scholarly journals Evolution of Anthocyanin Biosynthesis in Maize Kernels: The Role of Regulatory and Enzymatic Loci

Genetics ◽  
1996 ◽  
Vol 143 (3) ◽  
pp. 1395-1407 ◽  
Author(s):  
Michael A Hanson ◽  
Brandon S Gaut ◽  
Adrian O Stec ◽  
Susan I Fuerstenberg ◽  
Major M Goodman ◽  
...  
Keyword(s):  
Protein Function ◽  
Sequence Data ◽  
Anthocyanin Biosynthesis ◽  
Regulatory Protein ◽  
Regulatory Elements ◽  
Kernel Development ◽  
Genetic Tests ◽  
Anthocyanin Pathway ◽  
Regulatory Loci ◽  
Functional Alleles

Abstract Understanding which genes contribute to evolutionary change and the nature of the alterations in them are fundamental challenges in evolution. We analyzed regulatory and enzymatic genes in the maize anthocyanin pathway as related to the evolution of anthocyanin-pigmented kernels in maize from colorless kernels of its progenitor, teosinte. Genetic tests indicate that teosinte possesses functional alleles at all enzymatic loci. At two regulatory loci, most teosintes possess alleles that encode functional proteins, but ones that are not expressed during kernel development and not capable of activating anthocyanin biosynthesis there. We investigated nucleotide polymorphism at one of the regulatory loci, c1. Several observations suggest that c1 has not evolved in a strictly neutral manner, including an exceptionally low level of polymorphism and a biased representation of haplotypes in maize. Curiously, sequence data show that most of our teosinte samples possess a promoter element necessary for the activation of the anthocyanin pathway during kernel development, although genetic tests indicate that teosinte c1 alleles are not active during kernel development. Our analyses suggest that the evolution of the purple kernels resulted from changes in cis regulatory elements at regulatory loci and not changes in either regulatory protein function nor the enzymatic loci.

scholarly journals Gateway cloning and in-planta transformation of drought stress responsive Ecmyb1 gene isolated from Eleusine coracana var.PRM 6107

2021 ◽  
Vol 22 (1) ◽  
pp. 205-211
Author(s):  
Megha Bhatt ◽  
Prafull Salvi ◽  
Pushpa Lohani
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Drought Stress ◽  
Stress Responses ◽  
Anthocyanin Biosynthesis ◽  
Regulatory Protein ◽  
Regulatory Elements ◽  
Growth And Yield ◽  
Yield Potential ◽  
Gateway Cloning

Drought is one of the key abiotic stress that critically influences the crops by restraining their growth and yield potential. Being sessile, plants tackle the detrimental effects of drought stress via modulating the cellular state by changing the gene expression. Such alteration of gene expression is essentially driven by the transcriptional syndicate. Transcription factors (TF) are the key regulatory protein that controls the expression of their target gene by binding to the cis-regulatory elements present in the promoter region. Myb-TFs ubiquitously present in all eukaryotes belong to one of the largest TF family, and play wide array of biological functions in plants including anthocyanin biosynthesis, vasculature system, cell signaling, seed maturation and abiotc stress responses. In the present study the full length Myb TF from Eleusine corocana was subcloned using Gateway cloning system and further transformed into Arabidopsis thaliana through floral dip method. Transgenic Arabidopsis thaliana plants harbouring Ecmyb1 gene were screened and grown in transgenic glasshouse under controlled conditions.

Knockdown of duplicated zebrafishhoxb1genes reveals distinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention

Development ◽  
2002 ◽  
Vol 129 (10) ◽  
pp. 2339-2354 ◽  
Author(s):  
James M. McClintock ◽  
Mazen A. Kheirbek ◽  
Victoria E. Prince
Keyword(s):  
Protein Function ◽  
Cranial Nerve ◽  
Duplicate Gene ◽  
Regulatory Elements ◽  
Duplicate Genes ◽  
Duplicated Genes ◽  
Gene Retention ◽  
Redundant Functions ◽  
Group 1 ◽  
Rhombomere 4

We have used a morpholino-based knockdown approach to investigate the functions of a pair of zebrafish Hox gene duplicates, hoxb1a and hoxb1b, which are expressed during development of the hindbrain. We find that the zebrafish hoxb1 duplicates have equivalent functions to mouse Hoxb1 and its paralogue Hoxa1. Thus, we have revealed a ‘function shuffling’ among genes of paralogue group 1 during the evolution of vertebrates. Like mouse Hoxb1, zebrafish hoxb1a is required for migration of the VIIth cranial nerve branchiomotor neurons from their point of origin in hindbrain rhombomere 4 towards the posterior. By contrast, zebrafish hoxb1b, like mouse Hoxa1, is required for proper segmental organization of rhombomere 4 and the posterior hindbrain. Double knockdown experiments demonstrate that the zebrafish hoxb1 duplicates have partially redundant functions. However, using an RNA rescue approach, we reveal that these duplicated genes do not have interchangeable biochemical functions: only hoxb1a can properly pattern the VIIth cranial nerve. Despite this difference in protein function, we provide evidence that the hoxb1 duplicate genes were initially maintained in the genome because of complementary degenerative mutations in defined cis-regulatory elements.

