflorescence Morphology ◽  
Key Factor ◽  
Flanking Sequences

Grass inflorescences support floral structures that each bear a single grain, where variation in branch architecture directly impacts yield. The maize RAMOSA1 (ZmRA1) transcription factor acts as a key regulator of inflorescence development by imposing branch meristem determinacy. Here, we show RA1 transcripts accumulate in boundary domains adjacent to spikelet meristems in Sorghum bicolor (Sb) and Setaria viridis (Sv) inflorescences similar as in the developing maize tassel and ear. To evaluate functional conservation of syntenic RA1 orthologs and promoter cis sequences in maize, sorghum and setaria, we utilized interspecies gene transfer and assayed genetic complementation in a common inbred background by quantifying recovery of normal branching in highly ramified ra1-R mutants. A ZmRA1 transgene that includes endogenous upstream and downstream flanking sequences recovered normal tassel and ear branching in ra1-R. Interspecies expression of two transgene variants of the SbRA1 locus, modeled as the entire endogenous tandem duplication or just the non-frameshifted downstream copy, complemented ra1-R branching defects and induced novel fasciation and branch patterns. The SvRA1 locus lacks conserved, upstream noncoding cis sequences found in maize and sorghum; interspecies expression of an SvRA1 transgene did not or only partially recovered normal inflorescence forms. Driving expression of the SvRA1 coding region by the ZmRA1 upstream region, however, recovered normal inflorescence morphology in ra1-R. These data leveraging interspecies gene transfer suggest that cis-encoded temporal regulation of RA1 expression is a key factor in modulating branch meristem determinacy that ultimately impacts grass inflorescence architecture.

scholarly journals Roles of Horizontal Gene Transfer and Gene Integration in Evolution of 1,3-Dichloropropene- and 1,2-Dibromoethane-Degradative Pathways

2000 ◽  
Vol 182 (8) ◽  
pp. 2191-2199 ◽  
Author(s):  
Gerrit J. Poelarends ◽  
Leonid A. Kulakov ◽  
Michael J. Larkin ◽  
Johan E. T. van Hylckama Vlieg ◽  
Dick B. Janssen
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Regulatory Protein ◽  
Constitutive Expression ◽  
Haloalkane Dehalogenase ◽  
Coding Region ◽  
Integrase Gene ◽  
Gene Acquisition ◽  
Degrading Bacteria ◽  
Flanking Sequences

ABSTRACT The haloalkane-degrading bacteria Rhodococcus rhodochrous NCIMB13064, Pseudomonas pavonaceae 170, and Mycobacterium sp. strain GP1 share a highly conserved haloalkane dehalogenase gene (dhaA). Here, we describe the extent of the conserved dhaA segments in these three phylogenetically distinct bacteria and an analysis of their flanking sequences. The dhaA gene of the 1-chlorobutane-degrading strain NCIMB13064 was found to reside within a 1-chlorobutane catabolic gene cluster, which also encodes a putative invertase (invA), a regulatory protein (dhaR), an alcohol dehydrogenase (adhA), and an aldehyde dehydrogenase (aldA). The latter two enzymes may catalyze the oxidative conversion of n-butanol, the hydrolytic product of 1-chlorobutane, to n-butyric acid, a growth substrate for many bacteria. The activity of the dhaR gene product was analyzed in Pseudomonas sp. strain GJ1, in which it appeared to function as a repressor of dhaA expression. The 1,2-dibromoethane-degrading strain GP1 contained a conserved DNA segment of 2.7 kb, which included dhaR, dhaA, and part of invA. A 12-nucleotide deletion indhaR led to constitutive expression of dhaA in strain GP1, in contrast to the inducible expression of dhaAin strain NCIMB13064. The 1,3-dichloropropene-degrading strain 170 possessed a conserved DNA segment of 1.3 kb harboring little more than the coding region of the dhaA gene. In strains 170 and GP1, a putative integrase gene was found next to the conserveddhaA segment, which suggests that integration events were responsible for the acquisition of these DNA segments. The data indicate that horizontal gene transfer and integrase-dependent gene acquisition were the key mechanisms for the evolution of catabolic pathways for the man-made chemicals 1,3-dichloropropene and 1,2-dibromoethane.

