Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families

Extremely reduced evolutionary rate of TATA-box binding protein in higher vertebrates and its evolutionary implications

Previously we showed that the evolutionary rates of the Pax proteins are markedly reduced in higher vertebrates, as compared with those in the ancestral lineage of vertebrates, and we suggested that the reduced Pax protein evolution might be explained by increased functional constraints due to gene recruitment for other purposes or repeated expression in different developmental stages. To clarify the problem of whether the evolutionary rate variation found in the Pax proteins is an evolutionary feature generally recognized in most transcription factors, we have cloned and sequenced cDNAs encoding the TATA-box binding protein (TBP), a general transcription factor of eukaryotes, from Oryzias latipes, a Japanese medaka, Lampetra reissneri, a lamprey, and Ephydatia fluviatilis, a freshwater sponge. An evolutionary rate analysis of TBP has revealed that the evolutionary rate of TBP is extremely low in higher vertebrates, but not in the ancestral lineage of vertebrates, as found in the Pax proteins. In contrast, no marked reduction of the evolutionary rate in higher vertebrates is observed in the aldolase C, a house keeping enzyme. It is therefore likely that the increased functional constraint on TBP is responsible for the extremely low evolutionary rate in higher vertebrates. The temporal pattern of the evolutionary rate variation during vertebrate evolution was discussed.

Gene expression and molecular evolution

The combination of complete genome sequence information and estimates of mRNA abundances have begun to reveal causes of both silent and protein sequence evolution. Translational selection appears to explain patterns of synonymous codon usage in many prokaryotes as well as a number of eukaryotic model organisms (with the notable exception of vertebrates). Relationships between gene length and codon usage bias, however, remain unexplained. Intriguing correlations between expression patterns and protein divergence suggest some general mechanisms underlying protein evolution.

Divergence pattern of animal gene families and relationship with the Cambrian explosion

There are many gene families that are specific to multicellular animals. These have either diverged from ancestral genes that are shared with fungi and/or plants or evolved from an ancestral gene unique to animals. The evolution of gene families involved in cell-cell communication and developmental control has been studied to establish whether the number of member genes increased dramatically immediately prior to or in concert with the Cambrian explosion. A molecular phylogeny-based analysis of several animal-specific gene families has revealed that gene diversification by duplication occurred during two active periods interrupted by a long intervening quiescent period. Intriguingly, the Cambrian explosion is situated in the silent period, indicating that there is no direct link between the first burst of gene diversification and the Cambrian explosion itself. The importance of gene recruitment as a possible molecular mechanism for morphological diversity, and its possible role for the Cambrian explosion, are discussed.

Postembryonic expression of the myosin heavy chain genes in the limb, tail, and heart muscles of metamorphosing amphibian tadpoles

Thyroid hormone is presumed to play a role in initiating and/or orchestrating the postembryonic expression of the genes encoding isoforms of the myosin heavy chains (MHCs) that characterize the muscle fibres in an adult organism. The fact that the postembryonic development of a free-living amphibian tadpole takes place during its thyroid hormone-dependent metamorphosis has made the metamorphosing tadpole an ideal system for elucidating the molecular mechanism(s) by which this hormone affects these postembryonic changes. In this review, we summarize the results from recent studies focused on the postembryonic expression of the MHC genes in the skeletal muscles and hearts of metamorphosing anuran (Rana catesbeiana) tadpoles. The demonstration that mRNAs encoding at least five of the MHC isoforms present in the tadpole tail muscles are also present in the adult hind-limb muscles and that an mRNA encoding a cardiac-specific MHC isoform is present in the heart of both the tadpole and adult organism, rules out the possibility that thyroid hormone initiates the expression of these MHC genes. Instead, it seems more likely that this hormone acts by modulating the expression of one or more of the genes encoding these particular MHC isoforms. Whatever the case, the fact that sequence homology suggests that the five distinct skeletal muscle-specific MHCs are all "fast" isoforms raises the question of how these MHCs are distributed among the three different fibre types described for Rana. On the other hand, the possibility exists that the mRNAs for one or more of these fast MHC isoforms encode developmental isoforms that are present but not translated in the muscles of the tadpole and/or adult frog. Finally, an evaluation of the evolutionary relatedness of the R. catesbeiana MHCs to the MHCs in another species of Rana and to the MHCs in other vertebrates discloses, among other things, that the nucleotide sequence in the R. catesbeiana cardiac MHC isoform is more closely related to the chicken ventricular MHC isoform than it is to any of the other MHC isoforms examined.

