Characterization of mouse sialyltransferase genes: their evolution and diversity

Sialic acids are negatively charged acidic sugars, and sialylglycoconjugates often play important roles in various biological phenomena. Sialyltransferases are involved in the synthesis of sialylglycoconjugates, and 20 members of the mammalian sialyltransferase family have been identified to date. These sialyltransferases are grouped into four families according to the carbohydrate linkages they synthesize: beta-galactoside alpha2,3-sialyltransferases (ST3Gal I-VI), beta-galactoside alpha2,6-sialyltransferases (ST6Gal I and II), GalNAc alpha2,6-sialyltransferases (ST6GalNAc I-VI), and alpha2,8-sialyltransferases (ST8Sia I-VI). Analysis of the amino acid sequence similarities, substrate specificities, and gene structures of mouse sialyltransferases has revealed that they can be further divided into seven subfamilies. The genomic structural resemblance of members of the same subfamily suggests that they arose from a common ancestral gene through gene duplication events. These multiple sialyltransferase genes are needed for fine control of the expression of sialylglycoconjugates, resulting in a variety of developmental stage- and tissue-specific glycosylation patterns.     

High mutation rates in human and ape pseudoautosomal genes

It has been suggested that recombination may be mutagenic, which, if true, would inflate intraspecies diversity and interspecies silent divergence in regions of high recombination. Here, we test this hypothesis comparing human/orangutan genome-wide non-coding divergence (K) to that in the pseudoautosomal genes which were reported to recombine much more frequently than the rest of the genome. We demonstrate that, compared to the average human/orangutan non-coding divergence (K=3%), the substitution rate is significantly elevated in the introns of SHOX (K=5.7%), PPP2R3L (K=8.7%) and ASMT (K=6.5%) genes located in the human and orangutan Xp/Yp pseudoautosomal region (p-PAR), where recombination is over 20-fold higher than the genomic average. On the other hand, human/orangutan non-coding divergence at the Xp/Yp pseudoautosomal boundary (K=3.5%) and in the SYBL1 gene (K=2.7%), located in the human Xq/Yq pseudoautosomal region (q-PAR), where recombination is known to be less frequent than in p-PAR, was not significantly higher than the genome average. The data are consistent with the hypothesis that recombination may be mutagenic.     

Composite human VK genes and a model of their evolution.

A phage library and two cosmid libraries were screened for human VK genes. Two recombinant phage and four cosmid clones were analysed in detail by restriction mapping and sequencing. Each one contained a single VKI sequence. Two of these six sequences are potentially functional VK genes and four are pseudogenes. Two pseudogenes derived from different genomic DNAs are highly homologous and are therefore either allelic variants or the products of a recent duplication event. Comparisons of our sequences with all fully determined human VKI amino acid and DNA sequences reveal identical segments which at first sight appear like minigenes. But these segments do not coincide with the subregions and some of the segments include both, framework and complementarity determining regions (FR, CDR, ref. 2). The findings may be explained by an evolutionary model generating composite genes by gene conversion and selection.     

Rapid divergency of rodent CD99 orthologs: implications for the evolution of the pseudoautosomal region

The human pseudoautosomal region 1 (PAR1) is essential for the obligatory X-Y crossover in male meiosis. Despite its critical role, comparative studies of human and mouse pseudoautosomal genes have been limited owing to the scarcity of genes conserved between the two species. Human CD99 is a 32-kDa cell surface protein that is encoded by the MIC2 gene localized to the PAR1. Although several sequences such as CD99L2, PBDX, and CD99L1 are related to CD99, its murine ortholog, Cd99, has not yet been identified. Here we report a novel mouse Cd99, designated D4, which shows overall sequence homology to CD99, with the highest conservation between the two genes being found in the transmembrane regions. In addition, the D4 protein displays biochemical characteristics, functional homology, and expression patterns similar to those of CD99. The D4 gene is localized on an autosome, chromosome 4, reflecting a common mapping feature with other mouse orthologs of human PAR1 genes. Furthermore, a phylogenetic analysis of CD99-related genes confirmed that the D4 gene is indeed an ortholog of CD99 and exhibits the accelerated evolution pattern of CD99 orthologs, as compared to the CD99L2 orthologs. On the basis of these findings, we suggest that CD99 belongs to the ancient PAR genes, and that the rapid interspecies divergence of its present sequence and map position is due to a high recombination frequency and the occurrence of chromosomal translocation, supporting the addition-attrition hypothesis for PAR evolution.     

