Identification and Developmental Expression of Xenopus laevis SUMO Proteases

SUMO proteins are small ubiquitin-related modifiers. All SUMOs are synthesized as propeptides that are post-translationally cleaved prior to conjugation. After processing, SUMOs become covalently conjugated to cellular targets through a pathway that is similar to ubiquitination. Ubiquitin like protein proteases/Sentrin specific proteases (Ulp/SENPs) mediate both processing and deconjugation of SUMOs. The action of Ulp/SENPs makes SUMOylation a highly dynamic post-translational modification. To investigate how Ulp/SENPs are regulated in a developmental context, we isolated and characterized all Ulp/SENPs in Xenopus laevis. Xenopus possess homologues of mammalian SENP3, 5, 6 and 7. All of these enzymes reacted with HA-tagged vinyl sulfone derivatives of SUMO-2 (HA-SU2-VS) but not SUMO-1 (HA-SU1-VS), suggesting that they act primarily on SUMO-2 and -3. In contrast, Xenopus possess a single member of the SENP1/SENP2 subfamily of Ulp/SENPs, most closely related to mammalian SENP1. Xenopus SENP1 reacted with HA-SU1-VS and HA-SU2-VS, suggesting that it acts on all SUMO paralogues. We analyzed the mRNA and protein levels for each of the Ulp/SENPs through development; we found that they show distinct patterns of expression that may involve both transcriptional and post-transcriptional regulation. Finally, we have characterized the developmental function of the most abundant Ulp/SENP found within Xenopus eggs, SENP3. Depletion of SENP3 using morpholino antisense oligonucleotides (morpholinos) caused accumulation of high molecular weight SUMO-2/3 conjugated species, defects in developing embryos and changes in the expression of some genes regulated by the transforming growth factor beta (TGF-β) pathway. These findings collectively indicate that SUMO proteases are both highly regulated and essential for normal development

Development of polymorphic markers in the immune gene complex loci of cattle

Publication history: Accepted - 18 January 2021; Published online - 6 March 2021The addition of cattle health and immunity traits to genomic selection indices holds promise to increase individual animal longevity and productivity, and decrease economic losses from disease. However, highly variable genomic loci that contain multiple immune-related genes were poorly assembled in the first iterations of the cattle reference genome assembly and underrepresented during the development of most commercial genotyping platforms. As a consequence, there is a paucity of genetic markers within these loci that may track haplotypes related to disease susceptibility. By using hierarchical assembly of bacterial artificial chromosome inserts spanning 3 of these immune-related gene regions, we were able to assemble multiple full-length haplotypes of the major histocompatibility complex, the leukocyte receptor complex, and the natural killer cell complex. Using these new assemblies and the recently released ARS-UCD1.2 reference, we aligned whole-genome shotgun reads from 125 sequenced Holstein bulls to discover candidate variants for genetic marker development. We selected 124 SNPs, using heuristic and statistical models to develop a custom genotyping panel. In a proof-of-principle study, we used this custom panel to genotype 1,797 Holstein cows exposed to bovine tuberculosis (bTB) that were the subject of a previous GWAS study using the Illumina BovineHD array. Although we did not identify any significant association of bTB phenotypes with these new genetic markers, 2 markers exhibited substantial effects on bTB phenotypic prediction. The models and parameters trained in this study serve as a guide for future marker discovery surveys particularly in previously unassembled regions of the cattle genome.Hammond, Heimeier, and Schwartz were supported by United Kingdom Research and Innovation, Biotechnology and Biological Sciences Research Council (UKRI-BBSRC) funding awards BB/M027155/1, BBS/E/I/00007031, BBS/E/I/00007038, BBS/E/I/00007039, BBS/OS/GC/000015B, and BBS/OS/GC/200016. Glass was supported by UKRI-BBSRC funding awards BB/J004227/1, BB/J004235/1, and BB/P013740; Glass, Skuce, and Allen were also supported by UKRI-BBSRC BB/E018386/1, BB/E018335/1 and 2, and BB/L004054/1; Glass was also supported by UKRI-BBSRC award BB/M027155/1 and BB/P013740/1. Wilkinson was supported by UKRI-BBSRC BB/L004054/1. We gratefully acknowledge the Agri-Food and Biosciences Institute (AFBI, Northern Ireland) who collected and provided samples in the form of phenotyped bTB case/control samples for use within this project. Bickhart, Bakshy, McClure, and Null were supported by appropriated projects 5090-31000-026-00-D, Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency, and 8042-31000-001-00-D, Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection, of the Agricultural Research Service (ARS) of the USDA. Cole and Null were supported by appropriated project 8042-31000-002-00-D, “Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals of ARS-USDA. Cole was also partially supported by the grant “Reducing Mastitis in the Dairy Cow by Increasing the Prevalence of Beneficial Polymorphisms in Genes Associated with Mastitis Resistance” from the Minnesota Agricultural Experiment Station Rapid Agricultural Response Fund. Smith was supported by appropriated project 3040-31000-100-00-D, “Developing a Systems Biology Approach to Enhance Efficiency and Sustainability of Beef and Lamb Production,” of ARS-USDA. Bickhart, Bakshy, Young, and Smith were supported by USDA NIFA grant number 2015-67015-22970, “US-UK Collaborative project: “Reassembly of cattle immune gene clusters for quantitative analysis.

