Genome-wide characterization of 2OGD superfamily for mining of susceptibility factors responding to various biotic stresses in Musa spp

Bananas are an important staple food and cash crop, but they are vulnerable to a variety of pests and diseases that substantially reduce yield and quality. Banana diseases are challenging to control and necessitate an integrated strategy, and development of resistant cultivars is one of the effective ways of managing diseases. Lasting disease resistance is the main goal in crop improvement and resistance mediated by a single resistant (R) gene mostly lack durability. However, long-term resistance can be obtained by inactivating susceptibility factors (S), which facilitate pathogen infection and proliferation. Identification and inactivation of susceptibility factors against the major pathogens like Fusarium oxysporum f. sp. cubense (Foc), Pseudocercospora eumusae and Pratylenchus coffeae in banana will be an effective way in developing banana varieties with more durable resistance. Downy mildew resistance 6 (DMR6) and DMR-like oxygenases (DLO1) are one such susceptibility factors and they belong to 2-oxoglutarate Fe(II) dependent oxygenases (2OGD) superfamily. 2OGDs are known to catalyze a plethora of reactions and also confer resistance to different pathogens in various crops, but not much is known about the 2OGD in Musa species. Through a comprehensive genome-wide analysis, 133 and 122 potential 2OGDs were systematically identified and categorized from the A and B genomes of banana, respectively. Real time expression of dmr6 and dlo1 genes showed positive correlation with transcriptome data upon Foc race1 and TR4 infection and examination of expression pattern of Macma4_04_g22670 (Ma04_g20880) and Macma4_02_g13590 (Ma02_g12040) genes revealed their involvement in Foc race1 and TR4 infections, respectively. Further the expression profile of 2OGDs, specifically Macma4_04_g25310 (Ma04_g23390), Macma4_08_g11980 (Ma08_g12090) and Macma4_04_g38910 (Ma04_g36640) shows that they may play a significant role as a susceptibility factor, particularly against P. eumusae and P. coffeae, implying that they can be exploited as a candidate gene for editing in developing resistant cultivars against these diseases. In summary, our findings contribute to a deeper comprehension of the evolutionary and functional aspects of 2OGDs in Musa spp. Furthermore, they highlight the substantial functions of these family constituents in the progression of diseases. These insights hold significance in the context of enhancing the genetic makeup of bananas to attain extended and more durable resistance against pathogens.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01380-y.

Functional analysis of a susceptibility gene (HIPP27) in the Arabidopsis thaliana-Meloidogyne incognita pathosystem by using a genome editing strategy

BACKGROUND

Plant-parasitic root-knot nematodes cause immense yield declines in crop plants that ultimately obviate global food security. They maintain an intimate relationship with their host plants and hijack the host metabolic machinery to their own advantage. The existing resistance breeding strategies utilizing RNAi and resistance (R) genes might not be particularly effective. Alternatively, knocking out the susceptibility (S) genes in crop plants appears to be a feasible approach, as the induced mutations in S genes are likely to be long-lasting and may confer broad-spectrum resistance. This could be facilitated by the use of CRISPR/Cas9-based genome editing technology that precisely edits the gene of interest using customizable guide RNAs (gRNAs) and Cas9 endonuclease.

RESULTS

Initially, we characterized the nematode-responsive S gene HIPP27 from Arabidopsis thaliana by generating HIPP27 overexpression lines, which were inoculated with Meloidogyne incognita. Next, two gRNAs (corresponding to the HIPP27 gene) were artificially synthesized using laboratory protocols, sequentially cloned into a Cas9 editor plasmid, mobilized into Agrobacterium tumefaciens strain GV3101, and transformed into Arabidopsis plants using the floral dip method. Apart from 1-3 bp deletions and 1 bp insertions adjacent to the PAM site, a long deletion of approximately 161 bp was documented in the T0 generation. Phenotypic analysis of homozygous, 'transgene-free' T2 plants revealed reduced nematode infection compared to wild-type plants. Additionally, no growth impairment was observed in gene-edited plants.

CONCLUSION

Our results suggest that the loss of function of HIPP27 in A. thaliana by CRISPR/Cas9-induced mutagenesis can improve host resistance to M. incognita.

