Biology subjects

Kamran, M.

Publications and source records attributed to Kamran, M..

10 recordsLinked to original sources

bioRxiv2026

CRK5 preserves antioxidant homeostasis and prevents cell death during dark-induced senescence through inhibiting the salicylic acid signaling pathway

BackgroundDark-induced senescence (DIS) is a widely used model for dissecting the regulatory mechanisms that manage leaf aging, redox imbalance, and cell death (CD) in plants. Salicylic acid (SA) is a central hormonal regulator of these processes. However, the mechanism involving upstream components, which integrate SA-dependent pathways with antioxidant homeostasis during DIS, remains unresolved. CYSTEINE-RICH RECEPTOR-LIKE KINASE 5 (CRK5) is a membrane-localized protein that plays a role in developmental and stress-responsive pathways. Its promoter contains multiple W-box cis-elements, indicating regulation by WRKY factors in SA-mediated pathways. This study investigates how CRK5 modulates SA-dependent CD and antioxidant dynamics during DIS. ResultsIn this study, SA-accumulating mutant crk5 exhibited accelerated senescence, elevated electrolyte leakage, enhanced micro-lesion formation, and markedly increased reactive oxygen species (ROS) accumulation under both control and dark conditions. These phenotypes were accompanied by a substantial reduction in carotenoid and xanthophyll pools, enhanced accumulation of phenolic compounds, and increased free radical scavenging capacity, including ascorbate peroxidase, catalase, and superoxide dismutase activities. Importantly, crk5 phenotype was fully reverted in crk5sid2 and crk5NahG double mutants, confirming that crk5 DIS phenotype is induced by activation of the SA-signaling pathway. Transcriptome profiling revealed extensive deregulation of senescence-, CD-, and redox-associated genes in crk5 during darkness, including strong induction of SAGs, metacaspases, autophagy, and antioxidant-related transcripts. The line with constitutively enhanced SA level (cpr1), used as a control, showed similar phenotypes to crk5, although transcriptional reprogramming was largely absent in cpr1 after darkness, highlighting CRK5 as a key upstream negative regulator of SA-mediated CD and positive regulator of antioxidant homeostasis. ConclusionOur work presents CRK5 as a central regulatory hub that inhibits the SA-signaling, ROS burst, and CD activation during DIS. Loss of CRK5 function is associated with the activation of SA-signaling, altered antioxidant systems, increased ROS burden, and ROS-driven CD acceleration, resulting in accelerated senescence. Conversely, suppression of SA-biosynthesis or -catabolism in a crk5 background restores the wild-type phenotype. These findings position this receptor kinase as a key mediator that coordinates hormonal, metabolic, and oxidative pathways to maintain leaf viability, providing mechanistic insight into the control of stress-induced senescence and CD in Arabidopsis.

plant biology↗

bioRxiv2025

Role of CIA2 and CIL in the regulation of chloroplast photomorphogenesis in Arabidopsis

Chloroplast development plays a crucial role in plant de-etiolation, a process in which plants switch from growth in darkness to light-driven development, known as photomorphogenesis. This study provides evidence that CIA2 (Chloroplast Import Apparatus 2) and CIL (CIA2-Like) contribute to chloroplast biogenesis, likely by affecting and regulating PSII assembly and related gene expression. Although their precise molecular roles remain unclear, our findings support their involvement in chloroplast development. This is indicated by deregulation of foliar chlorophyll content, chlorophyll a fluorescence parameters, chloroplast size, and gene expression of PSII molecular markers in cia2cil double mutant during de-etiolation. Chlorophyll a fluorescence and quantitative gene expression analysis during de-etiolation revealed a significant reduction in PSII maximal efficiency and non-photochemical quenching, as well as deregulated transcription of genes such as LHCB2.1 and psbA. According to the immunoblotting and microscopy imaging results, there is an impaired assembly of PSII and a compromised ultrastructure of the chloroplast membranes in cia2cil plants. However, in CIA2p::CIA2cia2cil and 35Sp::CIA2cia2cil complementation lines, reversion of this phenotype was observed. These results suggest a supporting role for CIA2 and CIL in the plant de-etiolation process, expanding our understanding of chloroplast biogenesis regulation.

