Evolutionary implications of three novel members of the human sarcomeric myosin heavy chain gene family

Fast skeletal muscle myosin heavy chain gene cluster of medaka Oryzias latipes enrolled in temperature adaptation

To disclose mechanisms involved in temperature acclimation of fish muscle, we subjected eurythermal fish of medaka Oryzias latipes to cloning of myosin heavy chain genes (MYHs). We cloned cDNAs encoding fast skeletal muscle myosin heavy chain (MYH) isoforms from cDNA libraries of medaka acclimated to 10 and 30 degrees C and observed that different MYH cDNA clones are expressed in the two temperature-acclimated fish. Subsequently, we isolated several overlapping MYH contigs by shotgun cloning strategy from a medaka genomic library. Contig assembly of the complete medaka MYH (mMYH) locus of 219 kbp revealed a cluster of tandemly arrayed 11 mMYHs, in which eight genes are actually transcribed, with the remaining three being pseudogenes. Expression analysis of the transcribed genes revealed that two genes were each highly expressed in medaka acclimated to 10 and 30 degrees C, whereas comparatively lower expression levels of the three genes were exclusively observed in medaka acclimated to 30 degrees C. cDNAs of the remaining genes were too underrepresented in the libraries to determine the expression levels, and the transcripts could only be obtained by reverse transcription-polymerase chain reaction. Deduced amino acid sequences in the loop 1 and loop 2 regions of mMYHs were highly variable, suggesting that these isoforms were functionally different. The present findings consolidate our knowledge on teleost MYH multigene family and would provide further insight into the mechanisms by which expressions of individual MYH molecules are fine-tuned with environmental temperature fluctuations with further functional analysis of the genes concerned.

The Mammalian 2′-5′ Oligoadenylate Synthetase Gene Family: Evidence for Concerted Evolution of Paralogous Oas1 Genes in Rodentia and Artiodactyla

Multiple 2'-5' oligoadenylate (2-5A) synthetases are important components of innate immunity in mammals. Gene families encoding these proteins have previously been studied mainly in humans and mice. To reconstruct the evolution of this gene family in mammals, a search for additional 2-5A synthetase genes was performed in rat, cattle, pig, and dog. Twelve 2'-5' oligoadenylate synthetase (Oas) genes were identified in the rat genome, including eight Oas1 genes, two Oas1 pseudogenes, single copies of Oas2 and Oas3, and two Oas-like genes, Oasl1 and Oasl2. Four OAS genes were detected in the pig genome and five OAS genes were found in both the cattle and dog genomes. An OAS3 gene was not found in either the cattle or the pig genome. While two tandemly duplicated OAS-like (OASL) genes were identified in the dog genome, only a single OASL orthologue was found in both the cattle and the pig genomes. The bovine and porcine OASL genes contain premature stop codons and encode truncated proteins, which lack the typical C-terminal double ubiquitin domains. The cDNA sequences of the rat, cattle, pig, and dog OAS genes were amplified, sequenced and compared with each other and with those in the human, mouse, horse, and chicken genomes. Evidence of concerted evolution of paralogous 2'-5' oligoadenylate synthetase 1 genes was obtained in rodents (Rodentia) and even-toed ungulates (Artiodactyla). Calculations using the nonparametric Kolmogorov-Smirnov test suggested that the homogenization of paralogous OAS1 sequences was due to gene conversion rather than stabilizing selection.

The sarcomeric myosin heavy chain gene family in the dog: analysis of isoform diversity and comparison with other mammalian species

Sarcomeric myosin heavy chains (MyHC) are the major contractile proteins of cardiac and skeletal muscles and belong to class II MyHC. In this study the sequences of nine sarcomeric MyHC isoforms were obtained by combining assembled contigs of the dog genome draft available in the NCBI database. With this information available the dog becomes the second species, after human, for which the sequences of all members of the sarcomeric MyHC gene family are identified. The newly determined sequences of canine MyHC isoforms were aligned with their orthologs in mammals, forming a set of 38 isoforms, to search for the molecular features that determine the structural and functional specificity of each type of isoform. In this way the structural motifs that allow identification of each isoform and are likely determinants of functional properties were identified in six specific regions (surface loop 1, loop 2, loop 3, converter, MLC binding region, and S2 proximal segment).