Delimiting regulatory sequences of the Drosophila melanogaster Ddc gene

1986 ◽  
Vol 6 (12) ◽  
pp. 4548-4557
Author(s):  
J Hirsh ◽  
B A Morgan ◽  
S B Scholnick
Keyword(s):  
Drosophila Melanogaster ◽  
Germ Line ◽  
Regulatory Elements ◽  
P Element ◽  
Developmental Expression ◽  
Upstream Region ◽  
Regulatory Sequences ◽  
Flanking Sequences

We delimited sequences necessary for in vivo expression of the Drosophila melanogaster dopa decarboxylase gene Ddc. The expression of in vitro-altered genes was assayed following germ line integration via P-element vectors. Sequences between -209 and -24 were necessary for normally regulated expression, although genes lacking these sequences could be expressed at 10 to 50% of wild-type levels at specific developmental times. These genes showed components of normal developmental expression, which suggests that they retain some regulatory elements. All Ddc genes lacking the normal immediate 5'-flanking sequences were grossly deficient in larval central nervous system expression. Thus, this upstream region must contain at least one element necessary for this expression. A mutated Ddc gene without a normal TATA boxlike sequence used the normal RNA start points, indicating that this sequences is not required for start point specificity.

Identification of upstream regulatory regions in the heart-expressed homeobox gene Nkx2-5

Development ◽  
1999 ◽  
Vol 126 (4) ◽  
pp. 839-849 ◽  
Author(s):  
J.M. Reecy ◽  
X. Li ◽  
M. Yamada ◽  
F.J. DeMayo ◽  
C.S. Newman ◽  
...  
Keyword(s):  
Homeobox Gene ◽  
Protein Isoforms ◽  
Proximal Promoter ◽  
Coding Region ◽  
Heart Tube ◽  
Regulatory Regions ◽  
Regulatory Domains ◽  
Exon 1 ◽  
Flanking Sequences ◽  
Upstream Exon

Nkx2-5 marks the earliest recognizable cardiac progenitor cells, and is activated in response to inductive signals involved in lineage specification. Nkx2-5 is also expressed in the developing foregut, thyroid, spleen, stomach and tongue. One approach to elucidate the signals involved in cardiogenesis was to examine the transcriptional regulation of early lineage markers such as Nkx2-5. We generated F0 transgenic mice, which carry Nkx2-5 flanking sequences linked to a lacZ reporter gene. We identified multiple regulatory regions located within the proximal 10.7 kb of the Nkx2-5 gene. In addition to a proximal promoter, we identified a second promoter and a novel upstream exon that could participate in the regulation of Nkx2-5 transcription. Although used rarely in normal development, this novel exon could be spliced into the Nkx2-5 coding region in several ways, thereby potentially creating novel Nkx2-5 protein isoforms, whose transcriptional activity is greatly diminished as compared to wild-type Nkx2-5. An enhancer that directs expression in pharynx, spleen, thyroid and stomach was identified within 3.5 kb of exon 1 between the coding exon 1 and the novel upstream exon 1a. Two or more enhancers upstream of exon 1a were capable of driving expression in the cardiac crescent, throughout the myocardium of the early heart tube, then in the outflow tract and right ventricle of the looped heart tube. A negative element was also located upstream of exon1a, which interacted in complex ways with enhancers to direct correct spatial expression. In addition, potential autoregulatory elements can be cooperatively stimulated by Nkx2-5 and GATA-4. Our results demonstrate that a complex suite of interacting regulatory domains regulate Nkx2-5 transcription. Dissection of these elements should reveal essential features of cardiac induction and positive and negative signaling within the cardiac field.

