Nacht über Median (German Edition)

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Business Development Manager - Germany. Business Development Manager - France. Support Engineer High Tech machinery. Gerente de Ventas para la zona sur de Europa. Looking for German Teacher. Business Development Manager for EU. Full Stack Developer, with frontend focus. User Training Administrator VN18 Group 2b genes are now found exclusively in a cluster on chromosome 22, which suggests that they arose via local duplications of a single precursor gene that had lost its B Similarly, group 3a genes are clustered together on chromosome 4, with group 3b and 3c genes arranged on chromosomes 1 and 17, respectively.

Group 4 genes are found mostly on chromosome 15, some on chromosome 1, but are notably excluded from chromosome 4. Both group 2 and group 3 have a few individual genes dispersed over other chromosomes; careful inspection of the evidence on which this allocation is based revealed no indications that it is incorrect. Some of the group 3 members on other chromosomes are more divergent from the consensus for this group, suggesting they may indeed have separated from the group early. Within chromosome 4, no clear pattern can be detected in the distribution of the genes.

We are, however, aware of possible shortcomings in the assembly of the long arm of chromosome 4; the highly repetitive nature of the sequence makes it difficult to exclude with absolute certainty shuffling of gene locations. We noted that the NLR-B In some cases, older gene models had joined B However, our manual analyses showed that the B A possible explanation for the erroneous annotation is that the predictions created apparent fintrim ftr genes. Fintrim proteins, members of the larger tripartite motif TRIM protein family, are composed of multiple Zn-fingers combined with a B We therefore analysed the distribution of the NLR-B We established a list of ftr -related genes found in the zebrafish genome.

Total number of Zn-finger encoding gene predictions: Inner circles light to dark blue: We found gene models encoding Zn-fingers of this type, with the number of repeats per gene ranging from 1 to The encoded proteins with small numbers of Zn-fingers included many known proteins, including the Sna and Opa transcription factor families. By contrast, genes encoding those proteins with larger numbers of Zn-finger domains are progressively clustered in restricted regions of the genome.

Outside chromosome 4, some multi-Zn-finger genes co-locate with subsets of the trim genes, for example on chromosomes 3, 16 and 19, whereas others are located in regions where neither NLR-B Similar to the NLR-B In summary, the local duplications that may have led to the expansion of the NLR-B The family of NLR-B These include repeated gene amplifications, shuffling of exons and gene fusions, gene conversion and positive selection for diversity.

These proteins have not been reported to have immune functions. Apaf1, originally discovered as CED-4 in Caenorhabditis elegans , is an ancient regulator of apoptosis. The so far only function reported for NWD1, first identified in the zebrafish genome as NACHTP1 [ 7 ], is its involvement in androgen signalling in the context of prostate cancer [ 22 ]. It will be interesting to learn whether this is a special case of a more general immune function yet to be discovered, or whether, like Apaf1, this old gene does not have immune functions.

The other conserved genes first appear at the base of the jawed vertebrates, and all have roles in immunity or inflammation, whether as transcription factors or as inflammasome components. NLR genes have duplicated and often undergone extensive species-specific expansions throughout evolution. The largest of the known early expansions were in the sponge Amphimedon queenslandica , the sea urchin Strongylocentrotus purpuratus and the lancelet Branchiostoma floridae , with , 92 and genes, respectively [ 17 , 23 ].

As more genomes are sequenced, it is likely that additional NLR expansions will be discovered. In vertebrates, the largest expansions are those of the NLR-B The expansion of the families argues in favour of their involvement in immunity or broader stress reactions, as seen in numerous other examples of expanded gene families.

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

Expansions can increase the amount of gene product, for example to adapt to stressful environmental conditions [ 24 , 25 ], as in the cold adaptation in several gene families expressed in Antarctic icefish [ 26 ]. Expansions can also allow the creation of the variety of sequences that are needed for immune recognition, as in the case of antibodies and T-cell receptors, or the more recent example of the VLR genes in lampreys and hagfish [ 27 ].

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The likely scenario for the origin of the current NLR-B Unfortunately, the available data are not sufficient to trace these earliest duplications. In particular, the extensive expansion of the NLR-B The paralogues that were present in the common ancestor of the teleost lineage then diversified into groups in the Clupeocephala superorder. Whether the common ancestor of the Clupeocephala had four genes or a similarly small number or whether each of the four genes had already begun to be duplicated to form small families is not clear.

We see low rates of synonymous substitutions in the NACHT domain when comparing the members within each group, and similarly low rates of synonymous substitutions for the B A low rate of synonymous sequence substitutions can be interpreted as a sign of recent gene duplication. If we apply this interpretation using the low divergence of the B However, this is not consistent with the significant divergence of the NACHT domains between the groups, the different tree topologies of the two domains, or with our finding that the split into NLR families occurred before the divergence of zebrafish and carp.

