A VpreB3 homologue in a marsupial, the gray short-tailed opossum, Monodelphis domestica

A VpreB surrogate light (SL) chain was identified for the first time in a marsupial, the opossum Monodelphis domestica. Comparing the opossum VpreB to homologues from eutherian (placental mammals) and avian species supported the marsupial gene being VpreB3. VpreB3 is a protein that is not known to traffic to the cell surface as part of the pre-B cell receptor. Rather, VpreB3 associates with nascent immunoglobulin chains in the endoplasmic reticulum. Homologues of other known SL chains VpreB1, VpreB2, and λ5, which are found in eutherian mammals, were not found in the opossum genome, nor have they been identified in the genomes of nonmammals. VpreB3 likely evolved from earlier gene duplication, independent of that which generated VpreB1 and VpreB2 in eutherians. The apparent absence of VpreB1, VpreB2, and λ5 in marsupials suggests that an extracellular pre-B cell receptor containing SL chains, as it has been defined in humans and mice, may be unique to eutherian mammals. In contrast, the conservation of VpreB3 in marsupials and its presence in nonmammals is consistent with previous hypotheses that it is playing a more primordial role in B cell development.     

Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex

The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used theMonodelphis domestica (gray short-tailed opossum) sequence to construct the first map of a marsupial major histocompatibility complex (MHC). The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral “immune supercomplex” that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes.     

An analysis of the factors that influence the level and scaling of mammalian BMR

The factors influencing the basal rate of metabolism (BMR) in 639 species of mammals include body mass, food habits, climate, habitat, substrate, a restriction to islands or highlands, use of torpor, and type of reproduction. They collectively account for 98.8% of the variation in mammalian BMR, but often interact in complex ways. The factor with the greatest impact on BMR, as always, is body mass (accounting for 96.8% of its variation), the extent of its impact reflecting the 10(6.17)-fold range of mass in measured species. The attempt to derive mathematically the power relationship of BMR in mammals is complicated by the necessity to include all of the factors that influence BMR that are themselves correlated with body mass. BMR also correlates with taxonomic affiliation because many taxa are distinguished by their ecological and behavioral characteristics. Phylogeny, reflecting previous commitments, may influence BMR either through a restriction on the realized range of behaviors or by opening new behavioral and ecological opportunities. A new opportunity resulted from the evolution by eutherians of a type of reproduction that permitted species feeding on high quality resources to have high BMRs. These rates facilitated high rates of gas, nutrient, and waste exchange between a pregnant eutherian and her placental offspring. This pattern led to high rates of reproduction in some eutherians, a response denied all monotremes and marsupials, thereby permitting eutherians to occupy cold-temperate and polar environments and to dominate other mammals in all environments to which ecologically equivalent eutherians had access.     

C-->U editing of apolipoprotein B mRNA in marsupials: identification and characterisation of APOBEC-1 from the American opossum Monodelphus domestica.

The C->U editing of RNA is widely found in plant and animal species. In mammals it is a discrete process confined to the editing of apolipoprotein B (apoB) mRNA in eutherians and the editing of the mitochondrial tRNA for glycine in marsupials. Here we have identified and characterised apoB mRNA editing in the American opossum Monodelphus domestica. The apoB mRNA editing site is highly conserved in the opossum and undergoes complete editing in the small intestine, but not in the liver or other tissues. Opossum APOBEC-1 cDNA was cloned, sequenced and expressed. The encoded protein is similar to APOBEC-1 of eutherians. Motifs previously identified as involved in zinc binding, RNA binding and catalysis, nuclear localisation and a C-terminal leucine-rich domain are all conserved. Opossum APOBEC-1 contains a seven amino acid C-terminal extension also found in humans and rabbits, but not present in rodents. The opossum APOBEC-1 gene has the same intron/exon organisation in the coding sequence as the eutherian gene. Northern blot and RT-PCR analyses and an editing assay indicate that no APOBEC-1 was expressed in the liver. Thus the far upstream promoter responsible for hepatic expression in rodents does not operate in the opossum. An APOBEC-1-like enzyme such as might be involved in C->U RNA editing of tRNA in marsupial mitochondria was not demonstrated. The activity of opossum APOBEC-1 in the presence of both chicken and rodent auxiliary editing proteins was comparable to that of other mammals. These studies extend the origins of APOBEC-1 back 170 000 000 years to marsupials and help bridge the gap in the origins of this RNA editing process between birds and eutherian mammals.     

Marsupial genetics and genomics

Marsupials, the 'other' mammals, are found only in Australasia and the Americas. They are quite different from eutherian ('placental') mammals, as well they might be after 130 million years of separate evolution. They display a unique pattern of mammalian organization and development that is reflected by differences in their genomes. Here, we introduce marsupials as alternative (but not inferior!) mammals and summarize the state of knowledge of marsupial relationships, marsupial chromosomes, maps, genes and genetic regulatory systems. We shamelessly present the case for a Kangaroo Genome Project.     

