Showing papers by "Bruce W. Birren published in 2002"

Initial sequencing and comparative analysis of the mouse genome.

Abstract: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

The Genome of M. Acetivorans Reveals Extensive Metabolic and Physiological Diversity

Abstract: The Archaea remain the most poorly understood domain of life despite their importance to the biosphere. Methanogenesis, which plays a pivotal role in the global carbon cycle, is unique to the Archaea. Each year, an estimated 900 million metric tons of methane are biologically produced, representing the major global source for this greenhouse gas and contributing significantly to global warming (Schlesinger 1997). Methanogenesis is critical to the waste-treatment industry and biologically produced methane also represents an important alternative fuel source. At least two-thirds of the methane in nature is derived from acetate, although only two genera of methanogens are known to be capable of utilizing this substrate. We report here the first complete genome sequence of an acetate-utilizing (acetoclastic) methanogen, Methanosarcina acetivorans C2A. The Methanosarcineae are metabolically and physiologically the most versatile methanogens. Only Methanosarcina species possess all three known pathways for methanogenesis (Fig. ​(Fig.1)1) and are capable of utilizing no less than nine methanogenic substrates, including acetate. In contrast, all other orders of methanogens possess a single pathway for methanogenesis, and many utilize no more than two substrates. Among methanogens, the Methanosarcineae also display extensive environmental diversity. Individual species of Methanosarcina have been found in freshwater and marine sediments, decaying leaves and garden soils, oil wells, sewage and animal waste digesters and lagoons, thermophilic digesters, feces of herbivorous animals, and the rumens of ungulates (Zinder 1993). Figure 1 Three pathways for methanogenesis. Methanogenesis is a form of anaerobic respiration using a variety of one-carbon (C-1) compounds or acetic acid as a terminal electron acceptor. All three pathways converge on the reduction of methyl-CoM to methane (CH ... The Methanosarcineae are unique among the Archaea in forming complex multicellular structures during different phases of growth and in response to environmental change (Fig. ​(Fig.2).2). Within the Methanosarcineae, a number of distinct morphological forms have been characterized, including single cells with and without a cell envelope, as well as multicellular packets and lamina (Macario and Conway de Macario 2001). Packets and lamina display internal morphological heterogeneity, suggesting the possibility of cellular differentiation. Moreover, it has been suggested that cells within lamina may display differential production of extracellular material, a potential form of cellular specialization (Macario and Conway de Macario 2001). The formation of multicellular structures has been proposed to act as an adaptation to stress and likely plays a role in the ability of Methanosarcina species to colonize diverse environments. Figure 2 Different morphological forms of Methanosarcina acetivorans. Thin-section electron micrographs showing M. acetivorans growing as both single cells (center of micrograph) and within multicellular aggregates (top left, bottom right). Cells were harvested ... Significantly, powerful methods for genetic analysis exist for Methanosarcina species. These tools include plasmid shuttle vectors (Metcalf et al. 1997), very high efficiency transformation (Metcalf et al. 1997), random in vivo transposon mutagenesis (Zhang et al. 2000), directed mutagenesis of specific genes (Zhang et al. 2000), multiple selectable markers (Boccazzi et al. 2000), reporter gene fusions (M. Pritchett and W. Metcalf, unpubl.), integration vectors (Conway de Macario et al. 1996), and anaerobic incubators for large-scale growth of methanogens on solid media (Metcalf et al. 1998). Furthermore, and in contrast to other known methanogens, genetic analysis can be used to study the process of methanogenesis: Because Methanosarcina species are able to utilize each of the three known methanogenic pathways, mutants in a single pathway are viable (M. Pritchett and W. Metcalf, unpubl.). The availability of genetic methods allowing immediate exploitation of genomic sequence, coupled with the genetic, physiological, and environmental diversity of M. acetivorans make this species an outstanding model organism for the study of archaeal biology. For these reasons, we set out to study the genome of M. acetivorans.

Lymphopenia in the BB rat model of type 1 diabetes is due to a mutation in a novel immune-associated nucleotide (Ian)-related gene.