plant biology↗

bioRxiv2025

Transpiration, Photoinhibition and Non-photochemical Quenching Reciprocally Control Foliar Heat Emission

Global warming intensifies heat waves and drought, causing energy absorption in excess (EAE) in plants, thereby inhibiting transpiration and photosynthesis. Non-photochemical quenching (NPQ) contributes significantly to EAE dissipation as heat, with leaves emitting ca. 107 W m-2 while absorbing ca. 417 W m-2. Foliar temperature is further elevated when transpiration is inhibited, but NPQ is not increased. Surprisingly, during generic photosynthetic electron transport and NPQ partial inhibition, foliar temperature under EAE was reduced considerably. Our findings emphasize the importance of mutual co-regulation of photosynthetic electron transport, NPQ, and transpiration in foliar temperature regulation and suggest that overall heat emission from forest ecosystems may conditionally vary on a terawatt (TW) scale per 1,000,000 km-2. Global warming models do not take into account this putative phenomenon. One Sentence SummaryPhotosynthesis and Foliar Thermoregulation

plant biology↗

bioRxiv2025

Structure and Activity of the Essential UCH Family Deubiquitinase DUB16 from Leishmania donovani

In Leishmania parasites, as for their hosts, the ubiquitin proteasome system is important for cell viability. As part of a systematic gene deletion study, it was discovered that four cysteine protease type deubiquitinases (DUBs) are essential for parasite survival in the promastigote stage, including DUB16. Here we have purified and characterised recombinant DUB16 from Leishmania donovani, which belongs to the ubiquitin C-terminal hydrolase (UCH) family. DUB16 efficiently hydrolyses C-terminal aminocoumarin and rhodamine conjugates of ubiquitin consistent with proposed cellular roles of UCH-type DUBs in regenerating free monomeric ubiquitin from small molecule ubiquitin adducts arising from adventitious metabolic processes. The crystal structure of DUB16 reveals a typical UCH-type deubiquitinase fold, and a relatively short and disordered crossover loop that appears to restrict access to the catalytic cysteine. At close to stoichiometric enzyme to substrate ratios, DUB16 exhibits deubiquitinase activity towards diubiquitins linked through isopeptide bonds between Lys11, Lys48 or Lys63 residues of the proximal ubiquitin and the C-terminus of the distal ubiquitin. With 100-1000-fold higher turnover rates, DUB16 cleaves the ubiquitin-ribosomal L40 fusion protein to give the mature products. A DUB-targeting cysteine-reactive cyanopyrrolidine compound, IMP-1710, inhibits DUB16 activity. IMP-1710 was shown in promastigote cell viability assays to have parasite killing activity with EC50 values of 1-2 M, comparable to the anti-leishmanial drug, miltefosine. L. mexicana parasites engineered to overproduce DUB16 showed a modest increase in resistance to IMP-1710, providing evidence that IMP-1710 inhibits DUB16 in vivo. Together these results suggest on-target activity and that DUB16 may be a druggable target to develop new anti-leishmania compounds.

biochemistry↗

bioRxiv2023

Perception of butenolides by Bacillus subtilis via the α/β-hydrolase RsbQ

The regulation of behavioural and developmental decisions by small molecules is common to all domains of life. In plants, strigolactones and karrikins are butenolide growth regulators that influence several aspects of plant growth and development, as well as interactions with symbiotic fungi1-3. DWARF14 (D14) and KARRIKIN INSENSITIVE2 (KAI2) are homologous receptors that perceive strigolactones and karrikins, respectively, and that hydrolyse their ligands to effect signal transduction4-7. RsbQ, a homologue of D14 and KAI2 from the Gram-positive bacterium Bacillus subtilis, regulates growth responses to nutritional stress via the alternative transcription factor SigmaB ({sigma}B)8,9. However, the molecular function of RsbQ is unknown. Here we show that RsbQ perceives butenolide compounds that are bioactive in plants. RsbQ is thermally destabilised by the synthetic strigolactone GR24 and its desmethyl butenolide equivalent dGR24. We show that, like D14 and KAI2, RsbQ is a functional butenolide hydrolase that undergoes covalent modification of the catalytic histidine residue. Exogenous application of both GR24 and dGR24 inhibited the endogenous signalling function of RsbQ in vivo, with dGR24 being 10-fold more potent. Application of dGR24 to B. subtilis phenocopied loss-of-function rsbQ mutations and led to a significant down-regulation of {sigma}B-regulated transcripts. We also discovered that exogenous butenolides promoted the transition from planktonic to biofilm growth. Our results suggest that butenolides may serve as inter-kingdom signalling compounds between plants and bacteria to help shape rhizosphere communities.