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Therefore, there must be an alternative explanation. The pattern of synonymous divergence of the two domains between groups is most parsimoniously explained by ongoing gene conversion. Gene conversion in the NACHT domain appears to be restricted to conversion within each group, keeping the groups homogeneous and distinct from each other. In contrast, gene conversion between B The process is not uncommon in gene families involved in immunity see [ 30 ] for review.

It can create diversity, for example, in antibodies [ 31 ] or in the MHC reviewed in [ 32 ] , but it can also homogenize genes, e. The substitutions are concentrated in the same hypervariable regions of the B These correspond to regions exposed on the surface of TRIM5 [ 34 ] and are therefore presumed to be involved in pathogen interactions.

Once substitutions have been introduced in one of the genes, gene conversion can then spread these throughout the family. If conversion tracts are shorter than the entire B At the same time, because gene conversion in the B This can prevent the groups from being characterized by a defined subset of B It is striking that the three groups of genes that show gene conversion in the B At this point, gene conversion may already have been occurring and if the early prototypes had already amplified into gene families in the common ancestor, then gene conversion may have acted within each group.

Gene conversion must have stopped occurring between NACHT domains of different groups to allow for the observed divergence, but continued in the B Because not all currently extant fish have representatives of all four groups, it may be that either whole sets of these genes can be easily lost, or else that the common precursor had only one gene from each group, and that not all lineages inherited all four prototypes. The near-identity of some of the genes we find in zebrafish difference between paralogues lower than the rate of polymorphism shows that duplications continue to occur.

It is worth speculating about the functional and selective forces that prevent sequence homogenization between the NACHT domains of different groups. If the proteins form large multimeric complexes, as the known inflammasome NLRs do, then their efficient functioning might require that only proteins from the same group can multimerize, for instance to elicit distinct downstream signalling events.

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This is supported by the fact that the group members feature different N-terminal domains. A mixed multimer may not be able to assemble a functional N-terminal effector complex. This is not without precedent, because gene conversion often proceeds across DNA segments of limited length see [ 35 ] for review and parts of a gene can escape sequence homogenization [ 35 , 36 ]. Both LRRs and B LRRs have been implicated in the recognition of pathogen-associated molecular patterns both in the LRR-containing transmembrane proteins of the Toll-like receptor proteins, and in the NLR proteins in plants and animals reviewed in [ 38 — 40 ].

It may therefore have the same function as the related B It is conceivable that the acquisition of the B Not many salt-water fish genome assemblies are available. We did not find the NLR-B We are tempted to speculate that the massive inflation of the NLR-B We have not investigated whether the presence of NLR-B A mechanism involved in the initial creation of the NLR-B For example, the N-terminal peptide repeats occur in several variants, but a given variant is not strictly associated with any particular group: We also find evidence for recombination with other immune genes.

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This suggests that exon shuffling occurred during the generation of the ancestral genes of the NLR-B Apart from this possible case of exon exchange, the relationship between the three large and partially related families—the NLR-B While it is striking that the fintrims share the B By contrast, the multi-Zn-finger genes are mostly found on chromosome 4, interspersed between the NLR-B The C-terminal part of pyrin contains a Zn-finger and a B The most likely interpretation for the origin of this gene, which must have arisen at the base of the tetrapods, is therefore a recombination between an NLR gene and a neighbouring fintrim gene.

The zebrafish chromosome 4 has unusual properties. Its long arm is entirely heterochromatic, replicates late and shows a reduced recombination rate. The sex determination region in the grass carp may also be associated with NACHT domain encoding genes [ 45 ]. This was concluded from the comparison of the genome sequences of one male and one female carp, where those regions present in the male and absent in the female were interpreted as sex determining.

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While the co-location between sex determination and immune signalling molecules we describe here may support this conclusion, it is of course equally possible that the finding in the grass carp is simply caused by allelic diversity in these highly variable genes between the two individuals. It is nevertheless intriguing that two fast evolving genetic systems are located in such close proximity in zebrafish.

Perhaps, after an initial round of NLR gene duplications, a run-away evolutionary process of further amplification created the present chromosome 4, which is now a hotspot for rapid evolutionary processes. To establish a complete list of all genes encoding NLR proteins in the zebrafish genome, we first conducted a search of the Zv9 genome assembly for sequences that encoded the characteristic protein domains, using a combination of approaches.

As an alternative approach to identify NACHT domains specific for the novel NLRs, we ran electronic PCRs [ 15 ] with primer sets for a segment stretching from the C-domain into the winged helix domain that we had used for experimental analysis of the genes , unpublished work. Each set of primers was specific for one of the NLR groups electronic supplementary material, Methods. This resulted in hits. To find regions in the genome encoding B Second, we collected all Ensembl genes overlapping the above motifs predicted genes and also all manually annotated genes vega.