M6P/IGF2R imprinting evolution in mammals

Imprinted gene identification in animals has been limited to eutherian mammals, suggesting a significant role for intrauterine fetal development in the evolution of imprinting. We report herein that M6P/IGF2R is not imprinted in monotremes and does not encode for a receptor that binds IGF2. In contrast, M6P/IGF2R is imprinted in a didelphid marsupial, the opossum, but it strikingly lacks the differentially methylated CpG island in intron 2 postulated to be involved in imprint control. Thus, invasive placentation and gestational fetal growth are not required for imprinted genes to evolve. Unless there was convergent evolution of M6P/ IGF2R imprinting and receptor IGF2 binding in marsupials and eutherians, our results also demonstrate that these two functions evolved in a mammalian clade exclusive of monotremes.     

The genome of a Gondwanan mammal

Australia is thought of as the home of marsupials, but South America has 60 or so species of these interesting mammals. The genome of one of these, the South American grey short-tailed opossum, Monodelphis domestica, has just been sequenced and published in June.1 The high quality 6x coverage is the first marsupial genome completed, pipping the 2x coverage of the Australian tammar wallaby at the post by half a year. The opossum genome has an unusual structure with fewer chromosomes than the human genome (9 pairs versus 23 pairs) but a longer total length (3.4 billion versus 3 billion bases). The opossum autosomes, like those of all marsupials, are extremely large but, in contrast, the X chromosome is only 76 Mb long. The opossum genome has turned up several surprises and provided critical new information on the evolution of mammalian genomes.     

A eutherian X-linked gene, PDHA1, is autosomal in marsupials:A model for the evolution of a second, testis-specific variant in eutherian mammals

We report the cloning and mapping of a gene (PDHA)for the pyruvate dehydrogenase E1α subunit in marsupials. In situ hybridization and Southern blot analysis show that PDHA is autosomal in marsupials, mapping to chromosome 3q in Sminthopsis macroura and 5p in Macropus eugenii. Since these locations represent a region that was translocated to the p arm of the human X chromosome following marsupial/eutherian divergence, we suggest that the marsupial PDHA gene is homologous to PDHA1, the somatic eutherian isoform located on human Xp and mouse X. Only one copy of PDHA is found in marsupials, whereas a second, testis-specific, intronless form is observed in eutherian mammals. We also suggest that translocation of PDHA to the eutherian X chromosome, which is inactivated during spermatogenesis, led to the evolution of a second testis-specific locus by retroposition to an autosome.     

Housekeeping genes for phylogenetic analysis of eutherian relationships

The molecular relationship of placental mammals has attracted great interest in recent years. However, 2 crucial and conflicting hypotheses remain, one with respect to the position of the root of the eutherian tree and the other the relationship between the orders Rodentia, Lagomorpha (rabbits, hares), and Primates. Although most mitochondrial (mt) analyses have suggested that rodents have a basal position in the eutherian tree, some nuclear data in combination with mt-rRNA genes have placed the root on the so-called African clade or on a branch that includes this clade and the Xenarthra (e.g., anteater and armadillo). In order to generate a new and independent set of molecular data for phylogenetic analysis, we have established cDNA sequences from different tissues of various mammalian species. With this in mind, we have identified and sequenced 8 housekeeping genes with moderately fast rate of evolution from 22 placental mammals, representing 11 orders. In order to determine the root of the eutherian tree, the same genes were also sequenced for 3 marsupial species, which were used as outgroup. Inconsistent with the analyses of nuclear + mt-rRNA gene data, the current data set did not favor a basal position of the African clade or Xenarthra in the eutherian tree. Similarly, by joining rodents and lagomorphs on the same basal branch (Glires hypothesis), the data set is also inconsistent with the tree commonly favored in mtDNA analyses. The analyses of the currently established sequences have helped examination of problematic parts in the eutherian tree at the same time as they caution against suggestions that have claimed that basal eutherian relationships have been conclusively settled.     

Growth inhibition and chromosomal instability of cultured marsupial (opossum) cells after treatment with DNA polymerase α inhibitor

The DNA replication mechanism has been well established for eutherian mammals (placental mammals such as humans, mice, and cattle), but not, to date, for metatherian mammals (marsupials such as kangaroos, koalas, and opossums). In this study, we found that dehydroaltenusin, a selective inhibitor of mammalian (eutherian) DNA polymerase α, clearly suppressed the growth of metatherian (opossum and rat kangaroo) cultured cells. In cultured opossum (OK) cells, dehydroaltenusin also suppressed the progression of DNA replication. These results suggest that dehydroaltenusin inhibits metatherian as well as eutherian DNA replication. Dehydroaltenusin treatment of OK cells engendered fluctuations in the numbers of chromosomes in the OK cells as well as inhibition of cell growth and DNA replication. This suggests that partial inhibition of DNA replication by dehydroaltenusin causes chromosomal instability in cultured cells.     

