Isolation and characterization of tri‐ and tetra‐repeat microsatellite loci in the white‐spotted charr Salvelinus leucomaenis (Salmonidae)

Tri‐ and tetra‐motif repeat microsatellite marker loci were developed for the white‐spotted charr Salvelinus leucomaenis. The 454 pyrosequencing was used to discover repeat arrays, and eight microsatellite‐primer sets, available for the estimation of polymorphisms, were identified. The number of alleles in a wild population ranged from two to four and the observed and expected heterozygosities were 0·180–0·600 and 0·188–0·599, respectively.     

Uncovering the dynamic evolution of nucleotide‐binding site‐leucine‐rich repeat (NBS‐LRR) genes in Brassicaceae

Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat(NBS-LRR) genes;however,the long-term evolutionary history of these resistance genes has not been fully understood. This study focuses on five Brassicaceae genomes and the Carica papaya genome to explore changes in NBS-LRR genes that have taken place in this Rosid II lineage during the past 72 million years. Various numbers of NBS-LRR genes were identified from Arabidopsis lyrata(198),A. thaliana(165),Brassica rapa(204),Capsella rubella(127),Thellungiella salsuginea(88),and C. papaya(51). In each genome,the identified NBS-LRR genes were found to be unevenly distributed among chromosomes and most of them were clustered together.Phylogenetic analysis revealed that,before and after Brassicaceae speciation events,both toll/interleukin-1receptor-NBS-LRR(TNL) genes and non-toll/interleukin-1receptor-NBS-LRR(n TNL) genes exhibited a pattern of first expansion and then contraction,suggesting that both subclasses of NBS-LRR genes were responding to pathogen pressures synchronically. Further,by examining the gain/loss of TNL and n TNL genes at different evolutionary nodes,this study revealed that both events often occurred more drastically in TNL genes. Finally,the phylogeny of n TNL genes suggested that this NBS-LRR subclass is composed o two separate ancient gene types: RPW8-NBS-LRR and Coiled-coil-NBS-LRR.     

Genetic diversity of Ligula intestinalis (Cestoda: Diphyllobothriidea) based on analysis of inter‐simple sequence repeat markers

In order to investigate the genetic diversity of Ligula intestinalis populations, nine inter‐simple sequence repeat (ISSR) markers were applied to populations from nine geographical areas around the world and 10 host species. The 110 loci selected from the ISSR patterns produced revealed high variability among the analysed samples, with a polymorphism of 100% and a global coefficient of gene differentiation estimated by Nei’s index (G_ST) of 0.776. Major genetic differentiation was found to be correlated to five broad geographical regions (Europe, China, Canada, Australia and Algeria). Nevertheless, no significant genetic variation was found among European isolates, although they originated from disparate geographical localities and/or unrelated hosts. Classical classification methods: maximum parsimony and factorial correspondence analysis were compared with an advanced statistical method: the self‐organizing map (SOM). The results demonstrated that the ISSR approach is rapid and inexpensive and provides reliable markers to assess genetic diversity of L. intestinalis. Furthermore, SOM artificial neuronal networks are considered to provide an efficient alternative tool for mapping the genetic structures of parasite populations.     

Microsatellite markers from an expressed sequence tag library of half‐smooth tongue sole (Cynoglossus semilaevis) and their application in other related fish species

Microsatellite markers have been developed from a cDNA library of half‐smooth tongue sole, Cynoglossus semilaevis. Twenty‐five microsatellites were selected for designing microsatellite primers, of which 11 gave working primer pairs. They had between four and 12 alleles. Observed and expected heterozygosities varied from 0.60 to 0.90 and from 0.57 to 0.88, respectively. Five additional fish species assessed for cross‐species amplification revealed between one and four positive amplifications and between 0 and four polymorphic loci per species.     

The NIN‐like protein 5 (ZmNLP5) transcription factor is involved in modulating the nitrogen response in maize

Maize exhibits marked growth and yield response to supplemental nitrogen (N). Here, we report the functional characterization of a maize NIN‐like protein ZmNLP5 as a central hub in a molecular network associated with N metabolism. Predominantly expressed and accumulated in roots and vascular tissues, ZmNLP5 was shown to rapidly respond to nitrate treatment. Under limited N supply, compared with that of wild‐type (WT) seedlings, the zmnlp5 mutant seedlings accumulated less nitrate and nitrite in the root tissues and ammonium in the shoot tissues. The zmnlp5 mutant plants accumulated less nitrogen than the WT plants in the ear leaves and seed kernels. Furthermore, the mutants carrying the transgenic ZmNLP5 cDNA fragment significantly increased the nitrate content in the root tissues compared with that of the zmnlp5 mutants. In the zmnlp5 mutant plants, loss of the ZmNLP5 function led to changes in expression for a significant number of genes involved in N signalling and metabolism. We further show that ZmNLP5 directly regulates the expression of nitrite reductase 1.1 (ZmNIR1.1) by binding to the nitrate‐responsive cis‐element at the 5′ UTR of the gene. Interestingly, a natural loss‐of‐function allele of ZmNLP5 in Mo17 conferred less N accumulation in the ear leaves and seed kernels resembling that of the zmnlp5 mutant plants. Our findings show that ZmNLP5 is involved in mediating the plant response to N in maize.     