Case-only approach applied in environmental epidemiology: 2 examples of interaction effect using the US National Health and Nutrition Examination Survey (NHANES) datasets

INTRODUCTION

By substituting the general 'susceptibility factor' concept for the conventional 'gene' concept in the case-only approach for gene-environment interaction, the case-only approach can also be used in environmental epidemiology. Under the independence between the susceptibility factor and environmental exposure, the case-only approach can provide a more precise estimate of an interaction effect.

METHODS

Two analysis examples of the case-only approach in environmental epidemiology are provided using the 2015-2016 and 2017-2018 US National Health and Nutritional Examination Survey (NHANES): (i) the negative interaction effect between blood chromium level and glycohemoglobin level on albuminuria and (ii) the positive interaction effect between blood cobalt level and old age on albuminuria. The second part of the methods (theoretical backgrounds) summarized the logic and equations provided in previous studies about the case-only approach.

RESULTS

(i) When a 1 μg/L difference of both blood chromium level (mcg/L) and a 1% difference in blood glycohemoglobin level coincide, the multiplicative interaction contrast ratio (ICR_c/nc) was 0.72 (95% CI 0.35-1.60), with no statistical significance. However, when only the cases were analyzed, the case-only ICR (ICR_CO) was 0.59 (95% CI 0.28-0.95), with a statistical significance (a negative interaction effect). (ii) When a 1 μg/L difference of both blood cobalt levels and a 1-year difference in age coincide, the multiplicative interaction contrast ratio (ICR_c/nc) was 1.13 (95% CI 0.99-1.37), with no statistical significance. However, when only the cases were analyzed, the case-only ICR (ICR_CO) was 1.21 (95% CI 1.06-1.51), with a statistical significance (a positive interaction effect).

DISCUSSION

The discussion suggested the theoretical background and previous literature about the possible protective interaction effect between blood chromium levels and blood glycohemoglobin levels on the incidence of albuminuria and the possible aggravating interaction effect between blood cobalt levels and increasing ages on the incidence of albuminuria. If the independence assumption between a susceptibility factor and environmental exposure in a study with cases and non-cases is kept, the case-only approach can provide a more precise interaction effect estimate than conventional approaches with both cases and non-cases.

Effects of short-term selenium exposure on respiratory activity and proximate body composition of early-life stages of Catla catla, Labeo rohita and Cirrhinus mrigala

Metal exposure impairs respiration, increases metabolic demand, and reduces energy storage/fitness in aquatic species. Respiratory impairment and energy storage was examined in acute selenium-exposed Indian major carps, Catla catla, Labeo rohita and Cirrhinus mrigala fry and were correlated with exposure concentrations. Toxicity effects were determined in a renewal bioassay using 96 h lethal selenium concentrations. Species sensitivity distribution (SSD) was also used to derive predicted no-effect concentrations, toxicity exposure ratios, for selenium exposures to early-life fish stages. Mortality was proportional with increasing concentrations. Oxygen consumption and lipid content compared to moisture and ash and of all protein content in tissues of C. catla and C. mrigala indicates that lowered oxygen consumption is directly predictive of lowered lipid content and selenium-induced hypoxia impacts the energy/nutritional status of the early-life stage of carp. This cross-taxa comparison will have major implications for advancing impact assessment and allow better targeting of species for conservation measures.

Impaired serine metabolism complements LRRK2-G2019S pathogenicity in PD patients

Parkinson's disease (PD) is a multifactorial disorder with complex etiology. The most prevalent PD associated mutation, LRRK2-G2019S is linked to familial and sporadic cases. Based on the multitude of genetic predispositions in PD and the incomplete penetrance of LRRK2-G2019S, we hypothesize that modifiers in the patients' genetic background act as susceptibility factors for developing PD. To assess LRRK2-G2019S modifiers, we used human induced pluripotent stem cell-derived neuroepithelial stem cells (NESCs). Isogenic controls distinguish between LRRK2-G2019S dependent and independent cellular phenotypes. LRRK2-G2019S patient and healthy mutagenized lines showed altered NESC self-renewal and viability, as well as impaired serine metabolism. In patient cells, phenotypes were only partly LRRK2-G2019S dependent, suggesting a significant contribution of the genetic background. In this context we identified the gene serine racemase (SRR) as a novel patient-specific, developmental, genetic modifier contributing to the aberrant phenotypes. Its enzymatic product, d-serine, rescued altered cellular phenotypes. Susceptibility factors in the genetic background, such as SRR, could be new targets for early PD diagnosis and treatment.