In silico identification of opossum cytokine genes suggests the complexity of the marsupial immune system rivals that of eutherian mammals

Background

Cytokines are small proteins that regulate immunity in vertebrate species. Marsupial and eutherian mammals last shared a common ancestor more than 180 million years ago, so it is not surprising that attempts to isolate many key marsupial cytokines using traditional laboratory techniques have been unsuccessful. This paucity of molecular data has led some authors to suggest that the marsupial immune system is 'primitive' and not on par with the sophisticated immune system of eutherian (placental) mammals.

Results

The sequencing of the first marsupial genome has allowed us to identify highly divergent immune genes. We used gene prediction methods that incorporate the identification of gene location using BLAST, SYNTENY + BLAST and HMMER to identify 23 key marsupial immune genes, including IFN-γ, IL-2, IL-4, IL-6, IL-12 and IL-13, in the genome of the grey short-tailed opossum (Monodelphis domestica). Many of these genes were not predicted in the publicly available automated annotations.

Conclusion

The power of this approach was demonstrated by the identification of orthologous cytokines between marsupials and eutherians that share only 30% identity at the amino acid level. Furthermore, the presence of key immunological genes suggests that marsupials do indeed possess a sophisticated immune system, whose function may parallel that of eutherian mammals.     

哺乳动物基础代谢率的主要影响因素

综述了影响哺乳动物基础代谢率的主要因素, 包括体重、系统发育、食性、气候和栖息地、季节、生活习性和繁殖, 以及激素、器官、线粒体和质子漏的理化特征等, 并对这些因素可能的作用机理进行了简要的分析。     

Energetic trade-offs between brain size and offspring production: Marsupials confirm a general mammalian pattern

Recently, Weisbecker and Goswami presented the first comprehensive comparative analysis of brain size, metabolic rate, and development periods in marsupial mammals. In this paper, a strictly energetic perspective is applied to identify general mammalian correlates of brain size evolution. In both marsupials and placentals, the duration or intensity of maternal investment is a key correlate of relative brain size, but here I show that allomaternal energy subsidies may also play a role. In marsupials, an energetic constraint on brain size in adults is only revealed if we consider both metabolic and reproductive rates simultaneously, because a strong trade-off between encephalization and offspring production masks the positive correlation between basal metabolic rate and brain size in a bivariate comparison. In conclusion, starting from an energetic perspective is warranted to elucidate relations between ecology, social systems, life history, and brain size in all mammals.     

Energy expenditure and protein turnover in three species of wallabies (Marsupialia: Macropodidae)

Summary Relationships between basal and fed metabolic rates and whole-body protein turnover rates were examined in three species of wallabies, the red-necked pademelon (Thylogale thetis), parma wallaby (Macropus parma) and tammar wallaby (M. eugenii).There were no significant differences among wallaby species in basal metabolic rate (BMR) which was 30% below eutherian mammals. However, the fed metabolic rate of the tammar was lower than that of the other two species (P<0.05), as was the protein turnover rate (P<0.01) which is consistent with its lower voluntary feed intake and with its lower maintenance nitrogen requirement.Protein turnover rates in the wallabies were 23–47% lower than in eutherian mammals. Similarly, protein synthesis made a lower contribution to fed metabolic rates in the wallabies (7–8%) than in eutherians (17–25%).Thus, compared with several eutherian species, macropodid marsupials have low rates of both energy and protein metabolism, but within the macropodids there is not necessarily a close link between basal metabolic rate and whole-body protein turnover.Abbreviations BMR basal metabolic rate - DEE daily energy expenditure - EE energy expenditure - LSD least significant difference - RQ respiratory quotient     

First-generation linkage map of the gray, short-tailed opossum, Monodelphis domestica, reveals genome-wide reduction in female recombination rates

The gray, short-tailed opossum, Monodelphis domestica, is the most extensively used, laboratory-bred marsupial resource for basic biologic and biomedical research worldwide. To enhance the research utility of this species, we are building a linkage map, using both anonymous markers and functional gene loci, that will enable the localization of quantitative trait loci (QTL) and provide comparative information regarding the evolution of mammalian and other vertebrate genomes. The current map is composed of 83 loci distributed among eight autosomal linkage groups and the X chromosome. The autosomal linkage groups appear to encompass a very large portion of the genome, yet span a sex-average distance of only 633.0 cM, making this the most compact linkage map known among vertebrates. Most surprising, the male map is much larger than the female map (884.6 cM vs. 443.1 cM), a pattern contrary to that in eutherian mammals and other vertebrates. The finding of genome-wide reduction in female recombination in M. domestica, coupled with recombination data from two other, distantly related marsupial species, suggests that reduced female recombination might be a widespread metatherian attribute. We discuss possible explanations for reduced female recombination in marsupials as a consequence of the metatherian characteristic of determinate paternal X chromosome inactivation.