Abstract: The BB (BioBreeding) rat is one of the best models of spontaneous autoimmune diabetes and is used to study non-MHC loci contributing to Type 1 diabetes. Type 1 diabetes in the diabetes-prone BB (BBDP) rat is polygenic, dependent upon mutations at several loci. Iddm1, on chromosome 4, is responsible for a lymphopenia (lyp) phenotype and is essential to diabetes. In this study, we report the positional cloning of the Iddm1/lyp locus. We show that lymphopenia is due to a frameshift deletion in a novel member (Ian5) of the Immune-Associated Nucleotide (IAN)-related gene family, resulting in truncation of a significant portion of the protein. This mutation was absent in 37 other inbred rat strains that are nonlymphopenic and nondiabetic. The IAN gene family, lying within a tight cluster on rat chromosome 4, mouse chromosome 6, and human chromosome 7, is poorly characterized. Some members of the family have been shown to be expressed in mature T cells and switched on during thymic T-cell development, suggesting that Ian5 may be a key factor in T-cell development. The lymphopenia mutation may thus be useful not only to elucidate Type 1 diabetes, but also in the function of the Ian gene family as a whole.

Structure and evolution of the Smith-Magenis syndrome repeat gene clusters, SMS-REPs.

Abstract: Smith-Magenis syndrome (SMS) is caused in >90% of cases by a common deletion of an ∼4-Mb gene-rich genomic segment in 17p11.2. Recently, the same chromosome region has been shown to be duplicated in patients with the reciprocal chromosome duplication, dup(17)(p11.2p11.2) (Chen et al. 1997; Potocki et al. 2000). Physical mapping studies have shown that the SMS-common-deletion interval is flanked by large (∼200 kb), highly homologous, low-copy repeat (LCR) gene clusters termed SMS-REPs (Chen et al. 1997). The proximal and distal SMS-REPs likely act as substrates for nonallelic homologous recombination (NAHR; also known as unequal crossing-over), resulting in both common deletions and reciprocal duplications of the same chromosome segment. A third copy, the middle SMS-REP, has been mapped in 17p11.2 between the proximal and distal SMS-REPs (Chen et al. 1997). The chromosome 17p11.2 genomic region is involved in several other rearrangements. Isodicentric chromosomes idic(17)(p11), with breakpoints mapping within or just adjacent to the SMS critical region, have been identified in various hematological malignancies, including chronic myeloid leukemia, and in solid tumors, such as childhood primitive neuroectodermal tumors (Fioretos et al. 1999; Scheurlen et al. 1999). Chromosome amplifications within 17p11.2 have been described in patients with osteosarcoma and leiomyosarcoma (Tarkkanen et al. 1995; Otano-Joos et al. 2000). In medulloblastomas, an aberrant hypermethylation of the major breakpoint cluster region in 17p11.2 has been proposed to be an additional genomic feature responsible for the chromosomal fragility (Fruhwald et al. 2001). These data, together with identified somatic mosaicism for SMS deletions (Zori et al. 1993; Juyal et al. 1996), indicate that the presence of unique genome architecture features, including highly homologous SMS-REPs, makes the chromosome 17p11.2 a highly unstable region in the human genome, prone to both meiotic and mitotic rearrangements. To delineate the genomic structure and evolution of the SMS-REPs, we constructed and sequenced a complete bacterial artificial chromosome/P1 artifical chromosome (BAC/PAC) contig. Based on genomic sequence analysis, we elucidated the size and the orientation of each SMS-REP, the extent of homology among the SMS-REPs, genes within the SMS-REPs, and here provide a model for the evolution of SMS-REPs. Sequence-based structural analysis of the SMS-REPs is essential to determine the molecular mechanism of chromosome rearrangements in SMS, as well as other genomic disorders (Lupski 1998). These studies add to a growing body of evidence that implicate genome architecture in DNA rearrangements responsible for genomic disorders (Lupski 1998; Mazzarella and Schlessinger 1998; Ji et al. 2000; Shaffer and Lupski 2000; Emanuel and Shaikh 2001; Stankiewicz and Lupski 2002).

Mapping of Myxococcus xanthus Social Motility dsp Mutations to the dif Genes

Abstract: Myxococcus xanthus dsp and dif mutants have similar phenotypes in that they are deficient in social motility and fruiting body development. We compared the two loci by genetic mapping, complementation with a cosmid clone, DNA sequencing, and gene disruption and found that 16 of the 18 dsp alleles map to the dif genes. Another dsp allele contains a mutation in the sglK gene. About 36.6 kb around the dsp-dif locus was sequenced and annotated, and 50% of the genes are novel.