Drought-induced protein (Di19-3) plays a role in auxin signaling by interacting with IAA14 in Arabidopsis

The C2H2-type zinc finger transcription factor ZmDi19-7 regulates plant height and organ size by promoting cell size in maize

The drought-induced protein 19 (Di19) gene family encodes a Cys2/His2 zinc-finger protein implicated in responses to diverse plant stressors. To date, potential roles of these proteins as transcription factors remain largely elusive in maize. Here, we show that ZmDi19-7 gene exerts pivotal functions in regulation of plant height and organ growth by modulating the cell size in maize. ZmDi19-7 physically interacts with ubiquitin receptor protein ZmDAR1b, which is indispensable in ubiquitination of ZmDi19-7 and affects its protein stability. Further genetic analysis demonstrated that ZmDAR1b act in a common pathway with ZmDi19-7 to regulate cell size in maize. ZmDi19-7, severing as a transcriptional factor, is significantly enriched in conserved DiBS element in the promoter region of ZmHSP22, ZmHSP18c, ZmSAUR25, ZmSAUR55, ZmSAUR7 and ZmXTH23 and orchestrates the expression of these genes involving in auxin-mediated cell expansion and protein processing in the endoplasmic reticulum. Thus, our findings demonstrate that ZmDi19-7 is an important newfound component of the ubiquitin-proteasome pathway in regulation of plant height and organ size in maize. These discoveries highlight potential targets for the genetic improvement of maize in the future.

A point mutation in the IAA14 promoter enhances callus formation and regeneration

Callus formation induced by auxin accumulation is considered the first step of in vitro plant regeneration. In Arabidopsis, degradation of the Aux/IAA protein, IAA14, in response to auxin signaling, which activates the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 along with a series of downstream transcription factors, also plays a critical role in this process. However, the specific mechanism by which auxin regulates callus formation remains unclear. By screening mutant library in the solitary root 1 (iaa14/slr) Arabidopsis background we obtained the callus formation related 2 (cfr2) mutant. The cfr2 mutant exhibited a stronger capacity for callus formation, as well as lateral root and adventitious root regeneration from leaf explants than wild type (WT) seedlings, but did not recover gravitropism capability. The auxin signal in cfr2 was significantly enhanced, and the expression of some downstream transcription factors was increased. Map-based cloning, whole genome resequencing, and phenotypic complementation experiments showed that the phenotypes observed in the cfr2 mutant were caused by a point mutation in the IAA14 promoter region. This mutation, which is predicted to disrupt the binding of LBD16, LBD19, and LBD30 to the IAA14 promoter, changed the expression pattern of IAA14 in cfr2. Taken together, our results identified a new mutation in the IAA14 promoter region, which affects the expression pattern of IAA14 and in turn its ability to control plant regeneration.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01493-y.

Functional annotation of Candida albicans hypothetical proteins: a bioinformatics approach

Candida albicans is a member of the ascomycetes class of fungi and it is an opportunistic pathogen species responsible for a wide range of fungal infections in humans. Bioinformatics and sequencing analysis of Candida proteomics has disclosed that around 69% proteome is still uncharacterized which needs to be annotated with functions. The NCBI-Genome has termed them as hypothetical proteins (HPs) in the whole proteome of Candida. Interpretation of this substantial portion of the proteome can reveal novel pharmacological targets for markers, drug development, and other therapeutics and so on. In this article, we have assigned functional annotation to these hypothetical proteins using bioinformatics methodologies. The advanced and robust computational models have been used to assign the preliminary functions to these putative HPs with high level of confidence. The findings of this study unveil some novel pharmacological targets for drug therapy and vaccines and it would help to identify novel molecular mechanisms underlying the fungal pathogenesis.

