Lamins of the sea lamprey (Petromyzon marinus) and the evolution of the vertebrate lamin protein family

Identification and evolution of transcription factors RHR gene family (NFAT and RBPJ) involving lamprey (Lethenteron reissneri) innate immunity

Nuclear factor of activated T cells (NFAT) and recombination signal binding protein (RBP) belong to the family of Rel homology region (RHR) transcription factors which regulate the expression of genes involved in different aspects of the immune response. To gain insights into the evolution and characterisation of RHR genes in lampreys, a jawless vertebrate, four RHR genes, including nuclear factor of activated T cells (NFAT) and recombination signal binding protein for immunoglobulin kappa J region (RBPJ), have been identified and cloned from the lamprey (Lethenteron reissneri) database. Evolutionary relationships of NFAT and RBPJ genes among different species were determined through molecular phylogenetic analysis. Motif, genetic structure, and tertiary structure analyses showed that NFATs and RBPJ are conserved and contain RHD and IPT domains. Moreover, synteny analysis showed that the neighbourhood genes of Lr-NFATs and Lr-RBPJ have undergone significant changes compared to jawed vertebrates. Real-time quantitative results demonstrated that the RHR gene family plays a significant role in immune defence. This study provides a new understanding of the origin and evolution of the RHR gene family in different species.

A novel protein upstream stimulatory factor 2 identified in lamprey, Lethenteron reissneri

Upstream stimulatory factors are kinds of multi-functional transcription factors, which are expressed in eukaryotes widely, including Upstream stimulatory factor 1 (USFl) and upstream stimulatory factor 2 (USF2). USF protein has a typical basic helix-loop-helix leucine zipper (b-HLH-LZ) structure, which is involved in cell cycle, cell proliferations, glucose and lipid metabolism, and other biochemical processes. Although the USF family is an important regulator of cellular processes, little is known about the USF genes of lampreys, especially their evolutionary relationships, expression profiles, and biological functions. Here, an upstream stimulatory factor 2 (USF2) homolog from lamprey (Lethenteron reissneri) was identified and characterized (designated as L-USF2) because it is closer to USF2 subfamily than to USF1 subfamily. The cDNA fragment of L-USF2 has an open reading frame (ORF) of 765-bp length, encodes 254 amino acids, and contains an HLH domain at the c-terminal of amino acids. Meanwhile, motifs and genetic structure analysis reveal that USF2 gene exons are conserved. Moreover, the 3D structure analysis indicates that L-USF2 adopts the general USF2 folding and has a high structural similarity with H-USF2. The synteny results showed that the L-USF2 adjacent gene changed greatly compared with the jaw vertebrates. By real-time quantitative experiment and Western blot analysis, we found that L-USF2 gene played a significant role in the immune responses. This study not only provides us with a further understanding of the evolution and function of the USF gene family but also provides a basis for exploring its immune responses and immune defenses in lampreys.

Molecular evolution of the tnfr gene family and expression profiles in response to pathogens in lamprey(Lethenteron reissneri)

Tumor necrosis factor receptor superfamilies (TNFRSF) are one of essential cytokines and can trigger inflammation, apoptosis, participating lymphocyte homeostasis and tissue development in vertebrates. To gain insights into the evolution and characterization of tnfr genes in lamprey, a jawless vertebrate, we performed a genome-wide and transcriptome survey and identified 7 tnfr genes in the lamprey (Lethenteron reissneri) database. Based on the molecular phylogenetic analysis, 7 L-tnfr genes are divided into three different clusters, and multiple members of tnfr genes family have appeared in lamprey. Meanwhile, protein domains and motifs analysis reveals that TNFRSF are conserved and have typical cysteine-rich domains (CRDs). Synteny results indicates that the L-tnfr neighborhood genes have taken place great changes compared to jawed vertebrates. Real-time quantitative results demonstrate that tnfr gene family plays an important role in the immune defense. This study has a new understanding for origin and evolution of the tnfr gene family in different vertebrates.