The collection was purged of gene models that did not match the criteria for being novel NLRs, excluding e. Comparison of the purged gene sets with the genomic regions that encoded parts of NLR proteins showed that many genes in this family had been annotated incorrectly, and for others there were no predictions at all, probably owing to the repetitive nature of this gene family and the limited availability of supporting evidence in the form of cDNAs. The regions containing the sequences identified in our searches were therefore re-annotated manually as described elsewhere [ 46 , 47 ], correcting and adding gene models to create full-length genes.

This re-annotation had to be restricted to regions located on finished sequence, because whole genome shotgun contigs in Zv9 were not accessible to manual annotation. The resulting protein sequences were then aligned using C lustal —O mega [ 48 ] or M uscle [ 49 ] and compared.

Sequences that appeared truncated were analysed further by searching for additional exons to complete them, until, in an iterative process, we had optimized them. Some sequences remained incomplete, either because they were located next to sequence gaps, or because no additional exons could be detected.

In these cases, it is not known whether the truncation of the gene is a true biological event caused by recent recombination, or whether it is due to a misassembly of the genome sequence. The optimized gene set was combined with the gene predictions in Ensembl Methods, hand-filtered alignments and location checks of the remaining genes to identify accordance. The final list of novel zebrafish NLR proteins contains members electronic supplementary material, table S1. A further 36 predictions for NLR genes had been annotated as pseudo-genes and were therefore not retrieved for this list electronic supplementary material.

However, because the annotation was performed on pre-GRCz10 paths, the latest GRCz10 gene set Ensembl80 might differ marginally from the described results. We used the zebrafish gene identifiers for the conserved NLRs in zebrafish to query the O rthoinspector v.

After removing redundant hits, we calculated alignments employing C lustal —O mega v. In a second inference, we also used trimal [ 51 ] to reduce the alignment to the conserved residues. We employed prottest v. We then ran RAxML v. Phylogenetic trees were visualized and edited in D endroscope v. Expanded gene families are not well annotated in most genomes.

Rather than relying on gene predictions for identifying NLR-B Latimeria chalumnae, Lepisosteus oculatus, Callorhinchus milii, Esox lucius, Astyanax mexicanus and Cyprinus carpio. We downloaded genome data either from NCBI servers or the genome project websites. The F igmop pipeline builds a profile of conserved motifs from a starting set of sequences and uses these to search a target database with the MEME software suite [ 56 ]. We used zebrafish NLR-B The resulting contigs were then subjected to the A ugustus v.

We used a recursive approach for identifying genes for the phylogeny that were representative of the overall sequence divergence in the gene family. We then recursively performed the following: As described for the conserved NLR genes above we based our phylogeny on an alignment calculated with C lustal —O mega v. We then used our own iP ython [ 62 ] script to sort data and calculated means, medians and errors in the R statistic software R Core Team We loaded the inferred trees into D endroscope and employed this software to visualize connection between branches belonging to the same gene in both trees.

All online supplementary material can be found on Figshare under the accession number http: We thank Robert Remy and Giuliano Crispatzu for some early work on this project and Jonathan Wood for verifying genomic locations of assembly components. We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

NLR-B gene family evolution | Open Biology

Learn about Open Biology articles on Faculty of Skip to main content. Kerstin Howe , Philipp H. Laird , John C. Published 27 April Abstract Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. Background The need to adapt to new environments is a strong driving force for diversification during evolution. View inline View popup. All NLR proteins in the zebrafish genome.

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  4. Origin of the NLR-B Expansion of the NLR-B Evolutionary age of the NLR-B Genomic location of the NLR-B Shuffling between genes and creation of new genes A mechanism involved in the initial creation of the NLR-B Chromosome 4 The zebrafish chromosome 4 has unusual properties. Re-annotation of NLR genes in the zebrafish genome To establish a complete list of all genes encoding NLR proteins in the zebrafish genome, we first conducted a search of the Zv9 genome assembly for sequences that encoded the characteristic protein domains, using a combination of approaches.

    Phylogenetic analyses of the NLR-B Data accessibility All online supplementary material can be found on Figshare under the accession number http: Competing interests We declare we have no competing interests. Acknowledgements We thank Robert Remy and Giuliano Crispatzu for some early work on this project and Jonathan Wood for verifying genomic locations of assembly components. Ting JPY et al. Immunity 28 , — USA , — Lapraz F et al. Howe K , Wood JM.

    Gigascience 4 , Sola L , Gornung E. Genetica , — Oncotarget 5 , — Huang S et al. B , —