Phenotyping and metabolome analysis reveal the role of AdoMetDC and Di19 genes in determining acquired tolerance to drought in rice

Water-saving attempts for rice cultivation often reduce yields. Maintaining productivity under drought is possible when rice genotypes are bred with improved metabolism and spikelet fertility. Although attempts have been made to introgress water mining and water use efficiency traits, combining acquired tolerance traits (ATTs), that is, specific traits induced or upregulated to better tolerate severe stress, appears equally important. In our study, we screened 90 rice germplasm accessions that represented the molecular and phenotypic variations of 851 lines of the 3 K rice panel. Utilising phenomics, we identified markers linked to ATTs through association analysis of over 0.2 million SNPs derived from whole-genome sequences. Propensity to respond to 'induction' stress varied significantly among genotypes, reflecting differences in cellular protection against oxidative stress. Among the ATTs, the hydroxyl radical and proline contents exhibited the highest variability. Furthermore, these significant variations in ATTs were strongly correlated with spikelet fertility. The 43 significant markers associated with ATTs were further validated using a different subset of contrasting genotypes. Gene expression studies and metabolomic profiling of two well-known contrasting genotypes, APO (tolerant) and IR64 (sensitive), identified two ATT genes: AdoMetDC and Di19. Our study highlights the relevance of polyamine biosynthesis in modulating ATTs in rice. Genotypes with superior ATTs and the associated markers can be effectively employed in breeding rice varieties with sustained spikelet fertility and grain yield under drought.

Two splice forms of OsbZIP1, a homolog of AtHY5, function to regulate skotomorphogenesis and photomorphogenesis in rice

Plants possess well-developed light sensing mechanisms and signal transduction systems for regulating photomorphogenesis. ELONGATED HYPOCOTYL5 (HY5), a basic leucine zipper (bZIP) transcription factor, has been extensively characterized in dicots. In this study, we show that OsbZIP1 is a functional homolog of Arabidopsis (Arabidopsis thaliana) HY5 (AtHY5) and is important for light-mediated regulation of seedling and mature plant development in rice (Oryza sativa). Ectopic expression of OsbZIP1 in rice reduced plant height and leaf length without affecting plant fertility, which contrasts with OsbZIP48, a previously characterized HY5 homolog. OsbZIP1 is alternatively spliced, and the OsbZIP1.2 isoform lacking the CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)-binding domain regulated seedling development in the dark. Rice seedlings overexpressing OsbZIP1 were shorter than the vector control under white and monochromatic light conditions, whereas RNAi knockdown seedlings displayed the opposite phenotype. While OsbZIP1.1 was light-regulated, OsbZIP1.2 showed a similar expression profile in both light and dark conditions. Due to its interaction with OsCOP1, OsbZIP1.1 undergoes 26S proteasome-mediated degradation under dark conditions. Also, OsbZIP1.1 interacted with and was phosphorylated by CASEIN KINASE2 (OsCK2α3). In contrast, OsbZIP1.2 did not show any interaction with OsCOP1 or OsCK2α3. We propose that OsbZIP1.1 likely regulates seedling development in the light, while OsbZIP1.2 is the dominant player under dark conditions. The data presented in this study reveal that AtHY5 homologs in rice have undergone neofunctionalization, and alternative splicing of OsbZIP1 has increased the repertoire of its functions.

Systematical Characterization of the Cotton Di19 Gene Family and the Role of GhDi19-3 and GhDi19-4 as Two Negative Regulators in Response to Salt Stress

Drought-induced 19 (Di19) protein is a Cys2/His2 (C2H2) type zinc-finger protein, which plays a crucial role in plant development and in response to abiotic stress. This study systematically investigated the characteristics of the GhDi19 gene family, including the member number, gene structure, chromosomal distribution, promoter cis-elements, and expression profiles. Transcriptomic analysis indicated that some GhDi19s were up-regulated under heat and salt stress. Particularly, two nuclear localized proteins, GhDi19-3 and GhDi19-4, were identified as being in potential salt stress responsive roles. GhDi19-3 and GhDi19-4 decreased sensitivity under salt stress through virus-induced gene silencing (VIGS), and showed significantly lower levels of H2O2, malondialdehyde (MDA), and peroxidase (POD) as well as significantly increased superoxide dismutase (SOD) activity. This suggested that their abilities were improved to effectively reduce the reactive oxygen species (ROS) damage. Furthermore, certain calcium signaling and abscisic acid (ABA)-responsive gene expression levels showed up- and down-regulation changes in target gene-silenced plants, suggesting that GhDi19-3 and GhDi19-4 were involved in calcium signaling and ABA signaling pathways in response to salt stress. In conclusion, GhDi19-3 and GhDi19-4, two negative transcription factors, were found to be responsive to salt stress through calcium signaling and ABA signaling pathways.