High penetrance of acute intermittent porphyria in a Spanish founder mutation population and CYP2D6 genotype as a susceptibility factor

BACKGROUND

Acute intermittent porphyria (AIP) is a low-penetrant genetic metabolic disease caused by a deficiency of hydroxymethylbilane synthase (HMBS) in the haem biosynthesis. Manifest AIP (MAIP) is considered when carriers develop typical acute neurovisceral attacks with elevation of porphyrin precursors, while the absence of attacks is referred to as latent AIP (LAIP). Attacks are often triggered by drugs, endocrine factors, fasting or stress. Although AIP penetrance is traditionally considered to be around 10-20%, it has been estimated to be below 1% in general population studies and a higher figure has been found in specific AIP populations. Genetic susceptibility factors underlying penetrance are still unknown. Drug-metabolizing cytochrome P450 enzymes (CYP) are polymorphic haem-dependent proteins which play a role in haem demand, so they might modulate the occurrence of AIP attacks. Our aim was to determine the prevalence and penetrance of AIP in our population and analyse the main hepatic CYP genes to assess their association with acute attacks. For this, CYP2C9*2, *3; CYP2C19*2; CYP2D6*4, *5; CYP3A4*1B and CYP3A5*3 defective alleles were genotyped in fifty AIP carriers from the Region of Murcia, a Spanish population with a high frequency of the HMBS founder mutation c.669_698del30.

RESULTS

AIP penetrance was 52%, and prevalence was estimated as 17.7 cases/million inhabitants. The frequency of defective CYP2D6 alleles was 3.5 times higher in LAIP than in MAIP. MAIP was less frequent among CYP2D6*4 and *5 carriers (p < 0.05). The urine porphobilinogen (PBG)-to-creatinine ratio was lower in these individuals, although it was associated with a lower prevalence of attacks (p < 0.05) rather than with the CYP2D6 genotype.

CONCLUSIONS

AIP prevalence in our region is almost 3 times higher than that estimated for the rest of Spain. The penetrance was high, and similar to other founder mutation AIP populations. This is very relevant for genetic counselling and effective health care. CYP2D6*4 and *5 alleles may be protective factors for acute attacks, and CYP2D6 may constitute a penetrance-modifying gene. Further studies are needed to confirm these findings, which would allow a further progress in clinical risk profile assessment based on the CYP genotype, leading to predictive personalized medicine for each AIP carrier in the future.

Can MTHFR C677T and A1298C Polymorphisms Alter the Risk and Severity of Sporadic Breast Cancer in Brazilian Women?

INTRODUCTION

Polymorphisms in the methylenetetrahydrofolate reductase gene (MTHFR) modify the risk and severity of sporadic breast cancer (BC). In this context, the MTHFR C677T and A1298C polymorphisms have been associated with risk and severity of sporadic BC.

PATIENTS AND METHODS

In total, 253 women with BC and 257 controls were enrolled in this study. Polymorphisms were analyzed using restriction fragment length polymorphism - polymerase chain reaction. Epidemiology, tumor characteristics, and reproductive factors were considered in the analysis. Statistical tests included the χ² test, the Fisher exact test, and the Mann-Whitney and Kruskal-Wallis tests, or parametric equivalents.

RESULTS

MTHFR polymorphisms were not a risk factor for BC. The 677CC genotype was associated with distant metastasis (odds ratio [OR] = 5.311; 95% confidence interval [CI] = 1.124-25.09) and lower estrogen receptor expression, whereas the 1298AA genotype was associated with stage 0 (OR = 0.244; 95% CI = 0.077-0.771) and increased estrogen receptor expression. In haplotype analysis, 677CC/1298AA was associated with hypertension (OR = 1.979; 95% CI = 1.036-3.782), and 677CT/1298AC was associated with invasive carcinoma of no special type (OR = 0.472; 95% CI = 0.243-0.918) and stage 0 (OR = 3.476; 95% CI = 1.341-10.47).

CONCLUSION

The MTHFR C677T and A1298C polymorphisms do not alter the risk of BC, but are associated with the clinical severity of BC.