CBFs Function in Anthocyanin Biosynthesis by Interacting with MYB113 in Eggplant (Solanum melongena L.)

2019 ◽  
Vol 61 (2) ◽  
pp. 416-426 ◽  
Author(s):  
Lu Zhou ◽  
Yongjun He ◽  
Jing Li ◽  
Yang Liu ◽  
Huoying Chen
Keyword(s):  
Low Temperature ◽  
Anthocyanin Biosynthesis ◽  
Solanum Melongena ◽  
Structural Genes ◽  
Cold Response ◽  
Anthocyanin Pathway ◽  
R2r3 Myb ◽  
Dependent Pathway ◽  
Shed Light ◽  
R2r3 Myb Transcription Factors

Abstract Eggplant is rich in anthocyanins. R2R3-MYB transcription factors play a key role in the anthocyanin pathway. Low temperature is vital abiotic stress that affects the anthocyanin biosynthesis in plants. CBFs (C-repeat binding factors) act as central regulators in cold response. In this study, we found that SmCBF1, SmCBF2 and SmCBF3, via their C-terminal, physically interacted with SmMYB113, a key regulator of anthocyanin biosynthesis in eggplant. SmCBF2 and SmCBF3 upregulated the expression of SmCHS and SmDFR via a SmMYB113-dependent pathway. In addition, the transient expression assays demonstrated that co-infiltrating SmCBFs and SmMYB113 significantly improved the contents of anthocyanin and the expression levels of anthocyanin structural genes in tobacco. When SmTT8, a bHLH partner of SmMYB113, coexpressed with SmCBFs and SmMYB113, the anthocyanin contents were significantly enhanced compared with SmCBFs and SmMYB113. Furthermore, overexpression of SmCBF2 and SmCBF3 could facilitate the anthocyanin accumulation under cold conditions in Arabidopsis. Taken together, these results shed light on the functions of SmCBFs and potential mechanisms of low-temperature-induced anthocyanin biosynthesis in eggplant.

scholarly journals Mutations in Transcriptional Regulators Allow Selective Engineering of Signal Integration Logic

mBio ◽  
2014 ◽  
Vol 5 (3) ◽  
Author(s):  
Szabolcs Semsey
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Regulatory Protein ◽  
Point Mutations ◽  
Building Blocks ◽  
Regulatory Elements ◽  
Regulatory Proteins ◽  
Single Amino Acid ◽  
Signal Integration ◽  
Gene Regulatory

ABSTRACT Bacterial cells monitor their environment by sensing a set of signals. Typically, these environmental signals affect promoter activities by altering the activity of transcription regulatory proteins. Promoters are often regulated by more than one regulatory protein, and in these cases the relevant signals are integrated by certain logic. In this work, we study how single amino acid substitutions in a regulatory protein (GalR) affect transcriptional regulation and signal integration logic at a set of engineered promoters. Our results suggest that point mutations in regulatory genes allow independent evolution of regulatory logic at different promoters. IMPORTANCE Gene regulatory networks are built from simple building blocks, such as promoters, transcription regulatory proteins, and their binding sites on DNA. Many promoters are regulated by more than one regulatory input. In these cases, the inputs are integrated and allow transcription only in certain combinations of input signals. Gene regulatory networks can be easily rewired, because the function of cis-regulatory elements and promoters can be altered by point mutations. In this work, we tested how point mutations in transcription regulatory proteins can affect signal integration logic. We found that such mutations allow context-dependent engineering of signal integration logic at promoters, further contributing to the plasticity of gene regulatory networks.

scholarly journals Regulation of enzyme activities in Drosophila: I. The detection of regulatory loci by gene dosage responses