Identification of rice TUBBY-like genes and their evolution

The identification of TUBBY-like genes in organisms ranging from single-celled to multicellular eukaryotes has allowed the phylogenetic history of this gene family to be traced back to the early evolutionary stages of eukaryote development. Rice TUBBY-like genes were located on chromosomes 1, 2, 3, 4, 5, 7, 8, 11 and 12 without any obvious clustering. On a genomic scale, it was revealed that the rice TUBBY-like gene family probably evolved mainly through segmental duplication produced by polyploidy. The altered selective constraints (or site-specific rate changes), related to functional divergence during protein evolution between plant and animal TUBBY-like genes, were statistically significant. Based on posterior probability analysis, five amino acid sites (103, 312, 315, 317 and 319) are thought to be responsible for functional divergence.     

Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs.

About 30 years have now passed since it was discovered that microbes synthesize RubisCO molecules that differ from the typical plant paradigm. RubisCOs of forms I, II, and III catalyze CO(2) fixation reactions, albeit for potentially different physiological purposes, while the RubisCO-like protein (RLP) (form IV RubisCO) has evolved, thus far at least, to catalyze reactions that are important for sulfur metabolism. RubisCO is the major global CO(2) fixation catalyst, and RLP is a somewhat related protein, exemplified by the fact that some of the latter proteins, along with RubisCO, catalyze similar enolization reactions as a part of their respective catalytic mechanisms. RLP in some organisms catalyzes a key reaction of a methionine salvage pathway, while in green sulfur bacteria, RLP plays a role in oxidative thiosulfate metabolism. In many organisms, the function of RLP is unknown. Indeed, there now appear to be at least six different clades of RLP molecules found in nature. Consideration of the many RubisCO (forms I, II, and III) and RLP (form IV) sequences in the database has subsequently led to a coherent picture of how these proteins may have evolved, with a form III RubisCO arising from the Methanomicrobia as the most likely ultimate source of all RubisCO and RLP lineages. In addition, structure-function analyses of RLP and RubisCO have provided information as to how the active sites of these proteins have evolved for their specific functions.     

Structural differences between the repertoires of mouse and human germline genes and their evolutionary implications

 Although human and mouse antibodies are similar when one considers their diversification strategies, they differ in the extent to which kappa and lambda light chains are present in their respective variable light chain repertoires. While the Igk-V germline genes are preponderant in mice (95% or more), they comprise only 60% in humans. This may account for differences in the structural repertoire encoded in the Igk-V germline genes of these species. However, this subject has not been properly investigated, partially because a systematic structural characterization of the mouse Igk-V germline genes has not been undertaken. In the present study we compiled all available information on mouse Igk-V germline genes to characterize their structural repertoire. As expected, comparison with the structural repertoire of human Igk-V germline genes indicates differences. The most interesting is that the mouse Igk-V germline gene repertoire is more diverse in structural terms than its human counterpart: the mouse encodes seven canonical structure classes (combination of canonical structures in L1 and L3). In contrast, the human encodes only four. Analysis of the evolutionary relationships of human and mouse Igk-V germline genes led us to propose that the difference reflects a strategy of mice to compensate for the small lambda chain contribution to the repertoire of their variable light chains. Received: 1 June 1997 / Revised: 6 October 1997     

Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control

Rapid rates of evolution can signify either a lack of selective constraint and the consequent accumulation of neutral alleles, or positive Darwinian selection driving the fixation of advantageous alleles. Based on a comparison of 1,350 orthologous gene pairs from human and mouse, we show that the evolution of gene expression profiles is so rapid that it is comparable to that of paralogous gene pairs or randomly paired genes. The expression divergence in the entire set of orthologous pairs neither strongly correlates with sequence divergence, nor focuses in any particular tissue. Moreover, comparing tissue expressions across the orthologous gene pairs, we observe that any human tissue is more similar to any other human tissue examined than to its corresponding mouse tissue. Collectively, these results indicate that, while some differences in expression profiles may be due to adaptive evolution, the levels of divergence are mostly compatible with a neutral mode of evolution, in which a mutation for ectopic expression may rise to fixation by random drift without significantly affecting the fitness. A disturbing corollary of these findings is that knowledge of where the gene is expressed may not carry information about its function.     