Thyroid Disruption by Di-n-Butyl Phthalate (DBP) and Mono-n-Butyl Phthalate (MBP) in Xenopus laevis

BACKGROUND: Di-n-butyl phthalate (DBP), a chemical widely used in many consumer products, is estrogenic and capable of producing seriously reproductive and developmental effects in laboratory animals. However, recent in vitro studies have shown that DBP and mono-n-butyl phthalate (MBP), the major metabolite of DBP, possessed thyroid hormone receptor (TR) antagonist activity. It is therefore important to consider DBP and MBP that may interfere with thyroid hormone system. METHODOLOGY/PRINCIPAL FINDINGS: Nieuwkoop and Faber stage 51 Xenopus laevis were exposed to DBP and MBP (2, 10 or 15 mg/L) separately for 21 days. The two test chemicals decelerated spontaneous metamorphosis in X. laevis at concentrations of 10 and 15 mg/L. Moreover, MBP seemed to possess stronger activity. The effects of DBP and MBP on inducing changes of expression of selected thyroid hormone response genes: thyroid hormone receptor-beta (TRβ), retinoid X receptor gamma (RXRγ), alpha and beta subunits of thyroid-stimulating hormone (TSHα and TSHβ) were detected by qPCR at all concentrations of the compounds. Using mammalian two-hybrid assay in vitro, we found that DBP and MBP enhanced the interactions between co-repressor SMRT (silencing mediator for retinoid and thyroid hormone receptors) and TR in a dose-dependent manner, and MBP displayed more markedly. In addition, MBP at low concentrations (2 and 10 mg/L) caused aberrant methylation of TRβ in head tissue. CONCLUSIONS: The current findings highlight potential disruption of thyroid signalling by DBP and MBP and provide data for human risk assessment

Seasonality of bivalve larvae within a high Arctic fjord

Paid Open Acces

Initial description of Major Histocompatibility Complex variation at two Class II loci (DQA-DQB) in Sotalia fluviatilis and Sotalia guianensis

Genes of the major histocompatibility complex (MHC) play a key role in the initiation of immune response in jawed vertebrates. Variation at MHC loci can be used as an indicator of the genetic ‘health’ of natural populations and offer insight into potential susceptibility to epizootics. Here we present the first characterization of the sequence variation at two MHC class II loci (DQA and DQB) in the neotropical coastal (Sotalia guianensis) and riverine (Sotalia fluviatilis) dolphins, using cloning and direct sequencing of amplified genomic DNA. Four DQA and four DQB alleles were identified in 33 and 32 Sotalia samples, respectively, and high nucleotide diversity among these alleles was detected, similar to the findings described for other cetacean species. Positive selection was evidenced by an excess of dn/ds at the Peptide-Binding-Region of the DQB of Sotalia. The presence of common alleles at both loci in S. fluviatilis and S. guianensis are consistent with trans-species mode of evolution in the MHC. In contrast to observed low levels of mtDNA diversity at the population level, there was an apparent lack of reduction of DQA and DQB allelic variation in the Brazilian Coast population unit. This suggests either present or past balancing selection acting to maintain MHC variation in this population unit