1974 ◽  
Vol 24 (1) ◽  
pp. 59-72 ◽  
Author(s):  
John M. Rawls ◽  
John C. Lucchesi
Keyword(s):  
Enzyme Activity ◽  
Drosophila Melanogaster ◽  
Alcohol Dehydrogenase ◽  
Gene Dosage ◽  
Regulatory Elements ◽  
Gpdh Activity ◽  
Regulatory Loci ◽  
Chromosome Ii ◽  
Chromosome Segments ◽  
Regulatory Sites

SUMMARYIn order to detect regulatory genetic sites in the autosomes of Drosophila melanogaster, the levels of X-linked glucose-6-phosphate dehydro-genase and autosomally linked α-glycerophosphate and isocitrate dehydrogenases have been monitored in extracts of flies aneuploid for regions of chromosomes II and III. In addition to expected structural gene dosage responses of α-GPDH and IDH, flies hyperploid for several autosome regions were found to display altered levels of one or more of the enzymes studied. While IDH activity was increased in flies hyperploid for segments of both chromosomes II and III, α-GPDH activity was decreased in specific hyperploids for chromosome II regions only. The latter group of segmental aneuploids were normal with respect to levels of chromosome II-linked alcohol dehydrogenase. To test if the observed responses were due to dosage changes of discrete genes lying within the larger effective segments, flies aneuploid for subdivisions of the chromosome segments 21A-25CD, 35A–40, and 70CD–71B were assayed. For two of these large segments so analysed, the apparent effects were attributable to specific small subdivisions, suggesting the presence of discrete regulatory sites within the latter. For the 35A–40 region the α-GPDH effect observed for subdivisions was not sufficient to account for the large α-GPDH decrease seen in flies hyperploid for the large, inclusive region. These observations are discussed with respect to the possible bases of effect of regulatory elements on enzyme activity.

scholarly journals Cooperative Assembly of an hnRNP Complex Induced by a Tissue-Specific Homolog of Polypyrimidine Tract Binding Protein

2000 ◽  
Vol 20 (20) ◽  
pp. 7463-7479 ◽  
Author(s):  
Vadim Markovtsov ◽  
Julia M. Nikolic ◽  
Joseph A. Goldman ◽  
Christoph W. Turck ◽  
Min-Yuan Chou ◽  
...  
Keyword(s):  
Binding Protein ◽  
Regulatory Protein ◽  
Regulatory Elements ◽  
Specific Protein ◽  
Regulatory Sequence ◽  
Polypyrimidine Tract ◽  
Tissue Specific ◽  
Polypyrimidine Tract Binding ◽  
Polypyrimidine Tract Binding Protein

ABSTRACT Splicing of the c-src N1 exon in neuronal cells depends in part on an intronic cluster of RNA regulatory elements called the downstream control sequence (DCS). Using site-specific cross-linking, RNA gel shift, and DCS RNA affinity chromatography assays, we characterized the binding of several proteins to specific sites along the DCS RNA. Heterogeneous nuclear ribonucleoprotein (hnRNP) H, polypyrimidine tract binding protein (PTB), and KH-type splicing-regulatory protein (KSRP) each bind to distinct elements within this sequence. We also identified a new 60-kDa tissue-specific protein that binds to the CUCUCU splicing repressor element of the DCS RNA. This protein was purified, partially sequenced, and cloned. The new protein (neurally enriched homolog of PTB [nPTB]) is highly homologous to PTB. Unlike PTB, nPTB is enriched in the brain and in some neural cell lines. Although similar in sequence, nPTB and PTB show significant differences in their properties. nPTB binds more stably to the DCS RNA than PTB does but is a weaker repressor of splicing in vitro. nPTB also greatly enhances the binding of two other proteins, hnRNP H and KSRP, to the DCS RNA. These experiments identify specific cooperative interactions between the proteins that assemble onto an intricate splicing-regulatory sequence and show how this hnRNP assembly is altered in different cell types by incorporating different but highly related proteins.

scholarly journals Can Power Laws Help Us Understand Gene and Proteome Information?

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
J. A. Tenreiro Machado ◽  
António C. Costa ◽  
Maria Dulce Quelhas
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Genetic Code ◽  
Protein Function ◽  
Sequence Data ◽  
Proteome Analysis ◽  
Power Laws ◽  
Linear Sequence ◽  
Graphical Visualization