Homologous Drought-Induced 19 Proteins, PtDi19-2 and PtDi19-7, Enhance Drought Tolerance in Transgenic Plants

Drought-induced 19 (Di19) proteins play important roles in abiotic stress responses. Thus far, there are no reports about Di19 family in woody plants. Here, eight Di19 genes were identified in poplar. We analyzed phylogenetic tree, conserved protein domain, and gene structure of Di19 gene members in seven species. The results showed the Di19 gene family was very conservative in both dicotyledonous and monocotyledonous forms. On the basis of transcriptome data, the expression patterns of Di19s in poplar under abiotic stress and ABA treatment were further studied. Subsequently, homologous genes PtDi19-2 and PtDi19-7 with strong response to drought stress were identified. PtDi19-2 functions as a nuclear transcriptional activator with a transactivation domain at the C-terminus. PtDi19-7 is a nuclear and membrane localization protein. Additionally, PtDi19-2 and PtDi19-7 were able to interact with each other in yeast two-hybrid system. Overexpression of PtDi19-2 and PtDi19-7 in Arabidopsis was found. Phenotype identification and physiological parameter analysis showed that transgenic Arabidopsis increased ABA sensitivity and drought tolerance. PtDi19-7 was overexpressed in hybrid poplar 84K (Populus alba × Populus glandulosa). Under drought treatment, the phenotype and physiological parameters of transgenic poplar were consistent with those of transgenic Arabidopsis. In addition, exogenous ABA treatment induced lateral bud dormancy of transgenic poplar and stomatal closure of transgenic Arabidopsis. The expression of ABA/drought-related marker genes was upregulated under drought treatment. These results indicated that PtDi19-2 and PtDi19-7 might play a similar role in improving the drought tolerance of transgenic plants through ABA-dependent signaling pathways.

Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm

Maize (Zea mays L.) production is constrained by drought and heat stresses. The combination of these two stresses is likely to be more detrimental. To breed for maize cultivars tolerant of these stresses, 162 tropical maize inbred lines were evaluated under combined heat and drought (CHD) and terminal drought (TD) conditions. The mixed linear model was employed for the genome-wide association study using 7834 SNP markers and several phenotypic data including, days to 50% anthesis (AD) and silking (SD), husk cover (HUSKC), and grain yield (GY). In total, 66, 27, and 24 SNPs were associated with the traits evaluated under CHD, TD, and their combined effects, respectively. Of these, four single nucleotide polymorphism (SNP) markers (SNP_161703060 on Chr01, SNP_196800695 on Chr02, SNP_195454836 on Chr05, and SNP_51772182 on Chr07) had pleiotropic effects on both AD and SD under CHD conditions. Four SNPs (SNP_138825271 (Chr03), SNP_244895453 (Chr04), SNP_168561609 (Chr05), and SNP_62970998 (Chr06)) were associated with AD, SD, and HUSKC under TD. Twelve candidate genes containing phytohormone cis-acting regulating elements were implicated in the regulation of plant responses to multiple stress conditions including heat and drought. The SNPs and candidate genes identified in the study will provide invaluable information for breeding climate smart maize varieties under tropical conditions following validation of the SNP markers.

Lack of ethylene does not affect reproductive success and synergid cell death in Arabidopsis

