Recent advances in designing synthetic plant regulatory modules.

Introducing novel functions in plants through synthetic multigene circuits requires strict transcriptional regulation. Currently, the use of natural regulatory modules in synthetic circuits is hindered by our limited knowledge of complex plant regulatory mechanisms, the paucity of characterized promoters, and the possibility of crosstalk with endogenous circuits. Synthetic regulatory modules can overcome these limitations.

The N-region sequence context impacts the chloroplast import efficiency of multi-TMD protein.

Targeting heterologous multi-transmembrane domain (TMD) proteins to plant chloroplasts requires sequences in addition to the chloroplast transit peptide (cTP). The N-terminal domain (N-region), located C-terminal to the cTP in chloroplast inner envelope membrane proteins, is an essential region for import. However, it was unclear if the N-region functions solely as a spacer sequence to facilitate cTP access or if it plays an active role in the import process.

Artificially designed synthetic promoter for a high level of salt induction using a cis-engineering approach.

This work aimed to design a synthetic salt-inducible promoter using a cis-engineering approach. The designed promoter (PS) comprises a minimal promoter sequence for basal-level expression and upstream cis-regulatory elements (CREs) from promoters of salinity-stress-induced genes. The copy number, spacer lengths, and locations of CREs were manually determined based on their occurrence within native promoters.

Effect of ACGT motif in spatiotemporal regulation of AtAVT6D, which improves tolerance to osmotic stress and nitrogen-starvation.

Plasma membrane-localized AtAVT6D importing aspartic acid can be targeted to develop plants with enhanced osmotic and nitrogen-starvation tolerance. AtAVT6D promoter can be exploited as a stress-inducible promoter for genetic improvements to raise stress-resilient crops. The AtAVT6 family of amino acid transporters in Arabidopsis thaliana has been predicted to export amino acids like aspartate and glutamate.

Genome-wide analysis of AAAG and ACGT cis-elements in Arabidopsis thaliana reveals their involvement with genes downregulated under jasmonic acid response in an orientation independent manner.

Cis-regulatory elements are regions of noncoding DNA that regulate the transcription of neighboring genes. The study of cis-element architecture that functions in transcription regulation are essential. AAAG and ACGT are a class of cis-regulatory elements, known to interact with Dof and bZIP transcription factors respectively, and are known to regulate the expression of auxin response, gibberellin response, floral development, light response, seed storage proteins genes, biotic and abiotic stress genes in plants.

Analysis of CCGAC and CATGTG Elements Across Genomes Reveals their Roles in Gene Regulation under Stress.

Background: Plant yield closely depends on its environment and is negatively affected by abiotic stress conditions like drought, salinity, heat, and cold. Analysis of the stress-inducible genes in has previously shown that CCGAC and CATGTG play a crucial role in controlling the gene expression through the binding of DREB/CBF and NAC TFs under various stress conditions, mainly drought and salinity.

Methods: The pattern of these motifs is conserved, which has been analyzed in this study to find the mechanism of gene expression through spacer specificity, inter motif distance preference, functional analysis, and statistical analysis for four different plants, namely and .

Primer Designing for Amplifying an AT-Rich Promoter from Arabidopsis thaliana.

The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats. The present study also covers the key parameters that need to be kept in mind while designing primers. Results show that successful can be achieved by performing a 2-step PCR reaction at a lower extension temperature of 65 ̊C for an increased extension period of 1.

Promoter profiling of Arabidopsis amino acid transporters: clues for improving crops.

The review describes the importance of amino acid transporters in plant growth, development, stress tolerance, and productivity. The promoter analysis provides valuable insights into their functionality leading to agricultural benefits. Arabidopsis thaliana genome is speculated to possess more than 100 amino acid transporter genes.

Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates.

SARS-CoV-2 pandemic has recently made the entire world come to a standstill. The number of cases in the world, especially India, have been increasing exponentially. The need of the hour is to assimilate as much data as possible to fast track the pipeline of bringing in new therapeutic tools against this fatal virus.

activity of reconstituted rubisco enzyme from .

RuBisCO (Ribulose 1,5 bisphosphate carboxylase/oxygenase) by virtue of its dual specificity towards oxygen and carbon dioxide is an important rate-limiting step in photosynthesis and is believed to be the key factor for limited productivity of higher plants and algae. The photoautotrophic growth rate of cyanobacteria is a culmination of several factors including, rates of photosynthetic reactions, stress combating mechanisms and basic biomass generation metabolism in combination with optimal nutrient availability, irradiance, gaseous environment, etc. In case of cyanobacteria, the effect of RuBisCO in affecting the multiplication rate has been observed to show varied response.

Role of Chromatin Architecture in Plant Stress Responses: An Update.

Sessile plants possess an assembly of signaling pathways that perceive and transmit environmental signals, ultimately resulting in transcriptional reprogramming. Histone is a key feature of chromatin structure. Numerous histone-modifying proteins act under different environmental stress conditions to help modulate gene expression.

Co-expression network analysis of protein phosphatase 2A (PP2A) genes with stress-responsive genes in Arabidopsis thaliana reveals 13 key regulators.

Abiotic and biotic stresses adversely affect plant growth and development and eventually result in less yield and threaten food security worldwide. In plants, several studies have been carried out to understand molecular responses to abiotic and biotic stresses. However, the complete circuitry of stress-responsive genes that plants utilise in response to those environmental stresses are still unknown.

Glutathione S-transferase: a versatile protein family.