LEU3 of Saccharomyces cerevisiae activates multiple genes for branched-chain amino acid biosynthesis by binding to a common decanucleotide core sequence

1988 ◽  
Vol 8 (7) ◽  
pp. 2690-2697
Author(s):  
P Friden ◽  
P Schimmel
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Upstream Region ◽  
Promoter Regions ◽  
Sequence Element ◽  
The Core ◽  
Core Sequence ◽  
Flanking Sequences ◽  
Branched Chain

LEU3 of Saccharomyces cerevisiae encodes an 886-amino-acid polypeptide that regulates transcription of a group of genes involved in leucine biosynthesis and has been shown to bind specifically to a 114-base-pair DNA fragment of the LEU2 upstream region (P. Friden and P. Schimmel, Mol. Cell. Biol. 7:2707-2717, 1987). We show here that, in addition to LEU2, LEU3 binds in vitro to sequences in the promoter regions of LEU1, LEU4, ILV2, and, by inference, ILV5. The largely conserved decanucleotide core sequence shared by the binding sites in these genes is CCGGNNCCGG. Methylation interference footprinting experiments show that LEU3 makes symmetrical contacts with the conserved bases that lie in the major groove. Synthetic oligonucleotides (19 to 29 base pairs) which contain the core decanucleotide and flanking sequences of LEU1, LEU2, LEU4, and ILV2 have individually been placed upstream of a LEU3-insensitive test promoter. The expression of each construction is activated by LEU3, although the degree of activation varies considerably according to the specific oligonucleotide which is introduced. A promoter construction with substitutions in the core sequence remains LEU3 insensitive, however. One of the oligonucleotides (based on a LEU2 sequence) was also tested and shown to confer leucine-sensitive expression on the test promoter. The results demonstrate that only a short sequence element is necessary for LEU3-dependent promoter binding and activation and provide direct evidence for an expanded repertoire of genes that are activated by LEU3.

scholarly journals Identification of somatostatin receptor type 5 gene polymorphisms associated with acromegaly

2011 ◽  
Vol 165 (4) ◽  
pp. 517-525 ◽  
Author(s):  
Darja Ciganoka ◽  
Inga Balcere ◽  
Ivo Kapa ◽  
Raitis Peculis ◽  
Andra Valtere ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Somatostatin Receptor ◽  
Strong Association ◽  
Upstream Region ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Additional Group ◽  
Unstandardized Regression Coefficient ◽  
Design And Methods

ObjectiveThe aim of this study was to characterize the genetic variance of somatostatin receptor 5 (SSTR5) and investigate the possible correlation of such variants with acromegaly risk and different disease characteristics.Design and methodsThe SSTR5 gene coding region and 2000 bp upstream region was sequenced in 48 patients with acromegaly and 96 control subjects. Further, three single nucleotide polymorphisms (SNPs) were analyzed in the same group of acromegaly patients and in an additional group of 475 age- and sex-matched controls.ResultsIn total, 19 SNPs were identified in the SSTR5 gene locus by direct sequencing. Three SNPs (rs34037914, rs169068, and rs642249) were significantly associated with the presence of acromegaly using the initial controls. The allele frequencies were significantly (P<0.01) different between the acromegaly patients and the additional large control group. rs34037914 and rs642249 remained significantly associated with acromegaly after Bonferroni correction and permutation tests (odds ratio (OR)=3.38; 95% confidence interval (CI), 1.78–6.42; P=0.00016 and OR=2.41; 95% CI, 1.41–4.13; P=0.0014 respectively). Haplotype reconstruction revealed two possible risk haplotypes determined by rs34037914 (633T) and rs642249 (1044A) alleles. Both haplotypes were found in significantly higher frequency in acromegaly patients compared with controls (P<0.001). In addition, the 663T allele was significantly associated with a younger age of acromegaly diagnosis (unstandardized regression coefficient β=−10.4; P=0.002), increased body mass index (β=4.1; P=0.004), higher number of adenoma resection (P<0.001) and lack of observable tumor shrinkage after somatostatin analog treatment (P=0.014).ConclusionsOur results demonstrate a previously undetected strong association of two SSTR5 SNPs with acromegaly. The data also suggest a possible involvement of SSTR5 variants in decreased suppression of GH production and increased tumor proliferation.