microbiology↗

bioRxiv2023

SARS-CoV-2 protein NSP2 enhances microRNA-mediated translational repression

microRNAs (miRNAs) inhibit mRNA translation initiation by recruiting the GIGYF2/4EHP translation repressor complex to the mRNA 5 cap structure. Viruses utilise miRNAs to impair the host antiviral immune system and facilitate viral infection by expressing their own miRNAs or co-opting cellular miRNAs. We recently reported that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encoded non-structural protein 2 (NSP2) interacts with GIGYF2. This interaction is critical for blocking translation of the Ifn1-b mRNA that encodes the cytokine Interferon-{beta}, and thereby impairs the host antiviral immune response. However, it is not known whether NSP2 also affects miRNA-mediated silencing. Here, we demonstrate the pervasive augmentation of the miRNA-mediated translational repression of cellular mRNAs by NSP2. We show that NSP2 interacts with Argonaute 2, the core component of the miRNA-Induced Silencing Complex (miRISC) and enhances the translational repression mediated by natural miRNA binding sites in the 3 UTR of cellular mRNAs. Our data reveal an additional layer of the complex mechanism by which SARS-CoV-2 and likely other coronaviruses manipulate the host gene expression program through co-opting the host miRNA-mediated silencing machinery.

cell biology↗

bioRxiv2021

The Magnaporthe oryzae MAP kinase Pmk1 regulates polycomb repressive complex 2 to reprogram genes expression for biotrophic growth

Biotrophic and hemibiotrophic fungi have evolved the ability to colonize living plant cells, but how they establish biotrophic growth by remodeling gene expression is poorly understood. By using in planta invasive hyphae (IH) of Magnaporthe oryzae to perform an integrated Chromatin immunoprecipitation sequencing (ChIPseq) and RNA-seq analysis, combining with biological and cellular analyses, we found Polycomb repressive complex 2 (PRC2)-mediated epigenetic repression plays a key role in regulating biotrophic growth. ChIPseq for biotrophic IH samples identified 1701 PRC2 target genes. RNA-seq analysis showed that expression of 462 PRC2 target genes were up-regulated in the {Delta}suz12 mutant, while 82 were down-regulated, indicating a major role of PRC2 in gene repression of IH. During biotrophic growth, PRC2 repressed fungal cell wall synthesis genes and extracellular enzyme genes required for penetration, and secondary metabolites biosynthesis genes required for necrotrophic growth. A great number of effector-encoding genes were repressed by PRC2, which were highly expressed during penetration stage, suggesting PRC2 coordinates biotrophic growth by regulating effector suppression for immune evasion. This regulation was finely coordinated by Pmk1, through regulating phosphorylation, nuclear localization and protein abundance of Suz12. Our results indicate that the Pmk1-PRC2 regulatory module is required for gene remodeling to facilitate biotrophic growth in M. oryzae. IMPORTANCEBiotrophic and hemibiotrophic fungi establish a biotrophic stage for infection in host cells. For example, M. oryzae forms appressoria to penetrate host cell and establish a biotrophic growth stage for infection. How gene expression patterns are elaborately controlled for fungal biotrophic growth is largely unknown. In this study, we found that, the PRC2-mediated H3K27me3 repressed fungal penetration-required cell wall synthesis genes and extracellular enzyme genes, and necrotrophic growth-required secondary metabolites biosynthesis genes for biotrophic growth. Interestingly, a great number of effector-encoding genes were also repressed by PRC2 at biotrophic stage, which were highly expressed at penetration stage, suggesting PRC2 coordinates biotrophic growth by regulating effector suppression for immune evasion. The PRC2-mediated epigenetic repression is therefore required for the gene expression remodeling during fungal infection. This regulation was finely coordinated by Pmk1, through regulating nuclear localization and protein abundance of the PRC2 component Suz12.