Glutathione-S transferase (GST) is a most ancient protein superfamily of multipurpose roles and evolved principally from gene duplication of an ancestral GSH binding protein. They have implemented in diverse plant functions such as detoxification of xenobiotic, secondary metabolism, growth and development, and majorly against biotic and abiotic stresses. The vital structural features of GSTs like highly divergent functional topographies, conserved integrated architecture with separate binding pockets for substrates and ligand, the stringent structural fidelity with high Tm values (50º-60º), and stress-responsive cis-regulatory elements in the promoter region offer this protein as most flexible plant protein for plant breeding approaches, biotechnological applications, etc.

Genome wide analysis of W-box element in Arabidopsis thaliana reveals TGAC motif with genes down regulated by heat and salinity.

To design, synthetic promoters leading to stress-specific induction of a transgene, the study of cis-regulatory elements is of great importance. Cis-regulatory elements play a major role in regulating the gene expression spatially and temporally at the transcriptional level. The present work focuses on one of the important cis-regulatory element, W-box having TGAC as a core motif which serves as a binding site for the members of the WRKY transcription factor family.

Optimization of PCR conditions for amplifying an AT-rich amino acid transporter promoter sequence with high number of tandem repeats from Arabidopsis thaliana.

Objective: The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats.

Result: Results show that successful amplification can be achieved by performing a 2-step PCR at a lower extension temperature of 65 °C for an increased extension period of 1.5 min/kb, with MgCl concentration ranging from 2.

Regulatory components of carbon concentrating mechanisms in aquatic unicellular photosynthetic organisms.

This review provides an insight into the regulation of the carbon concentrating mechanisms (CCMs) in lower organisms like cyanobacteria, proteobacteria, and algae. CCMs evolved as a mechanism to concentrate CO at the site of primary carboxylating enzyme Ribulose-1, 5-bisphosphate carboxylase oxygenase (Rubisco), so that the enzyme could overcome its affinity towards O which leads to wasteful processes like photorespiration. A diverse set of CCMs exist in nature, i.

Towards combinatorial transcriptional engineering.

The modular nature of the transcriptional unit makes it possible to design robust modules with predictable input-output characteristics using a ‘parts- off a shelf’ approach. Customized regulatory circuits composed of multiple such transcriptional units have immense scope for application in diverse fields of basic and applied research. Synthetic transcriptional engineering seeks to construct such genetic cascades.

Developments and challenges in biodiesel production from microalgae: A review.

The imminent depletion of fossil fuels and the surging global demand for renewable energy have led to the search for nonconventional energy sources. After a few decades of trial and error, the world is now testing the sources of the third generation of fossil fuels, which contain for most parts microalgae. With more than 80% oil content, being adaptable in growth parameters and highly versatile, microalgae are highly promising sources of biofuels in the present time.

ICRF-193, an anticancer topoisomerase II inhibitor, induces arched telophase spindles that snap, leading to a ploidy increase in fission yeast.

ICRF-193 [meso-4,4-(2,3-butanediyl)-bis(2,6-piperazinedione)] is a complex-stabilizing inhibitor of DNA topoisomerase II (topo II) that is used as an effective anticancer drug. ICRF-193 inhibits topo II catalytic activity in vitro and blocks nuclear division in vivo. Here, we examined the effects of ICRF-193 treatment on chromatin behavior and spindle dynamics using detailed live mitotic cell analysis in the fission yeast, Schizosaccharomyces pombe.

PP2C-like Promoter and Its Deletion Variants Are Induced by ABA but Not by MeJA and SA in Arabidopsis thaliana.

Gene expression is mediated through interaction between cis regulatory elements and its cognate transcription factors. Cis regulatory elements are defined as non-coding DNA sequences that provide the binding sites for transcription factors and are clustered in the upstream region of genes. ACGT cis regulatory element is one of the important cis regulatory elements found to be involved in diverse biological processes like auxin response, salicylic acid (SA) response, UV light response, ABA response and jasmonic acid (JA) response.

Role of habitat and great oxidation event on the occurrence of three multisubunit inorganic carbon-uptake systems in cyanobacteria.

The oxygenase reaction catalyzed by RuBisCO became an issue only after the evolution of the oxygenic photosynthesis in cyanobacteria. Several strategies were developed by autotrophic organisms as an evolutionary response to increase oxygen levels to help RuBisCO maximize its net carboxylation rate. One of the crucial advancements in this context was the development of more efficient inorganic carbon transporters which could help in increasing the influx of inorganic carbon (Ci) at the site of CO₂ fixation.

In Silico Analysis of the Endonuclease III Protein Family Identifies Key Residues and Processes During Evolution.

DNA repair refers to a collection of processes by which a cell identifies and corrects damage to genomic DNA molecules. DNA repair processes significantly overcome DNA damage and restore the normal nucleotide sequence and DNA structure. This study focuses on the evolution of the endonuclease III gene/protein family, which plays a key role in the base excision repair pathway.

Genome wide analysis of Arabidopsis thaliana reveals high frequency of AAAGN7CTTT motif.

Sequence specific elements in DNA regulate transcription by recruiting transcription factors. The Dof proteins are a large family of transcription factors that share a single highly conserved zinc finger. The core to which Dof proteins bind has a consensus AAAG or ACTTTA sequence.

Abscisic acid and abiotic stress tolerance - different tiers of regulation.

Abiotic stresses affect plant growth, metabolism and sustainability in a significant way and hinder plant productivity. Plants combat these stresses in myriad ways. The analysis of the mechanisms underlying abiotic stress tolerance has led to the identification of a highly complex, yet tightly regulated signal transduction pathway consisting of phosphatases, kinases, transcription factors and other regulatory elements.

Combinatorial control of gene expression.

The complexity and diversity of eukaryotic organisms are a feat of nature's engineering. Pulling the strings of such an intricate machinery requires an even more masterful and crafty approach. Only the number and type of responses that they generate exceed the staggering proportions of environmental signals perceived and processed by eukaryotes.