Choosing among alternative trees of multigene families

Estimation of gene trees is the first step in testing alternative hypotheses about the evolution of multigene families. The standard practice for inferring gene family history is to construct trees that meet some objective criteria based on the fit of the character state changes (nucleotide or amino acid changes) to the gene tree. Unfortunately, analysis of character state data can be misleading. In addition, this approach ignores information about the relationships of the species from which the genes have been sampled. In this paper I explore using statistics of fit between the character data and gene trees and the reconciliation of the gene and species trees for choosing among alternative evolutionary hypotheses of gene families. In particular, I advocate a two-pronged strategy for choosing among alternative gene trees. First, the character data are used to define a set of acceptable gene trees (i.e., trees that are not significantly different from the minimum length tree). Next, the set of acceptable gene trees is reconciled with a known species tree, and the gene tree requiring the fewest number of gene duplications and losses is adopted as the best estimate of evolutionary history. The approach is illustrated using three gene families: BMP, EGR, and LDH.

Vertebrates have conserved capping protein alpha isoforms with specific expression patterns

Capping protein (CP), a ubiquitous actin binding protein composed of an alpha and a beta subunit, is important for actin assembly and cell motility. Lower organisms have one gene and one isoform of each subunit. Chickens have two very similar alpha-subunit isoforms. To determine if vertebrates in general contain multiple alpha isoforms and if those alpha isoforms have conserved sequences, we isolated and analyzed alpha subunit cDNA's in mice and humans. Both mice and humans also have two alpha isoforms. Phylogenetic analysis of the alpha isoform sequences reveals that vertebrates have two highly conserved subfamilies, alpha1 and alpha2. The alpha1 and alpha2 subfamilies are very similar to each other but can be defined and distinguished from each other by a small number of key amino acid residues. In addition, 3' untranslated cDNA sequences are conserved within the isoform subfamilies. To investigate the function of the alpha isoforms, we examined their expression in mouse cells and tissues. Endothelial cells contain only the alpha2 isoform, and erythrocytes contain almost exclusively the alpha1 isoform. Most tissues have both alpha1 and alpha2 isoforms but the ratio of alpha1:alpha2 varies widely. Together, these findings support the hypothesis that the CP alpha isoforms have conserved, unique and essential roles in vertebrates.

Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate

To determine whether gene expression patterns affect mutation rates and/or selection intensity in mammalian genes, we studied the relationships between substitution rates and tissue distribution of gene expression. For this purpose, we analyzed 2,400 human/rodent and 834 mouse/rat orthologous genes, and we measured (using expressed sequence tag data) their expression patterns in 19 tissues from three development states. We show that substitution rates at nonsynonymous sites are strongly negatively correlated with tissue distribution breadth: almost threefold lower in ubiquitous than in tissue-specific genes. Nonsynonymous substitution rates also vary considerably according to the tissues: the average rate is twofold lower in brain-, muscle-, retina- and neuron-specific genes than in lymphocyte-, lung-, and liver-specific genes. Interestingly, 5' and 3' untranslated regions (UTRs) show exactly the same trend. These results demonstrate that the expression pattern is an essential factor in determining the selective pressure on functional sites in both coding and noncoding regions. Conversely, silent substitution rates do not vary with expression pattern, even in ubiquitously expressed genes. This latter result thus suggests that synonymous codon usage is not constrained by selection in mammals. Furthermore, this result also indicates that there is no reduction of mutation rates in genes expressed in the germ line, contrary to what had been hypothesized based on the fact that transcribed DNA is more efficiently repaired than nontranscribed DNA.

Assembly of force-expressed troponin-I isoforms in myofibrils of cultured cardiac and fast skeletal muscle cells as studied by epitope tagging

The isoform-specific assembly of cardiac and skeletal muscle troponin-I (CTnI and FTnI, respectively) on to myofibrils (MFs) was investigated. Epitope tagging was used to monitor the intracellular localization of exogenously introduced constructs to myofibrillar structures in cultured chicken cardiac and fast skeletal (breast) muscle cells. Exogenous CTnI and FTnI were incorporated into endogenous MFs of cardiac and breast muscle cells with high affinity, respectively. In the case of CTnI and FTnI with breast and cardiac muscle cells respectively, CTnI was not incorporated into breast MFs but FTnI was assembled on to cardiac MFs. To determine which portion of TnI is responsible for incorporation into these MFs, we constructed chimeric TnIs with the head and tail of CTnI replaced by those of FTnI. The behaviour of these chimeras depends on the tail of TnIs. These results suggest that the tail regions of TnIs bind to cardiac and breast MFs, and that this affinity of TnI tails is responsible for the assembly of FTnI on to cardiac MFs.

Heterogeneity of Atlantic salmon troponin-I

Three non-identical, full length troponin-I (Tn-I) clones were isolated from an Atlantic salmon myotomal (trunk) muscle cDNA library. The primary structures, which are predicted to range from 172 to 180 amino acids in length, exhibit similar percent identity scores when compared with fast, slow and cardiac specific Tn-Is from higher vertebrates. When the sequence data are considered along with the results of Western blotting it is evident that Tn-I is more heterogeneous in Atlantic salmon than has been previously shown in higher vertebrates.