Eligible strategies of drought response to improve drought resistance in woody crops: a mini-review

Drought is the main abiotic stress that negatively affects the crop yield. Due to the rapid climate change, actual plant defence mechanisms may be less effective against increased drought stress and other related or co-occurring abiotic stresses such as salt and high temperature. Thus, genetic engineering approaches may be an important tool for improving drought tolerance in crops. This mini-review focuses on the responses to drought stress of the woody crop species Olea europaea and Citrus sp., selecting in particular five main strategies adopted by plants in response to drought stress: aquaporin (AQPs) expression, antioxidant activity, ABA signalling, and trehalose and proline accumulation. Transgenic studies on both the herbaceous Arabidopsis and woody Populus plant models showed an improvement in drought resistance with increasing expression of these drought-inducible genes. Outcomes from the present study suggest the overexpression of the gene families associated with AQPs and ABA biosynthesis, mainly involved in regulating water transport and in preventing water loss, respectively, as candidate targets for improving drought resistance; antioxidants-, trehalose- and proline-related genes remain valid candidates for resistance to a wider spectrum of abiotic stressors, including drought. However, the contribution of an increased stiffness of the modulus elasticity of leaf parenchyma cell walls to the rapid recovery of leaf water potential, delaying by this way the stress onset, is not a secondary aspect of the transgenic optimization, in particular for Olea cultivars.

The salivary, metal-binding peptide histatin-5 buffers extracellular copper availability

The family of human salivary histidine-rich peptides known as histatins bind zinc (Zn) and copper (Cu), but whether they contribute to nutritional immunity by influencing Zn and/or Cu availability has not been examined. We hypothesised that histatin-5 (Hst5) limits Zn availability (and promotes bacterial Zn starvation) and/or raises Cu availability (and promotes bacterial Cu poisoning). To test this hypothesis, Group A Streptococcus (GAS), which colonises the human oropharynx, was used as a model bacterium. Contrary to our hypothesis, Hst5 did not strongly influence Zn availability. This peptide did not induce expression of Zn uptake genes in GAS, nor did it suppress growth of an ΔadcAI mutant strain that is impaired in Zn uptake. Equilibrium competition measurements confirmed that Hst5 binds Zn weakly and does not compete with the high-affinity Zn uptake protein AdcAI for binding Zn. By contrast, Hst5 bound Cu with a high affinity and strongly influenced Cu availability. However, contrary to our hypothesis, Hst5 did not promote Cu toxicity. Instead, this peptide suppressed expression of Cu-inducible genes in GAS, stopped intracellular accumulation of Cu, and rescued growth of a ΔcopA mutant strain that is impaired in Cu efflux in the presence of added Cu. These findings led us to propose a new role for Hst5 and salivary histatins as major Cu buffers in saliva that reduce the potential negative effects of Cu exposure to microbes. We speculate that histatins promote oral and oropharyngeal health by contributing to microbial homeostasis in these host niches.

Cavefish cope with environmental hypoxia by developing more erythrocytes and overexpression of hypoxia inducible genes

Dark caves lacking primary productivity can expose subterranean animals to hypoxia. We used the surface-dwelling (surface fish) and cave-dwelling (cavefish) morphs of Astyanax mexicanus as a model for understanding the mechanisms of hypoxia tolerance in the cave environment. Primitive hematopoiesis, which is restricted to the posterior lateral mesoderm in other teleosts, also occurs in the anterior lateral mesoderm in Astyanax, potentially pre-adapting surface fish for hypoxic cave colonization. Cavefish have enlarged both hematopoietic domains and develop more erythrocytes than surface fish, which are required for normal development in both morphs. Laboratory induced hypoxia suppresses growth in surface fish but not in cavefish. Both morphs respond to hypoxia by overexpressing hypoxia-inducible factor 1 (hif1) pathway genes, and some hif1 genes are constitutively upregulated in normoxic cavefish to similar levels as in hypoxic surface fish. We conclude that cavefish cope with hypoxia by increasing erythrocyte development and constitutive hif1 gene overexpression.

Real-time kinetic studies of Mycobacterium tuberculosis LexA-DNA interaction

Transcriptional repressor, LexA, regulates the “SOS” response, an indispensable bacterial DNA damage repair machinery. Compared to its E.coli ortholog, LexA from Mycobacterium tuberculosis (Mtb) possesses a unique N-terminal extension of additional 24 amino acids in its DNA binding domain (DBD) and 18 amino acids insertion at its hinge region that connects the DBD to the C-terminal dimerization/autoproteolysis domain. Despite the importance of LexA in “SOS” regulation, Mtb LexA remains poorly characterized and the functional importance of its additional amino acids remained elusive. In addition, the lack of data on kinetic parameters of Mtb LexA-DNA interaction prompted us to perform kinetic analyses of Mtb LexA and its deletion variants using Bio-layer Interferometry (BLI). Mtb LexA is seen to bind to different “SOS” boxes, DNA sequences present in the operator regions of damage-inducible genes, with comparable nanomolar affinity. Deletion of 18 amino acids from the linker region is found to affect DNA binding unlike the deletion of the N-terminal stretch of extra 24 amino acids. The conserved RKG motif has been found to be critical for DNA binding. Overall, this study provides insights into the kinetics of the interaction between Mtb LexA and its target “SOS” boxes. The kinetic parameters obtained for DNA binding of Mtb LexA would be instrumental to clearly understand the mechanism of “SOS” regulation and activation in Mtb.