Diversity of the pufferfish Takifugu rubripes fast skeletal myosin heavy chain genes

Myosin is a highly conserved, ubiquitous actin-based molecular motor that is distributed as diverse as from prokaryotes to mammalian tissues. Among various types in the myosin family proteins, class II, also called sarcomeric, myosin is a classical, conventional molecule that has been extensively studies on its functional and structural properties. It consists of two heavy chains (MYH) of about 200 kDa and four light chains of about 20 kDa. The exon-intron organization was determined for the major subunit of MYH, which contains ATP-hydrolysis and actin-binding sites, from torafugu (tiger pufferfish) Takifugu rubripes fast skeletal muscles. Comprehensive investigation for fast skeletal MYHs based on the fugu (torafugu) genome database and subsequent construction of their physical map revealed that torafugu contains at least 8 putative skeletal MYHs. Furthermore, genomic structural analysis revealed that skeletal MYHs are not clustered in a single locus, but rather spread to at least four loci, with two of them locating at the mammalian syntenic regions. Such arrangement of torafugu MYHs are in a marked contrast to mammalian fast skeletal MYHs that are clustered in a single locus. These data suggest that an ancient segmental duplication or whole-genome duplication occurred in fish lineage as in many other reported torafugu genes.

The complete genomic sequence of the carp fast skeletal myosin heavy chain gene

We have determined the complete DNA nucleotide sequence of the carp Cyprinus carpio fast skeletal myosin heavy chain (MYH) gene. Introns and exons were predicted by comparison with the corresponding carp MYH cDNAs previously reported. The gene encoded the entire mRNA transcript and contained 5958 nucleotides (nt) including 77 nt 5'-untranslated region, 5796 nt coding region for 1931 amino acids, and 85 nt 3'-untranslated region. The coding region was split by 38 introns and the complete gene contained 11,385 nt. This integration of the carp fast skeletal MYH gene was comparable to those of the rat and chicken embryonic MYH genes, which have 41 and 40 exons, respectively. However, the entire gene size of carp MYH was about half those of rat and chicken due to much smaller size of carp introns. We have also demonstrated that this carp MYH gene belonged to so-called intermediate type in a multigene family of carp fast skeletal muscle MYH in comparison of its nucleotide and deduced amino acid sequences to those of carp MYH cDNAs reported previously.

Laryngeal muscle fibre types

The internal laryngeal muscles have evolved to subserve the highly specialized functions of airways protection, respiration, and phonation. Their contractile properties, histochemistry, biochemical properties, myosin heavy chain (MyHC) expression and their regulation by nerves and hormones are reviewed and compared with limb muscle fibres. Cricothyroid, the vocal cord tensor, is limb-like in MyHC composition and fibre type properties, while the vocal fold abductor and adductors are allotypically different, with capacity for expressing an isoform of MyHC that is kinetically faster than the fastest limb MyHC. In rats and rabbits the faster isoform is the extraocular (EO) MyHC, while in carnivores, it is the IIB MyHC. These adaptations enable the abductor and adductor muscles to remain always faster than the cricothyroid as the latter changes in speed during evolution to match changing metabolic and respiratory rates in relation to scaling with body mass. Such phylogenetic plasticity is vital to the airways protection and respiratory functions of these muscles. The posterior cricoarythenoid, the abductor muscle, is tonically driven during expiration, and consequently has a slower fibre type profile than the principal adductor, the thyroarythenoid. The human thyroarythenoid appears not to express EO or IIB MyHC significantly, but is unique in expressing the slow-tonic MyHC. The concepts of allotype and phylogenetic plasticity help to explain differences in fibre type between limb and laryngeal muscles and between homologous laryngeal muscles in different species. Laryngeal muscle fibres exhibit physiological plasticity as do limb muscles, being subject to neural and hormonal modulation.

Comparative analyses reveal a complex history of molecular evolution for human MYH16

We describe the pattern of molecular evolution at a sarcomeric myosin gene, MYH16, using more than 30,000 bp of exon and intron sequence data from the chimpanzee and human genome sequencing projects to evaluate the timing and consequences of a human lineage-specific frameshift deletion. We estimate the age of the deletion at approximately 5.3 MYA. This estimate is consistent with the time of human and chimpanzee divergence and is significantly older than the first appearance of the genus Homo in the fossil record. We also find conflicting estimates of nonsynonymous fixation rates (d(N)) across different regions of this gene, revealing a complex pattern inconsistent with a simple model of pseudogene evolution for human MYH16.