The SCP2‐thiolase‐like protein (SLP) of Trypanosoma brucei is an enzyme involved in lipid metabolism

Bioinformatics studies have shown that the genomes of trypanosomatid species each encode one SCP2‐thiolase‐like protein (SLP), which is characterized by having the YDCF thiolase sequence fingerprint of the Cβ2‐Cα2 loop. SLPs are only encoded by the genomes of these parasitic protists and not by those of mammals, including human. Deletion of the Trypanosoma brucei SLP gene (TbSLP) increases the doubling time of procyclic T. brucei and causes a 5‐fold reduction of de novo sterol biosynthesis from glucose‐ and acetate‐derived acetyl‐CoA. Fluorescence analyses of EGFP‐tagged TbSLP expressed in the parasite located the TbSLP in the mitochondrion. The crystal structure of TbSLP (refined at 1.75 Å resolution) confirms that TbSLP has the canonical dimeric thiolase fold. In addition, the structures of the TbSLP‐acetoacetyl‐CoA (1.90 Å) and TbSLP‐malonyl‐CoA (2.30 Å) complexes reveal that the two oxyanion holes of the thiolase active site are preserved. TbSLP binds malonyl‐CoA tightly (K_d 90 µM), acetoacetyl‐CoA moderately (K_d 0.9 mM) and acetyl‐CoA and CoA very weakly. TbSLP possesses low malonyl‐CoA decarboxylase activity. Altogether, the data show that TbSLP is a mitochondrial enzyme involved in lipid metabolism. Proteins 2016; 84:1075–1096. © 2016 Wiley Periodicals, Inc.     

New discoveries of tetrapods (ichthyostegid‐like and whatcheeriid‐like) in the Famennian (Late Devonian) localities of Strud and Becco (Belgium)

The origin of tetrapods is one of the key events in vertebrate history. The oldest tetrapod body fossils are Late Devonian (Frasnian–Famennian) in age, most of them consisting of rare isolated bone elements. Here we describe tetrapod remains from two Famennian localities from Belgium: Strud, in the Province of Namur, and Becco, in the Province of Liège. The newly collected material consists of an isolated complete postorbital, fragments of two maxillae, and one putative partial cleithrum, all from Strud, and an almost complete maxilla from Becco. The two incomplete maxillae and cleithrum from Strud, together with the lower jaw previously recorded from this site, closely resemble the genus Ichthyostega, initially described from East Greenland. The postorbital from Strud and the maxilla from Becco do not resemble the genus Ichthyostega. They show several derived anatomical characters allowing their tentative assignment to a whatcheeriid‐grade group. The new tetrapod records show that there are at least two tetrapod taxa in Belgium and almost certainly two different tetrapod taxa at Strud. This locality joins the group of Devonian tetrapod‐bearing localities yielding more than one tetrapod taxon, confirming that environments favourable to early tetrapod life were often colonized by several tetrapod taxa.     

Chromosome‐level genome assembly of the greenfin horse‐faced filefish (Thamnaconus septentrionalis) using Oxford Nanopore PromethION sequencing and Hi‐C technology

The greenfin horse‐faced filefish, Thamnaconus septentrionalis, is a valuable commercial fish species that is widely distributed in the Indo‐West Pacific Ocean. This fish has characteristic blue–green fins, rough skin and a spine‐like first dorsal fin. Thamnaconus septentrionalis is of conservation concern because its population has declined sharply, and it is an important marine aquaculture fish species in China. Genomic resources for the filefish are lacking, and no reference genome has been released. In this study, the first chromosome‐level genome of T. septentrionalis was constructed using nanopore sequencing and Hi‐C technology. A total of 50.95 Gb polished nanopore sequences were generated and were assembled into a 474.31‐Mb genome, accounting for 96.45% of the estimated genome size of this filefish. The assembled genome contained only 242 contigs, and the achieved contig N50 was 22.46 Mb, a surprisingly high value among all sequenced fish species. Hi‐C scaffolding of the genome resulted in 20 pseudochromosomes containing 99.44% of the total assembled sequences. The genome contained 67.35 Mb of repeat sequences, accounting for 14.2% of the assembly. A total of 22,067 protein‐coding genes were predicted, 94.82% of which were successfully annotated with putative functions. Furthermore, a phylogenetic tree was constructed using 1,872 single‐copy orthologous genes, and 67 unique gene families were identified in the filefish genome. This high‐quality assembled genome will be a valuable resource for a range of future genomic, conservation and breeding studies of T. septentrionalis.     