scholarly journals Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Mao-Sheng Chen ◽  
Mei-Li Zhao ◽  
Gui-Juan Wang ◽  
Hui-Ying He ◽  
Xue Bai ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Metabolic Pathway ◽  
Jatropha Curcas ◽  
Woody Plant ◽  
Regulatory Mechanism ◽  
Adenosine Kinase ◽  
Inflorescence Architecture ◽  
Inflorescence Development ◽  
Order Branch ◽  
Important Regulator

Abstract Background In higher plants, inflorescence architecture is an important agronomic trait directly determining seed yield. However, little information is available on the regulatory mechanism of inflorescence development in perennial woody plants. Based on two inflorescence branching mutants, we investigated the transcriptome differences in inflorescence buds between two mutants and wild-type (WT) plants by RNA-Seq to identify the genes and regulatory networks controlling inflorescence architecture in Jatropha curcas L., a perennial woody plant belonging to Euphorbiaceae. Results Two inflorescence branching mutants were identified in germplasm collection of Jatropha. The duo xiao hua (dxh) mutant has a seven-order branch inflorescence, and the gynoecy (g) mutant has a three-order branch inflorescence, while WT Jatropha has predominantly four-order branch inflorescence, occasionally the three- or five-order branch inflorescences in fields. Using weighted gene correlation network analysis (WGCNA), we identified several hub genes involved in the cytokinin metabolic pathway from modules highly associated with inflorescence phenotypes. Among them, Jatropha ADENOSINE KINASE 2 (JcADK2), ADENINE PHOSPHORIBOSYL TRANSFERASE 1 (JcAPT1), CYTOKININ OXIDASE 3 (JcCKX3), ISOPENTENYLTRANSFERASE 5 (JcIPT5), LONELY GUY 3 (JcLOG3) and JcLOG5 may participate in cytokinin metabolic pathway in Jatropha. Consistently, exogenous application of cytokinin (6-benzyladenine, 6-BA) on inflorescence buds induced high-branch inflorescence phenotype in both low-branch inflorescence mutant (g) and WT plants. These results suggested that cytokinin is an important regulator in controlling inflorescence branching in Jatropha. In addition, comparative transcriptome analysis showed that Arabidopsis homologous genes Jatropha AGAMOUS-LIKE 6 (JcAGL6), JcAGL24, FRUITFUL (JcFUL), LEAFY (JcLFY), SEPALLATAs (JcSEPs), TERMINAL FLOWER 1 (JcTFL1), and WUSCHEL-RELATED HOMEOBOX 3 (JcWOX3), were differentially expressed in inflorescence buds between dxh and g mutants and WT plants, indicating that they may participate in inflorescence development in Jatropha. The expression of JcTFL1 was downregulated, while the expression of JcLFY and JcAP1 were upregulated in inflorescences in low-branch g mutant. Conclusions Cytokinin is an important regulator in controlling inflorescence branching in Jatropha. The regulation of inflorescence architecture by the genes involved in floral development, including TFL1, LFY and AP1, may be conservative in Jatropha and Arabidopsis. Our results provide helpful information for elucidating the regulatory mechanism of inflorescence architecture in Jatropha.

scholarly journals Analysis of a lin-42/period Null Allele Implicates All Three Isoforms in Regulation of Caenorhabditis elegans Molting and Developmental Timing

2016 ◽  
Vol 6 (12) ◽  
pp. 4077-4086 ◽  
Author(s):  
Theresa L B Edelman ◽  
Katherine A McCulloch ◽  
Angela Barr ◽  
Christian Frøkjær-Jensen ◽  
Erik M Jorgensen ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Null Allele ◽  
Postembryonic Development ◽  
Developmental Timing ◽  
Critical Element ◽  
Coding Region ◽  
Protein Coding ◽  
Temporal Regulation ◽  
Larval Stages ◽  
Hypomorphic Alleles