Characterization of photolyase/blue-light receptor homologs in mouse and human cells.

We isolated and characterized mouse photolyase-like genes, mCRY1 (mPHLL1) and mCRY2 (mPHLL2), which belong to the photolyase family including plant blue-light receptors. The mCRY1 and mCRY2 genes are located on chromosome 10C and 2E, respectively, and are expressed in all mouse organs examined. We raised antibodies specific against each gene product using its C-terminal sequence, which differs completely between the genes. Immunofluorescent staining of cultured mouse cells revealed that mCRY1 is localized in mitochondria whereas mCRY2 was found mainly in the nucleus. The subcellular distribution of CRY proteins was confirmed by immunoblot analysis of fractionated mouse liver cell extracts. Using green fluorescent protein fused peptides we showed that the C-terminal region of the mouse CRY2 protein contains a unique nuclear localization signal, which is absent in the CRY1 protein. The N-terminal region of CRY1 was shown to contain the mitochondrial transport signal. Recombinant as well as native CRY1 proteins from mouse and human cells showed a tight binding activity to DNA Sepharose, while CRY2 protein did not bind to DNA Sepharose at all under the same condition as CRY1. The different cellular localization and DNA binding properties of the mammalian photolyase homologs suggest that despite the similarity in the sequence the two proteins have distinct function(s).     

Rapid cloning of any rearranged mouse immunoglobulin variable genes

Immunoglobulins (Ig) have been the focus of extensive study for several decades and have become an important research area for immunologists and molecular biologist. The use of polymerase chain reaction (PCR) technology has accelerated the cloning, sequencing, and characterization of genes of the immune system. However, cloning and sequencing the Ig variable (V) genes using the PCR technology has been a challenging task, primarily due to the very diverse nature of Ig V region genes. We have developed a simple, rapid, and reproducible PCR-based technique to clone any rearranged mouse Ig heavy or light chain genes. A close examination of all Ig heavy and light chain V gene families has resulted in the design of 5 and 3 universal primers from regions that are highly conserved across all heavy or light chain V gene families, and the joining or constant regions, respectively. We present our strategy for designing universal primers for Ig V gene families. These primers were able to rapidly amplify the rearranged Ig V genes, belonging to diverse Ig V gene families from very different cell lines, i.e., J558, MOPC-21, 36–60, and a chicken ovalbumin specific B-cell hybridoma. In addition, the present study provides the complete alignment of nucleotide sequences of all heavy and light chain variable gene families. This powerful method of cloning Ig V genes, therefore, allows rapid and precise analysis of B-cell hybridomas, B-cell repertoire, and B-cell ontogeny.The nucloetide sequence data reported in this paper have been submitted to the EMBL/GenBank nucleotide sequence database and have been assigned the accession number U32111     

Helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic Sel1-like genes

Geographic partitioning is postulated to foster divergence of Helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. H. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. Sequenced H. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs that are characteristic of the eukaryotic Sel1 regulatory protein, whereas the related Campylobacter and Wolinella genomes each contain only one or two such “Sel1-like repeat” (SLR) genes (“slr genes”). Signatures of positive selection (ratio of nonsynonymous to synonymous mutations, d_N/d_S = ω > 1) were evident in the evolutionary history of H. pylori slr gene family expansion. Sequence analysis of six of these slr genes (hp0160, hp0211, hp0235, hp0519, hp0628, and hp1117) from representative East Asian, European, and African H. pylori strains revealed that all but hp0628 had undergone positive selection, with different amino acids often selected in different regions. Most striking was a divergence of Japanese and Korean alleles of hp0519, with Japanese alleles having undergone particularly strong positive selection (ω_J > 25), whereas alleles of other genes from these populations were intermingled. Homology-based structural modeling localized most residues under positive selection to SLR protein surfaces. Rapid evolution of certain slr genes in specific H. pylori lineages suggests a model of adaptive change driven by selection for fine-tuning of host responses, and facilitated by geographic isolation. Characterization of such local adaptations should help elucidate how H. pylori manages persistent infection, and potentially lead to interventions tailored to diverse human populations.