A temperature sensitive mutation in the CstF77 subunit of the polyadenylation complex reveals the critical function of mRNA 3' end formation for a robust heat stress response in plants

Background: Heat Shock Protein 101 (HSP101) in plants and orthologs in bacteria (Caseinolytic peptidase B, ClpB) and yeast (Hsp104) are essential for thermotolerance. To investigate molecular mechanisms of thermotolerance involving HSP101, we performed a suppressor screen in Arabidopsis thaliana of a semi-dominant, missense HSP101 allele, hot1-4 (A499T). Plants carrying the hot1-4 mutation are more heat-sensitive than an HSP101 null mutant (hot1-3), indicating the toxicity of hot1-4 allele. Results: We report that one suppressor (shot2, suppressor of hot1-4 2) has a temperature-sensitive, missense mutation (E170K) in the CstF77 (Cleavage stimulation factor 77) subunit of the polyadenylation complex, which is critical for 3' end maturation of pre-mRNA. RNA-Seq analysis of total RNA depleted of ribosomes reveals that heat treatment causes transcriptional readthrough events in shot2, specifically in highly heat-induced genes, including the toxic hot1-4 gene. In addition, failure of correct transcript processing leads to reduced accumulation of many HSP RNAs and proteins, suppressing heat sensitivity of the hot1-4 mutant, due to reduction of the toxic mutant HSP101 protein. Notably, the shot2 mutation makes plants more sensitive to heat stress in the HSP101 null (hot1-3) and wild-type backgrounds correlated with the reduced expression of other heat-inducible genes required for thermotolerance. Conclusions: Our study reveals the critical function of CstF77 for 3' end formation of mRNA during heat stress, as well as the dominant role of HSP101 in dictating the outcome of severe heat stress in plants.

Real-time kinetic studies of Mycobacterium tuberculosis LexA–DNA interaction

Transcriptional repressor, LexA, regulates the ‘SOS’ response, an indispensable bacterial DNA damage repair machinery. Compared with its Escherichia coli ortholog, LexA from Mycobacterium tuberculosis (Mtb) possesses a unique N-terminal extension of additional 24 amino acids in its DNA-binding domain (DBD) and 18 amino acids insertion at its hinge region that connects the DBD to the C-terminal dimerization/autoproteolysis domain. Despite the importance of LexA in ‘SOS’ regulation, Mtb LexA remains poorly characterized and the functional importance of its additional amino acids remained elusive. In addition, the lack of data on kinetic parameters of Mtb LexA–DNA interaction prompted us to perform kinetic analyses of Mtb LexA and its deletion variants using Bio-layer Interferometry (BLI). Mtb LexA is seen to bind to different ‘SOS’ boxes, DNA sequences present in the operator regions of damage-inducible genes, with comparable nanomolar affinity. Deletion of 18 amino acids from the linker region is found to affect DNA binding unlike the deletion of the N-terminal stretch of extra 24 amino acids. The conserved RKG motif has been found to be critical for DNA binding. Overall, the present study provides insights into the kinetics of the interaction between Mtb LexA and its target ‘SOS’ boxes. The kinetic parameters obtained for DNA binding of Mtb LexA would be instrumental to clearly understand the mechanism of ‘SOS’ regulation and activation in Mtb.

Molecular connectivity between extra-cytoplasmic sigma factors and PhoP accounts for integrated mycobacterial stress response

The main purpose of this study is to understand how mycobacteria can sense numerous stress conditions and mount an appropriate stress response. Recent studies suggest that at low pH M. tuberculosis encounters reductive stress, and in response, modulates redox homeostasis by utilizing the phoPR regulatory system. However, the mechanism of integrated regulation of stress response remains unknown. To probe how PhoP contributes to redox stress response, we find that a PhoP-depleted M. tuberculosis shows a significantly enhanced susceptibility to redox stress relative to the WT bacilli. In keeping with these results, PhoP was shown to contribute to mycothiol redox state. Because SigH, one of the alternative sigma factors of mycobacteria, is known to control expression of redox inducible genes, we probed whether previously-reported PhoP-SigH interaction accounts for mycobacterial redox stress response. We had shown that under acidic conditions PhoP functions in maintaining pH homeostasis via its interaction with SigE. In striking contrast, here we show that under redox stress, direct recruitment of SigH, but not PhoP-SigH interaction, controls expression of mycobacterial thioredoxin genes, a major mycobacterial anti-oxidant system. Together, these unexpected results uncover novel stress-specific enhanced or reduced interaction events of sigma factors and PhoP, as the underlying mechanisms of an adaptive programme, which couples low pH conditions and mycobacterial thiol redox homeostasis.