The evolutionary characteristics and structural biology of Gallus toll‐like receptor 21

Toll‐like receptors (TLRs) are an important part of the innate immune system, acting as a first line of defense against many invading pathogens. The ligand known to bind Gallus toll‐like receptor 21 (gTLR21) is the unmethylated cytosine phosphate guanine dideoxy nucleotide motif; however, the evolutionary characteristics and structural biology of gTLR21 are poorly elaborated. Our results suggest that gTLR21 is phylogenetically and evolutionarily related to the TLR11 family and is perhaps a close ortholog of the Mus TLR13. Structural biology of homology modeling of the gTLR21 ectodomain structure suggests that it has no Z‐loop like that seen in Mus TLR9. The cytosolic toll‐IL‐1 receptor region of gTLR21 contains a central 4‐stranded parallel β‐sheet (βA‐βD) surrounded by 5 α‐helices (αA‐αE) on both sides, a highly conserved structure also seen in other TLRs. Molecular docking analysis reveals that the gTLR21 ectodomain has the potential to distinguish between different ligands. Homodimer analysis results also suggest that Phe842 and Pro844 of the BB loop and Cys876 of the αC helix in gTLR21 are conserved in other cytosolic toll‐IL‐1 receptor domains of other TLRs and may contribute to the docking of homodimers. Our study on the evolutionary characteristics and structural biology of gTLR21 reveals that the molecule may have a broader role to play in innate immune system; however, further experimental validation is required to confirm our findings.     

The tomato I gene for Fusarium wilt resistance encodes an atypical leucine‐rich repeat receptor‐like protein whose function is nevertheless dependent on SOBIR1 and SERK3/BAK1

We have identified the tomato I gene for resistance to the Fusarium wilt fungus Fusarium oxysporum f. sp. lycopersici (Fol) and show that it encodes a membrane‐anchored leucine‐rich repeat receptor‐like protein (LRR‐RLP). Unlike most other LRR‐RLP genes involved in plant defence, the I gene is not a member of a gene cluster and contains introns in its coding sequence. The I gene encodes a loopout domain larger than those in most other LRR‐RLPs, with a distinct composition rich in serine and threonine residues. The I protein also lacks a basic cytosolic domain. Instead, this domain is rich in aromatic residues that could form a second transmembrane domain. The I protein recognises the Fol Avr1 effector protein, but, unlike many other LRR‐RLPs, recognition specificity is determined in the C‐terminal half of the protein by polymorphic amino acid residues in the LRRs just preceding the loopout domain and in the loopout domain itself. Despite these differences, we show that I/Avr1‐dependent necrosis in Nicotiana benthamiana depends on the LRR receptor‐like kinases (RLKs) SERK3/BAK1 and SOBIR1. Sequence comparisons revealed that the I protein and other LRR‐RLPs involved in plant defence all carry residues in their last LRR and C‐terminal LRR capping domain that are conserved with SERK3/BAK1‐interacting residues in the same relative positions in the LRR‐RLKs BRI1 and PSKR1. Tyrosine mutations of two of these conserved residues, Q922 and T925, abolished I/Avr1‐dependent necrosis in N. benthamiana, consistent with similar mutations in BRI1 and PSKR1 preventing their interaction with SERK3/BAK1.     

The protein interacting with C‐kinase (PICK1) interacts with and attenuates parkin‐associated endothelial‐like (PAEL) receptor‐mediated cell death

The parkin‐associated endothelial‐like receptor (PAELR, GPR37) is an orphan G protein‐coupled receptor that interacts with and is degraded by parkin‐mediated ubiquitination. Mutations in parkin are thought to result in PAELR accumulation and increase neuronal cell death in Parkinson's disease. In this study, we find that the protein interacting with C‐kinase (PICK1) interacts with PAELR. Specifically, the Postsynaptic density protein‐95/Discs large/ZO‐1 (PDZ) domain of PICK1 interacted with the last three residues of the c‐terminal (ct) located PDZ motif of PAELR. Pull‐down assays indicated that recombinant and native PICK1, obtained from heterologous cells and rat brain tissue, respectively, were retained by a glutathione S‐transferase fusion of ct‐PAELR. Furthermore, coimmunoprecipitation studies isolated a PAELR‐PICK1 complex from transiently transfected cells. PICK1 interacts with parkin and our data showed that PICK1 reduces PAELR expression levels in transiently transfected heterologous cells compared to a PICK1 mutant that does not interact with PAELR. Finally, PICK1 over‐expression in HEK293 cells reduced cell death induced by PAEALR over‐expression during rotenone treatment and these effects of PICK1 were attenuated during inhibition of the proteasome. These results suggest a role for PICK1 in preventing PAELR‐induced cell toxicity.