Lamprey contractile protein genes mark different populations of skeletal muscles during development

Agnathan lampreys retain ancestral characteristics of vertebrates in the morphology of skeletal muscles derived from two mesodermal regions: trunk myotomes and unsegmented head mesoderm. During lamprey development, some populations of myoblasts migrate via pathways that differ from those of gnathostomes. To investigate the evolution of skeletal muscle differentiation in vertebrates, we characterize multiple contractile protein genes expressed in the muscle cells of the Japanese lamprey, Lethenteron japonicum. Lamprey actin gene LjMA2, and myosin heavy chain (MyHC) genes LjMyHC1 and LjMyHC2 are all expressed in the developing skeletal muscle cells of early embryos. However, LjMyHC1 and LjMyHC2 are expressed only in cells originating from myotomes, while LjMA2 is expressed in both myotomal and head musculature. Thus, in lampreys, myotomes and head mesoderm differ in the use of genes encoding contractile protein isoforms. Phylogenetic tree analyses including lamprey MyHCs suggest that the variety of muscle MyHC isoforms in different skeletal muscles may correspond to the morphological complexity of skeletal muscles of different vertebrate species. Another lamprey actin gene LjMA1 is likely to be the first smooth muscle actin gene isolated from non-tetrapods. We conclude that, in vertebrate evolution, the different regulatory systems for striated and smooth muscle-specific genes may have been established before the agnathan/gnathostome divergence.

Structure and evolution of the luciferin-regenerating enzyme (LRE) gene from the firefly Photinus pyralis

To study the structural features of genes for the luciferin-regenerating enzyme (LRE), the entire gene along with 524 bp of upstream sequence was determined from Photinus pyralis (Coleoptera: Lampyridae). The LRE gene revealed an open reading frame composed of five exons divided by four introns ranging in size from 47 to 904 bp. The deduced LRE amino acid sequence showed identity to senescence marker protein-30 (SMP30) from a number of insects and mammals including four putative SMP30 sequences from Anopheles gambiae. Gene structure comparisons showed some intron/exon site conservation with A. gambiae and mammalian SMP30 proteins but not Drosophila. LRE and luciferase sequence comparisons revealed two conserved putative luciferin-binding sites. The evolution of LRE was discussed in relation to its function.

Myosin heavy-chain isoform composition of human single jaw-muscle fibers

Diversity in muscle contractile properties is based on the variability of contractile properties of single muscle fibers which in turn is related to the presence of different myosin heavy-chain (MyHC) isoforms. Human jaw muscles are featured by many hybrid fibers expressing more than one MyHC isoform. The purpose of this study was to determine the proportion of each isoform within these fibers for evaluation of the fiber's capacity of producing a large diversity in contractile properties. Electrophoretic separation of MyHC isoforms was performed on 218 single fibers of the temporalis and digastric muscles. Of these fibers, 100 were classified as hybrid fibers. Most hybrid fibers co-expressed MyHC-IIA and -IIX (n = 62); a smaller number co-expressed MyHC-I and -IIA (n = 14), MyHC-I and -IIX (n = 12), and MyHC-I, -IIA, and -IIX (n = 12). The proportions of the individual MyHC isoforms in the hybrid fibers varied highly, suggesting a large range of contractile properties among these fibers.

Modular organization of phylogenetically conserved domains controlling developmental regulation of the human skeletal myosin heavy chain gene family

The mammalian skeletal myosin heavy chain locus is composed of a six-membered family of tandemly linked genes whose complex regulation plays a central role in striated muscle development and diversification. We have used publicly available genomic DNA sequences to provide a theoretical foundation for an experimental analysis of transcriptional regulation among the six promoters at this locus. After reconstruction of annotated drafts of the human and murine loci from fragmented DNA sequences, phylogenetic footprint analysis of each of the six promoters using standard and Bayesian alignment algorithms revealed unexpected patterns of DNA sequence conservation among orthologous and paralogous gene pairs. The conserved domains within 2.0 kilobases of each transcriptional start site are rich in putative muscle-specific transcription factor binding sites. Experiments based on plasmid transfection in vitro and electroporation in vivo validated several predictions of the bioinformatic analysis, yielding a picture of synergistic interaction between proximal and distal promoter elements in controlling developmental stage-specific gene activation. Of particular interest for future studies of heterologous gene expression is a 650-base pair construct containing modules from the proximal and distal human embryonic myosin heavy chain promoter that drives extraordinarily powerful transcription during muscle differentiation in vitro.