B7–H3 regulates osteoclast differentiation via type I interferon-dependent IDO induction

While their function, as immune checkpoint molecules, is well known, B7-family proteins also function as regulatory molecules in bone remodeling. B7–H3 is a receptor ligand of the B7 family that functions primarily as a negative immune checkpoint. While the regulatory function of B7–H3 in osteoblast differentiation has been established, its role in osteoclast differentiation remains unclear. Here we show that B7–H3 is highly expressed in mature osteoclasts and that B7–H3 deficiency leads to the inhibition of osteoclastogenesis in human osteoclast precursors (OCPs). High-throughput transcriptomic analyses reveal that B7–H3 inhibition upregulates IFN signaling as well as IFN-inducible genes, including IDO. Pharmacological inhibition of type-I IFN and IDO knockdown leads to reversal of B7–H3-deficiency-mediated osteoclastogenesis suppression. Although synovial-fluid macrophages from rheumatoid-arthritis patients express B7–H3, inhibition of B7–H3 does not affect their osteoclastogenesis. Thus, our findings highlight B7–H3 as a physiologic positive regulator of osteoclast differentiation and implicate type-I IFN–IDO signaling as its downstream mechanism.

Expression of the Sonic Hedgehog Embryonic Signalling Pathway Components in Matched Pre-Treatment and Relapsed Small Cell Lung Cancer Biopsies

Cancer stem cells may be responsible for tumour regrowth and acquisition of resistance in small cell lung cancer (SCLC). The Hedgehog pathway regulates survival and proliferation of tissue progenitor and stem cell populations, promoting the expression of stem cell related and proliferative genes. We evaluated the Sonic Hedgehog (Shh) embryonic signalling pathway in relapsed SCLC. Expression levels of Shh related genes GLI1, SMO, SUFU, PTCH1, HHIP, BCL2, BMI, ZEB1, ZEB2, N-MYC, Twist1 were analysed by qRT-PCR in matched pre-treatment and relapsed tumour fresh frozen biopsies of three SCLC patients. Expression of each gene was compared using the paired samples t-test, as well as comparison of mean expression levels was done. Data were statistically interpreted using the MedCalc version 10.2.0.0 software. 2.9-fold lower mean mRNA expression of the major Hedgehog activation indicator GLI1 was observed in relapsed samples (p = 0.0529). Mean expression of six Shh inducible genes, PTCH1, HHIP, N-MYC, ZEB2, Twist1, ZEB1, was also downregulated by 2.6-, 2.2-, 1.9-, 1.8-, 1.2-, 1.1-fold, respectively (p = 0.4252, p = 0.1268, p = 0.2480, p = 0.1169, p = 0.1480, p = 0.7595, respectively). 1.8-fold mean expression decrease was found for Gli activator Smo (p = 0.4111). Only the Shh pathway inhibitor SUFU and two other examined Hedgehog signalling inducible genes BCL2 and BMI in relapsed SCLC showed 0.8-, 0.9-,and 0.8-fold increase of expression, respectively (p = 0.3074, p = 0.7921, and p = 0.3822, respectively). To our knowledge, this is the first report of comparison of Shh signalling in matched pre-treatment and relapsed SCLC biopsies. Our data show decreased activity for majority of Shh pathway components in relapsed SCLC, although difference did not reach statistical significance.

BRCA1-BARD1 regulates transcription through modulating topoisomerase IIβ

RNA polymerase II (Pol II)-dependent transcription in stimulus-inducible genes requires topoisomerase IIβ (TOP2B)-mediated DNA strand break and the activation of DNA damage response signalling in humans. Here, we report a novel function of the breast cancer 1 (BRCA1)-BRCA1-associated ring domain 1 (BARD1) complex in this process. We found that BRCA1 is phosphorylated at S1524 by the kinases ataxia-telangiectasia mutated and ATR during gene activation, and that this event is important for productive transcription. Our biochemical and genomic analyses showed that the BRCA1-BARD1 complex interacts with TOP2B in the EGR1 transcription start site and in a large number of protein-coding genes. Intriguingly, the BRCA1-BARD1 complex ubiquitinates TOP2B, which stabilizes TOP2B binding to DNA while BRCA1 phosphorylation at S1524 controls the TOP2B ubiquitination by the complex. Together, these findings suggest the novel function of the BRCA1-BARD1 complex in the regulation of TOP2B and Pol II-mediated gene expression.