Abstract The Caenorhabditis elegans heterochronic gene pathway regulates the relative timing of events during postembryonic development. lin-42, the worm homolog of the circadian clock gene, period, is a critical element of this pathway. lin-42 function has been defined by a set of hypomorphic alleles that cause precocious phenotypes, in which later developmental events, such as the terminal differentiation of hypodermal cells, occur too early. A subset of alleles also reveals a significant role for lin-42 in molting; larval stages are lengthened and ecdysis often fails in these mutant animals. lin-42 is a complex locus, encoding overlapping and nonoverlapping isoforms. Although existing alleles that affect subsets of isoforms have illuminated important and distinct roles for this gene in developmental timing, molting, and the decision to enter the alternative dauer state, it is essential to have a null allele to understand all of the roles of lin-42 and its individual isoforms. To remedy this problem and discover the null phenotype, we engineered an allele that deletes the entire lin-42 protein-coding region. lin-42 null mutants are homozygously viable, but have more severe phenotypes than observed in previously characterized hypomorphic alleles. We also provide additional evidence for this conclusion by using the null allele as a base for reintroducing different isoforms, showing that each isoform can provide heterochronic and molting pathway activities. Transcript levels of the nonoverlapping isoforms appear to be under coordinate temporal regulation, despite being driven by independent promoters. The lin-42 null allele will continue to be an important tool for dissecting the functions of lin-42 in molting and developmental timing.

A possible role for D8/PSF-A-like sequences in lactotroph versus somatotroph expression of the human prolactin gene

1996 ◽  
Vol 149 (3) ◽  
pp. 473-483 ◽  
Author(s):  
V Leite ◽  
E A Cardoso ◽  
M E Bock ◽  
L G Sobrinho ◽  
P A Cattini
Keyword(s):  
Hela Cells ◽  
Upstream Region ◽  
Internal Deletion ◽  
Mobility Shift ◽  
Significant Stimulation ◽  
Prolactin Gene ◽  
Flanking Sequences ◽  
Promoter Specificity ◽  
Repressor Activity ◽  
Prl Gene

Abstract The transcription factor GHF-1/Pit-1 is essential for the expression of GH and prolactin (PRL) by somatotrophs and lactotrophs respectively. However, PRL is not expressed in mature somatotrophs despite the presence of GHF-1/Pit-1. A possible mechanism is the presence of a somatotroph-specific repressor in the 5′-flanking sequences of the PRL gene. The region −3500/−1750 of the human (h) PRL gene is associated with negative regulatory activity and contains an element, designated D8, that resembles repressor PSF-A sequences which are located in the distal upstream region of placental members of the human GH family. An internal deletion of D8 sequences resulted in a significant stimulation of promoter activity in somatotroph GC (P<0·005) and somatolactotroph-like GH3 and GH4C1 cells (P<0·05), but not lactotroph-like 235–1 cells after gene transfer. However, D8 binding was observed by nuclease protection with lactotroph- as well as somatotroph-like cell nuclear protein. Although proteins that bind to the D8 element appear ubiquitous, this element does yield tissuespecific complexes in mobility shift assays. Further, competition studies do not suggest an interaction between GHF-1/Pit-1 and D8 proteins. The hPRL D8 element was inserted upstream of a thymidine kinase promoter and used to transfect pituitary and non-pituitary HeLa cells, to assess intrinsic repressor activity and/or promoter specificity. Although no repression was observed, a significant ninefold increase in expression was observed in HeLa cells (P<0·001) which was at least twofold greater than observed in any of the pituitary cell lines tested. These results implicate D8 in the somatotroph-specific repression of hPRL; however, they also suggest that D8 can act as a stimulator as well as a repressor, depending on the interaction of a ubiquitous D8 factor forming promoter and cell-specific complexes with other elements/factors. Journal of Endocrinology (1996) 149, 473–483

scholarly journals SISTER OF TM3 activates FRUITFULL1 to regulate inflorescence branching in tomato