Evolution of the lamin protein family at the base of the vertebrate lineage

Lamin proteins are major constituents of the nuclear lamina. They are required for fundamental nuclear activities, as evidenced by the large number of laminopathies. Mutations in the human lamin A/C gene exhibit a broad spectrum of clinical manifestations. Most non-vertebrates including the nearest relatives of the vertebrates have only a single lamin gene. In jawed vertebrates (Gnathostomata), four lamin subtypes (B1, B2, LIII, and A) are found. Lampreys and hagfish form the two orders of jawless vertebrates, Agnatha, which represent the sister group of the Gnathostomata at the base of the vertebrate lineage. Lamin sequence information of lampreys and hagfish sheds light on the evolution of the lamin protein family at the base of the vertebrate lineage. In the genomes of the lamprey (Petromyzon marinus) and the hagfish (Eptatretus burgeri), only three lamin genes are present, a lamin A gene is lacking. The presence of an LIII gene in both, lampreys and hagfish, proves that the distinguishing features of this gene had been established before the agnathan/gnathostome split. The other two agnathan lamins, LmnI and LmnII, deviate strongly in their sequences from those of the gnathostome lamins. For none of these two agnathan lamins can orthology be established to one of the gnathostome lamin types. In the direct chromosomal neighbourhood of all three hagfish lamin genes, a MARCH3 paralog is found. This can be interpreted as further evidence that the vertebrate lamin genes have arisen in the course of the two rounds of whole genome duplication that took place at the base of the vertebrate lineage.

Laminopathies: what can humans learn from fruit flies

Lamin proteins are type V intermediate filament proteins (IFs) located inside the cell nucleus. They are evolutionarily conserved and have similar domain organization and properties to cytoplasmic IFs. Lamins provide a skeletal network for chromatin, the nuclear envelope, nuclear pore complexes and the entire nucleus. They are also responsible for proper connections between the karyoskeleton and structural elements in the cytoplasm: actin and the microtubule and cytoplasmic IF networks. Lamins affect transcription and splicing either directly or indirectly. Translocation of active genes into the close proximity of nuclear lamina is thought to result in their transcriptional silencing. Mutations in genes coding for lamins and interacting proteins in humans result in various genetic disorders, called laminopathies. Human genes coding for A-type lamin (LMNA) are the most frequently mutated. The resulting phenotypes include muscle, cardiac, neuronal, lipodystrophic and metabolic pathologies, early aging phenotypes, and combined complex phenotypes. The Drosophila melanogaster genome codes for lamin B-type (lamin Dm), lamin A-type (lamin C), and for LEM-domain proteins, BAF, LINC-complex proteins and all typical nuclear proteins. The fruit fly system is simpler than the vertebrate one since in flies there is only single lamin B-type and single lamin A-type protein, as opposed to the complex system of B- and A-type lamins in Danio, Xenopus and Mus musculus. This offers a unique opportunity to study laminopathies. Applying genetic tools based on Gal4 and in vitro nuclear assembly system to the fruit fly model may successfully advance knowledge of laminopathies. Here, we review studies of the laminopathies in the fly model system.

Repurposing a pore: highly conserved perforin-like proteins with alternative mechanisms

Pore-forming proteins play critical roles in pathogenic attack and immunological defence. The membrane attack complex/perforin (MACPF) group of homologues represents, with cholesterol-dependent cytolysins, the largest family of such proteins. In this review, we begin by describing briefly the structure of MACPF proteins, outlining their common mechanism of pore formation. We subsequently discuss some examples of MACPF proteins likely implicated in pore formation or other membrane-remodelling processes. Finally, we focus on astrotactin and bone morphogenetic protein and retinoic acid-induced neural-specific proteins, highly conserved MACPF family members involved in developmental processes, which have not been well studied to date or observed to form a pore-and which data suggest may act by alternative mechanisms.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.

