Key Role In Adaptive Responses Research Articles

Advantages and limitations of UV cross-linking analysis of protein-RNA interactomes in microbes.

RNA-binding proteins (RBPs) govern the lifespan of nearly all transcripts and play key roles in adaptive responses in microbes. A robust approach to examine protein-RNA interactions involves irradiating cells with UV light to form covalent adducts between RBPs and their cognate RNAs. Combined with RNA or protein purification, these procedures can provide global RBP censuses or transcriptomic maps for all target sequences of a single protein in living cells. The recent development of novel methods has quickly populated the RBP landscape in microorganisms. Here, we provide an overview of prominent UV cross-linking techniques which have been applied to investigate RNA interactomes in microbes. By assessing their advantages and caveats, this technical evaluation intends to guide the selection of appropriate methods and experimental design as well as to encourage the use of complementary UV-dependent techniques to inspect RNA-binding activity.

Application of Outer Membrane Protein-Based Vaccines Against Major Bacterial Fish Pathogens in India.

Aquaculture is one of the fastest-growing food-producing sectors in the world. However, its growth is hampered by various disease problems due to infectious microorganisms, including Gram-negative bacteria in finfish aquaculture. Disease control in aquaculture by use of antibiotics is not recommended as it leads to antibiotic residues in the final product, selection, and spread of antibiotic resistance in the environment. Therefore, focus is on disease prevention by vaccination. All Gram-negative bacteria possess surface-associated outer membrane proteins (OMPs), some of which have long been recognized as potential vaccine candidates. OMPs are essential for maintaining the integrity and selective permeability of the bacterial membrane and play a key role in adaptive responses of bacteria such as solute and ion uptake, iron acquisition, antimicrobial resistance, serum resistance, and bile salt resistance and some adhesins have virulence attributes. Antigenic diversity among bacterial strains even within the same bacterial species has constrained vaccine developments, but OMPs that are conserved across serotypes could be used as potential candidates in vaccine development, and several studies have demonstrated their efficacy and potential as vaccine candidates. In this review, we will look into the application of OMPs for the design of vaccines based on recombinant proteins, subunit vaccines, chimeric proteins, and DNA vaccines as new-generation vaccine candidates for major bacterial pathogens of fish for sustainable aquaculture.

Adaptation to climate change through genetic accommodation and assimilation of plastic phenotypes.

Theory suggests that evolutionary changes in phenotypic plasticity could either hinder or facilitate evolutionary rescue in a changing climate. Nevertheless, the actual role of evolving plasticity in the responses of natural populations to climate change remains unresolved. Direct observations of evolutionary change in nature are rare, making it difficult to assess the relative contributions of changes in trait means versus changes in plasticity to climate change responses. To address this gap, this review explores several proxies that can be used to understand evolving plasticity in the context of climate change, including space for time substitutions, experimental evolution and tests for genomic divergence at environmentally responsive loci. Comparisons among populations indicate a prominent role for divergence in environmentally responsive traits in local adaptation to climatic gradients. Moreover, genomic comparisons among such populations have identified pervasive divergence in the regulatory regions of environmentally responsive loci. Taken together, these lines of evidence suggest that divergence in plasticity plays a prominent role in adaptation to climatic gradients over space, indicating that evolving plasticity is also likely to play a key role in adaptive responses to climate change through time. This suggests that genetic variation in plastic responses to the environment (G × E) might be an important predictor of species' vulnerabilities to climate-driven decline or extinction. This article is part of the theme issue 'The role of plasticity in phenotypic adaptation to rapid environmental change'.

An investigation of gene expression patterns that contribute to osmoregulation in Macrobrachium australiense: Assessment of adaptive responses to different osmotic niches

Osmoregulation is considered to be the principal mechanisms for survival and adaptation to different environmental salinity conditions. The present study was conducted to assess mRNA expression levels of five osmoregulatory genes in a Palaemonid prawn species, Macrobrachium australiense, exposed to three different salinities (0‰, 5‰ and 10‰) across six time intervals for a period of five days, using an RT-qPCR approach. Relative mRNA expression patterns revealed comparatively higher expression levels of Na+/K+-ATPase (NKA) and Na+/K+/2Cl− Co-transporter (NKCC) genes at raised salinities (5‰ and 10‰). At 0‰ vs 10‰, expression levels of these two genes were significantly higher (p < 0.05) and showed 2–3 fold and 4–6 fold higher (higher in 10‰ than 0‰) expression levels for NKA and NKCC, respectively. Significantly higher expression levels (p < 0.05) were observed at 0‰ for the Na+/H+ exchanger (NHE) and V-type H+-ATPase (VTA) genes over 5‰ and 10‰ throughout the experimental time period. But initially higher expression levels of VTA were observed at 5‰ and 10‰ up to 24 h and then dropped below the levels at 0‰. The water channel regulatory gene, Aquaporin (AQP) showed very high expression levels initially (1 h) that were significantly different among treatments (p < 0.05), expression levels then declined up to the end of the experiment. In general, AQP, NHE and VTA were up-regulated in freshwater while NKA and NKCC were up-regulated under raised salinities. Results of this study indicate that the genes examined here likely play key roles in adaptive responses to variable environmental salinity conditions broadly in aquatic crustaceans.