Proteins are biochemical entities consisting of one or more blocks typically folded in a 3D pattern. Each block (a polypeptide) is a single linear sequence of amino acids that are biochemically bonded together. The amino acid sequence in a protein is defined by the sequence of a gene or several genes encoded in the DNA-based genetic code. This genetic code typically uses twenty amino acids, but in certain organisms the genetic code can also include two other amino acids. After linking the amino acids during protein synthesis, each amino acid becomes a residue in a protein, which is then chemically modified, ultimately changing and defining the protein function. In this study, the authors analyze the amino acid sequence using alignment-free methods, aiming to identify structural patterns in sets of proteins and in the proteome, without any other previous assumptions. The paper starts by analyzing amino acid sequence data by means of histograms using fixed length amino acid words (tuples). After creating the initial relative frequency histograms, they are transformed and processed in order to generate quantitative results for information extraction and graphical visualization. Selected samples from two reference datasets are used, and results reveal that the proposed method is able to generate relevant outputs in accordance with current scientific knowledge in domains like protein sequence/proteome analysis.

scholarly journals Beyond Homology Transfer: Deep Learning for Automated Annotation of Proteins

2017 ◽  
Author(s):  
Mohammad Nauman ◽  
Hafeez Ur Rehman ◽  
Gianfranco Politano ◽  
Alfredo Benso
Keyword(s):  
Deep Learning ◽  
Protein Interactions ◽  
Protein Function ◽  
Sequence Data ◽  
3D Structure ◽  
Input Sequence ◽  
Sequence Information ◽  
Large Set ◽  
Automated Annotation ◽  
Protein Functions

ABSTRACTAccurate annotation of protein functions is important for a profound understanding of molecular biology. A large number of proteins remain uncharacterized because of the sparsity of available supporting information. For a large set of uncharacterized proteins, the only type of information available is their amino acid sequence. In this paper, we propose DeepSeq – a deep learning architecture – that utilizes only the protein sequence information to predict its associated functions. The prediction process does not require handcrafted features; rather, the architecture automatically extracts representations from the input sequence data. Results of our experiments with DeepSeq indicate significant improvements in terms of prediction accuracy when compared with other sequence-based methods. Our deep learning model achieves an overall validation accuracy of 86.72%, with an F1 score of 71.13%. Moreover, using the automatically learned features and without any changes to DeepSeq, we successfully solved a different problem i.e. protein function localization, with no human intervention. Finally, we discuss how this same architecture can be used to solve even more complicated problems such as prediction of 2D and 3D structure as well as protein-protein interactions.

scholarly journals Assessing predictors for new post translational modification sites: a case study on hydroxylation

2020 ◽  
Author(s):  
Damiano Piovesan ◽  
Andras Hatos ◽  
Giovanni Minervini ◽  
Federica Quaglia ◽  
Alexander Miguel Monzon ◽  
...  
Keyword(s):  
Protein Function ◽  
Sequence Data ◽  
High Specificity ◽  
The Self ◽  
Training Data ◽  
Test Case ◽  
Post Translational Modification ◽  
Specificity And Sensitivity ◽  
Training Examples ◽  
Better Than

AbstractPost-translational modification (PTM) sites have become popular for predictor development. However, with the exception of phosphorylation and a handful of other examples, PTMs suffer from a limited number of available training examples and their sparsity in protein sequences. Here, proline hydroxylation is taken as an example to compare different methods and evaluate their performance on new experimentally determined sites. As a proxy for an effective experimental design, predictors require both high specificity and sensitivity. However, the self-reported performance is often not indicative of prediction quality and detection of new sites is not guaranteed. We have benchmarked seven published hydroxylation site predictors on two newly constructed independent datasets. The self-reported performance widely overestimates the real accuracy measured on independent datasets. No predictor performs better than random on new examples, indicating the refined models are not sufficiently general to detect new sites. The number of false positives is high and precision low, in particular for non-collagen proteins whose motifs are not conserved. In short, existing predictors for hydroxylation sites do not appear to generalize to new data. Caution is advised when dealing with PTM predictors in the absence of independent evaluations, in particular for unique specific sites such as those involved in signalling.Author SummaryMachine learning methods are extensively used by biologists to design and interpret experiments. Predictors which take the only sequence as input are of particular interest due to the large amount of sequence data available and self-reported performance is often very high. In this work, we evaluated post-translational modification (PTM) predictors for hydroxylation sites and found that they perform no better than random, in strong contrast to performances reported in the original publications. PTMs are chemical amino acids alterations providing the cell with conditional mechanisms to fine tune protein function, thereby regulating complex biological processes such as signalling and cell cycle. Hydroxylation sites are a good PTM test case due to the availability of a range of predictors and an abundance of newly experimentally detected modification sites. Poor performances in our results highlight the overlooked problem of predicting PTMs when best practices are not followed and training data are likely incomplete. Experimentalists should be careful when using PTM predictors blindly and more independent assessments are needed to separate the wheat from the chaff in the field.

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