Evolutionary changes in lamin expression in the vertebrate lineage

The nuclear lamina is involved in fundamental nuclear functions and provides mechanical stability to the nucleus. Lamin filaments form a meshwork closely apposed to the inner nuclear membrane and a small fraction of lamins exist in the nuclear interior. Mutations in lamin genes cause severe hereditary diseases, the laminopathies. During vertebrate evolution the lamin protein family has expanded. While most vertebrate genomes contain 4 lamin genes, encoding the lamins A, B1, B2, and LIII, the majority of non-vertebrate genomes harbor only a single lamin gene. We have collected lamin gene and cDNA sequence information for representatives of the major vertebrate lineages. With the help of RNA-seq data we have determined relative lamin expression levels for representative tissues for species of 9 different gnathostome lineages. Here we report that the level of lamin A expression is low in cartilaginous fishes and ancient fishes and increases toward the mammals. Lamin B1 expression shows an inverse tendency to that of lamin A. Possible implications for the change in the lamin A to B ratio is discussed in the light of its role in nuclear mechanics.

Regulation of lamin properties and functions: does phosphorylation do it all?

The main functions of lamins are their mechanical and structural roles as major building blocks of the karyoskeleton. They are also involved in chromatin structure regulation, gene expression, intracellular signalling pathway modulation and development. All essential lamin functions seem to depend on their capacity for assembly or disassembly after the receipt of specific signals, and after specific, selective and precisely regulated interactions through their various domains. Reversible phosphorylation of lamins is crucial for their functions, so it is important to understand how lamin polymerization and interactions are modulated, and which sequences may undergo such modifications. This review combines experimental data with results of our in silico analyses focused on lamin phosphorylation in model organisms to show the presence of evolutionarily conserved sequences and to indicate specific in vivo phosphorylations that affect particular functions.

A peculiar lamin in a peculiar mammal: Expression of lamin LIII in platypus (Ornithorhynchus anatinus)

Platypus (Ornithorhynchus anatinus) holds a unique phylogenetic position at the base of the mammalian lineage due to an amalgamation of mammalian and sauropsid-like features. Here we describe the set of four lamin genes for platypus. Lamins are major components of the nuclear lamina, which constitutes a main component of the nucleoskeleton and is involved in a wide range of nuclear functions. Vertebrate evolution was accompanied by an increase in the number of lamin genes from a single gene in their closest relatives, the tunicates and cephalochordates, to four genes in the vertebrate lineage. Of the four genes the LIII gene is characterized by the presence of two alternatively spliced CaaX-encoding exons. In amphibians and fish LIII is the major lamin protein in oocytes and early embryos. The LIII gene is conserved throughout the vertebrate lineage, with the notable exception of marsupials and placental mammals, which have lost the LIII gene. Here we show that platypus has retained an LIII gene, albeit with a significantly altered structure and with a radically different expression pattern. The platypus LIII gene contains only a single CaaX-encoding exon and the head domain together with coil 1a and part of coil1b of the platypus LIII protein is replaced by a novel short non-helical N-terminus. It is expressed exclusively in the testis. These features resemble those of male germ cell-specific lamins in placental mammals, in particular those of lamin C2. Our data suggest (i) that the specific functions of LIII, which it fulfills in all other vertebrates, is no longer required in mammals and (ii) once it had been freed from these functions has undergone structural alterations and has adopted a new functionality in monotremes.

Evolutionary aspects in intermediate filament proteins

Intermediate filament (IF) proteins, together with tubulins and actins, constitute the majority of cytoskeletal proteins in metazoans. Proteins of the IF family fulfil increasingly diverse functions but share common structural features. Phylogenetic analysis within the metazoan lineage traces back their origin to a common lamin-like ancestor. Major steps in lamin evolution occurred at the base of the vertebrate radiation, while cytoplasmic IF protein subfamilies evolved independently in the major metazoan lineages.