microbiology↗

bioRxiv2020

The Clusters of Transcription Factors NFATC2, STAT5, GATA2, AP1,RUNX1 and EGR2 Binding Sites at the Induced Il13 Enhancers Mediate Il13 Gene Transcription in Response to Antigenic Stimulation

Interleukin-13 plays a critical role in mediating many biological processes responsible for allergic inflammation. Mast cells express Il13 mRNA and produce IL-13 protein in response to antigenic stimulation. Enhancers are essential in promoting gene transcription and are thought to activate transcription by delivering essential accessory co-factors to the promoter to potentiate gene transcription. However, enhancers mediating Il13 have not been identified. Furthermore, which Il13 enhancers detect signals triggered by antigenic stimulation have not yet been defined. In this study, we identified potential Il13 enhancers using histone modification monomethylation at lysine residue 4 on histone 3 (H3K4me1) ChIP-seq and acetylation at lysine residue 27 on histone 3 (H3K27ac) ChIP-seq. We used Omni-ATAC-seq to determine which accessible regions within the potential Il13 enhancers that responded to IgE receptor crosslinking. We also demonstrated that the transcription factor (TF) cluster consisting of the NFATC2, STAT5, GATA2, AP1, and RUNX1 binding sites at the proximal Il13 enhancer, the TF cluster consisting of the EGR2-binding site at the distal Il13 E+6.5 enhancer, are critical in sensing the signals triggered by antigenic stimulation. Those enhancers, which are responsive to antigenic stimulation and constitutively active, cooperate to generate greater transcriptional outputs. Our study reveals a novel mechanism underlying how antigenic stimulation induces robust Il13 mRNA expression in mast cells.

immunology↗

bioRxiv2020

GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super-enhancers

Mast cells (MCs) are critical effectors of allergic inflammation and protection against parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the MC lineage-determining factors (LDTFs). However, it is unclear whether these LDTFs regulate chromatin accessibility at MC enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of MC identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation. We found that the number and densities of GATA2-but not MITF-bound sites at the super-enhancers were several folds higher than that at the typical enhancers. Our studies revealed that GATA2 promotes robust gene transcription to maintain MC identity and respond to antigenic stimulation by binding to super-enhancer regions with dense GATA2 binding sites available at key MC genes.

molecular biology↗

bioRxiv2017

Split personality of Aluminum Activated Malate Transporter family proteins: facilitation of both GABA and malate transport

Plant aluminum activated malate transporters (ALMTs) are currently classified as anion channels; they are also known to be regulated by diverse signals leading to a range of physiological responses. Gamma-aminobutyric acid (GABA) regulation of anion flux through ALMT proteins requires the presence of a specific amino acid motif in ALMTs that shares similarity with a GABA-binding site in mammalian GABAA receptors. Here, we explore why TaALMT1-activation leads to a negative correlation between malate efflux and endogenous GABA concentrations ([GABA]i) in both wheat root tips and in heterologous expression systems. We show that TaALMT1 activation reduces [GABA]i because TaALMT1 facilitates GABA efflux. TaALMT1-expression also leads to GABA transport into cells, demonstrated by a yeast complementation assay and via 14CGABA uptake into TaALMT1-expressing Xenopus laevis oocytes; this was found to be a general feature of all ALMTs we examined. Mutation of the GABA motif (TaALMT1F213C) prevented both GABA influx and efflux, and uncoupled the relationship between malate efflux and [GABA]i. We conclude that ALMTs are likely to act as both GABA and anion transporters in planta. GABA and malate appear to interact with ALMTs in a complex manner regulating each others transport, suggestive of a role for ALMTs in communicating metabolic status.

plant biology↗