Abiotic Stress Responsive miRNA-Target Network and Related Markers (SNP, SSR) in Brassica juncea.

Abiotic stress is one of the major factors responsible for huge yield loss in crop plants. MicroRNAs play a key role in adaptive responses of plants under abiotic stress conditions through post-transcriptional gene regulations. In present study, 95 potential miRNAs were predicted in Brassica juncea using comparative genomics approach. It was noted that these miRNAs, target several transcription factors (TFs), transporter family proteins, signaling related genes, and protease encoding genes. Nineteen distinct miRNA-target regulatory networks were observed with significant involvement in regulation of transcription, response to stimulus, hormone and auxin mediated signaling pathway related gene ontology (GO) term. The sucrose-starch metabolism and pentose-gluconate interconversion pathways were found significantly enriched for these target genes. Molecular markers such as Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism (SNPs) were identified on miRNAs (miR-SSRs and miR-SNPs) and their target genes in B. juncea. Notably, one of the miR-SNP (C/T) was found at the 5th position on mature region of miR2926. This C/T transition led to the distorted and unstable hairpin structure of miR2926, consequently complete loss of target function. Hence, findings from this study will lay a foundation for marker assisted breeding for abiotic stress tolerant varieties of B. juncea.

Cloning, Characterization, and Functional Expression of Phospholipase Dα cDNA from Banana (Musa acuminate L.)

Phospholipase D (PLD) plays a key role in adaptive responses of postharvest fruits. A cDNA clone of banana (Musa acuminate L.) PLDα (MaPLDα) was obtained by RT-PCR in this study. The MaPLDα gene contains a complete open reading frame (ORF) encoding a 92-kDa protein composed of 832 amino acid residues and possesses a characteristic C2 domain and two catalytic H×K×××D (abbr. HKD) motifs. The two HKD motifs are separated by 341 amino acid residues in the primary structure. Relatively higher PLD activity and expression of MaPLDα mRNA were detected in developing tissues compared to senescent or mature tissues in individual leaves, flower, stem, and fruit organs, respectively. The expression profile of PLDα mRNA in postharvest banana fruits at different temperatures was determined, and the MaPLDα mRNA reached the highest expression peak on day 5 at 25°C and on day 7 at 12°C. The results provide useful information for maintaining postharvest quality and extending the storage life of banana fruit.

LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects.

BackgroundLeucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of plant RLKs. The functions of most LRR-RLKs have remained undiscovered, and a few that have been experimentally characterized have been shown to have important roles in growth and development as well as in defense responses. Although RLK subfamilies have been previously studied in many plants, no comprehensive study has been performed on this gene family in Citrus species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed in silico analysis to identify and classify LRR-RLK homologues in the predicted proteomes of Citrus clementina (clementine) and Citrus sinensis (sweet orange). In addition, we used large-scale phylogenetic approaches to elucidate the evolutionary relationships of the LRR-RLKs and further narrowed the analysis to the LRR-XII group, which contains several previously described cell surface immune receptors.ResultsWe built integrative protein signature databases for Citrus clementina and Citrus sinensis using all predicted protein sequences obtained from whole genomes. A total of 300 and 297 proteins were identified as LRR-RLKs in C. clementina and C. sinensis, respectively. Maximum-likelihood phylogenetic trees were estimated using Arabidopsis LRR-RLK as a template and they allowed us to classify Citrus LRR-RLKs into 16 groups. The LRR-XII group showed a remarkable expansion, containing approximately 150 paralogs encoded in each Citrus genome. Phylogenetic analysis also demonstrated the existence of two distinct LRR-XII clades, each one constituted mainly by RD and non-RD kinases. We identified 68 orthologous pairs from the C. clementina and C. sinensis LRR-XII genes. In addition, among the paralogs, we identified a subset of 78 and 62 clustered genes probably derived from tandem duplication events in the genomes of C. clementina and C. sinensis, respectively.ConclusionsThis work provided the first comprehensive evolutionary analysis of the LRR-RLKs in Citrus. A large expansion of LRR-XII in Citrus genomes suggests that it might play a key role in adaptive responses in host-pathogen co-evolution, related to the perennial life cycle and domestication of the citrus crop species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2930-9) contains supplementary material, which is available to authorized users.