The signaling pathway of the gaseous hormone ethylene is involved in plant reproduction, growth, development, and stress responses. During reproduction, the two synergid cells of the angiosperm female gametophyte both undergo programmed cell death (PCD)/degeneration but in a different manner: PCD/degeneration of one synergid facilitates pollen tube rupture and thereby the release of sperm cells, while PCD/degeneration of the other synergid blocks supernumerary pollen tubes. Ethylene signaling was postulated to participate in some of the synergid cell functions, such as pollen tube attraction and the induction of PCD/degeneration. However, ethylene-mediated induction of synergid PCD/degeneration and the role of ethylene itself have not been firmly established. Here, we employed the CRISPR/Cas9 technology to knock out the five ethylene-biosynthesis 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) genes and created Arabidopsis mutants free of ethylene production. The ethylene-free mutant plants showed normal triple responses when treated with ethylene rather than 1-aminocyclopropane-1-carboxylic acid, but had increased lateral root density and enlarged petal sizes, which are typical phenotypes of mutants defective in ethylene signaling. Using these ethylene-free plants, we further demonstrated that production of ethylene is not necessarily required to trigger PCD/degeneration of the two synergid cells, but certain components of ethylene signaling including transcription factors ETHYLENE-INSENSITIVE 3 (EIN3) and EIN3-LIKE 1 (EIL1) are necessary for the death of the persistent synergid cell.

OsRR6, a type-A response regulator in rice, mediates cytokinin, light and stress responses when over-expressed in Arabidopsis

Plants have evolved a complex network of components that sense and respond to diverse signals. In the present study, we have characterized OsRR6, a type-A response regulator, which is part of the two-component sensor-regulator machinery in rice. The expression of OsRR6 is induced by exogenous cytokinin and various abiotic stress treatments, including drought, cold and salinity stress. Organ-specific expression analysis revealed that its expression is high in anther and low in shoot apical meristem. The Arabidopsis plants constitutively expressing OsRR6 (OsRR6^OX) exhibited reduced cytokinin sensitivity, adventitious root formation and enhanced anthocyanin accumulation in seeds. OsRR6^OX plants were more tolerant to drought and salinity conditions when compared to wild-type. The hypocotyl growth in OsRR6^OX seedlings was significantly inhibited under red, far-red and blue-light conditions and also a decline in transcript levels of OsRR6 was observed in rice under the above monochromatic as well as white light treatments. Transcriptome profiling revealed that the genes associated with defense responses and anthocyanin metabolism are up-regulated in OsRR6^OX seedlings. Comparative transcriptome analysis showed that the genes associated with phenylpropanoid and triterpenoid biosynthesis are enriched among differentially expressed genes in OsRR6^OX seedlings of Arabidopsis, which is in conformity with reanalysis of the transcriptome data performed in rice transgenics for OsRR6. Further, genes like DREB1A/CBF3, COR15A, KIN1, ERD10 and RD29A are significantly upregulated in OsRR6^OX seedlings when subjected to ABA and abiotic stress treatments. Thus, a negative regulator of cytokinin signaling, OsRR6, plays a positive role in imparting abiotic stress tolerance.

A comprehensive transcriptome analysis of contrasting rice cultivars highlights the role of auxin and ABA responsive genes in heat stress response

Sensing a change in ambient temperature is key to survival among all living organisms. Temperature fluctuations due to climate change are a matter of grave concern since it adversely affects growth and eventually the yield of crop plants, including two of the major cereals, i.e., rice and wheat. Thus, to understand the response of rice seedlings to elevated temperatures, we performed microarray-based transcriptome analysis of two contrasting rice cultivars, Annapurna (heat tolerant) and IR64 (heat susceptible), by subjecting their seedlings to 37 °C and 42 °C, sequentially. The transcriptome analyses revealed a set of uniquely regulated genes and related pathways in red rice cultivar Annapurna, particularly associated with auxin and ABA as a part of heat stress response in rice. The changes in expression of few auxin and ABA associated genes, such as OsIAA13, OsIAA20, ILL8, OsbZIP12, OsPP2C51, OsDi19-1 and OsHOX24, among others, were validated under high-temperature conditions using RT-qPCR. In particular, the expression of auxin-inducible SAUR genes was enhanced considerably at both elevated temperatures. Further, using genes that expressed inversely under heat vs. cold temperature conditions, we built a regulatory network between transcription factors (TF) such as HSFs, NAC, WRKYs, bHLHs or bZIPs and their target gene pairs and determined regulatory coordination in their expression under varying temperature conditions. Our work thus provides useful insights into temperature-responsive genes, particularly under elevated temperature conditions, and could serve as a resource of candidate genes associated with thermotolerance or downstream components of temperature sensors in rice.