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Xiaotian Wang ◽  
Zhiqiang Liu ◽  
Shuai Sun ◽  
Jianxin Wu ◽  
Ren Li ◽  
...  
Keyword(s):  
Regulatory Mechanism ◽  
Luciferase Reporter ◽  
Crop Breeding ◽  
Inflorescence Architecture ◽  
Inflorescence Development ◽  
Branching Structures ◽  
Qpcr Analysis ◽  
Genetic Mechanisms ◽  
Reporter Assays ◽  
Selection For

AbstractSelection for favorable inflorescence architecture to improve yield is one of the crucial targets in crop breeding. Different tomato varieties require distinct inflorescence-branching structures to enhance productivity. While a few important genes for tomato inflorescence-branching development have been identified, the regulatory mechanism underlying inflorescence branching is still unclear. Here, we confirmed that SISTER OF TM3 (STM3), a homolog of Arabidopsis SOC1, is a major positive regulatory factor of tomato inflorescence architecture by map-based cloning. High expression levels of STM3 underlie the highly inflorescence-branching phenotype in ST024. STM3 is expressed in both vegetative and reproductive meristematic tissues and in leaf primordia and leaves, indicative of its function in flowering time and inflorescence-branching development. Transcriptome analysis shows that several floral development-related genes are affected by STM3 mutation. Among them, FRUITFULL1 (FUL1) is downregulated in stm3cr mutants, and its promoter is bound by STM3 by ChIP-qPCR analysis. EMSA and dual-luciferase reporter assays further confirmed that STM3 could directly bind the promoter region to activate FUL1 expression. Mutation of FUL1 could partially restore inflorescence-branching phenotypes caused by high STM3 expression in ST024. Our findings provide insights into the molecular and genetic mechanisms underlying inflorescence development in tomato.

scholarly journals Upstream region of OprD mutations in imipenem-resistant and imipenem-sensitive Pseudomonas aeruginosa isolates

2021 ◽  
Author(s):  
Masoumeh Kiani ◽  
Akram Astani ◽  
Nahid Rezaei Khozani ◽  
Mansoor Khaledi ◽  
Hamed Afkhami ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Point Mutations ◽  
Genomic Region ◽  
Upstream Region ◽  
Diffusion Method ◽  
Base Substitution ◽  
Coding Region ◽  
Biochemical Tests ◽  
Disk Diffusion Method ◽  
Study Results

Abstract The current study was aimed at investigating the prevalence of the mutations upstream of the oprD coding region and its promoters among imipenem-resistant and sensitive Pseudomonas aeruginosa isolated from educational hospitals in Yazd City, Iran. All isolates were identified by the conventional biochemical tests. Then, the antibiotic resistance of these isolates was determined using the disk diffusion method according to the CLSI guidelines. Also, the E.test was performed to determine the minimum inhibitory concentrations (MIC) of imipenem. The mutations of this gene were recognized by the amplification of this region and subsequently sequenced. Sequencing of the genomic region upstream of oprD these regions were done in the 29 clinical strains. Statistical analysis was done by the statistical software SPSS-18. Seventy (77.7%) of isolates had MIC ≥ 16 and were resistant to imipenem. Mutations of the upstream of the oprD gene and its promoters were seen in 25 (86.2%) isolates and 4 isolates had no mutation. One isolate had a base substitution A→Cat nt 25 in the coding region and this isolate had a point mutation leading to an amino acid change at positions 9 (I→L). Our study results indicated that none of the strains had mutation in Shine-Dalgarno and the point mutations were the most common mutations upstream of the oprD coding region among P. aeruginosa isolates. Mutations were observed in imipenem-resistant isolates and it seems this mechanism is effective in resistance of isolates to imipenem and this confirmed that the indiscriminate use of antibiotic should be controlled.

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