Multicellular Ascomycetous Fungal Genomes Contain More Than 8000 Genes

Fungi comprise a large monophyletic group of uni- and multicellular eukaryotic organisms in which many species are of economic or medical importance. Fungal genomes are variable in size (13–42 Mb), and multicellular species support true spatial and temporal cell-type-specific regulation of gene expression. In a 38.8-kbAspergillus nidulanscontiguous genomic DNA region, a transposable element and 12 potential genes were identified, 7 similar to genes in other organisms. This observation is consistent with the prediction that multicellular ascomycetous fungi harbor 8000–9000 genes in a 36-Mb average genome. Thus, the genomic DNA sequence of filamentous fungi will provide substantial amounts of genetic and functional information that is not available in yeast, for the human and other metazoan minimal gene complement.     

A Universal Method for the Study of CR1 Retroposons in Nonmodel Bird Genomes

Presence/absence patterns of retroposon insertions at orthologous genomic loci constitute straightforward markers for phylogenetic or population genetic studies. In birds, the convenient identification and utility of these markers has so far been mainly restricted to the lineages leading to model birds (i.e., chicken and zebra finch). We present an easy-to-use, rapid, and cost-effective method for the experimental isolation of chicken repeat 1 (CR1) insertions from virtually any bird genome and potentially nonavian genomes. The application of our method to the little grebe genome yielded insertions belonging to new CR1 subfamilies that are scattered all across the phylogenetic tree of avian CR1s. Furthermore, presence/absence analysis of these insertions provides the first retroposon evidence grouping flamingos + grebes as Mirandornithes and several markers for all subsequent branching events within grebes (Podicipediformes). Five markers appear to be species-specific insertions, including the hitherto first evidence in birds for biallelic CR1 insertions that could be useful in future population genetic studies.     

A Majority of Infectious Newcastle Disease Virus Particles Contain a Single Genome, while a Minority Contain Multiple Genomes

Paramyxoviruses produce pleiomorphic particles containing variable amounts of genetic material that correlate with virion diameter by electron microscopy. However, the infectious nature of these particles is unknown, and functional genomes are indistinguishable from defective RNA. A quantitative approach to paramyxovirus packaging revealed a majority of infectious Newcastle disease viruses contain one functional genome. Virions encapsidating two or three genomes (approximately 25% of total) were also observed by utilizing three different recombinant viruses expressing unique fluorescent reporters.     

测定胸腺肽含量几种定量方法的比较

本文用凯氏定氮法、双缩脲法及福林－酚法测定了胸腺肽含量,并加以比较,说明三种方法对其含量测定没有显著差异．在实践中可以根据不同条件选择适当的方法进行实验．     

逆转座子对灵长目动物基因组结构的影响

逆转座子(retroposon)是动物基因组中一类可移动的元件,它们首先通过转录产生一个RNA拷贝,然后利用逆转录酶将该RNA拷贝逆转录为c DNA后,再插入到基因组的新位点上。逆转座子在动物基因组中含量极为丰富,种类也很繁多,并随着动物进化在基因组中不断扩增。它们可通过形成插入突变、侧翼序列转导、基因逆转座、DNA断裂与修复、异常重组等机制对动物基因组结构的稳定性产生重要影响,并成为推动基因组进化的重要动力。本文综述了灵长目动物主要的逆转座子类型及其对基因组结构的影响方式,从而为深入理解逆转座子在灵长目动物基因组中的功能及灵长目动物的进化提供参考。     

Secretory Pathway of Trypanosomatid Parasites

The Trypanosomatidae comprise a large group of parasitic protozoa, some of which cause important diseases in humans. These include Trypanosoma brucei (the causative agent of African sleeping sickness and nagana in cattle), Trypanosoma cruzi (the causative agent of Chagas' disease in Central and South America), and Leishmania spp. (the causative agent of visceral and [muco]cutaneous leishmaniasis throughout the tropics and subtropics). The cell surfaces of these parasites are covered in complex protein- or carbohydrate-rich coats that are required for parasite survival and infectivity in their respective insect vectors and mammalian hosts. These molecules are assembled in the secretory pathway. Recent advances in the genetic manipulation of these parasites as well as progress with the parasite genome projects has greatly advanced our understanding of processes that underlie secretory transport in trypanosomatids. This article provides an overview of the organization of the trypanosomatid secretory pathway and connections that exist with endocytic organelles and multiple lytic and storage vacuoles. A number of the molecular components that are required for vesicular transport have been identified, as have some of the sorting signals that direct proteins to the cell surface or organelles in the endosome-vacuole system. Finally, the subcellular organization of the major glycosylation pathways in these parasites is reviewed. Studies on these highly divergent eukaryotes provide important insights into the molecular processes underlying secretory transport that arose very early in eukaryotic evolution. They also reveal unusual or novel aspects of secretory transport and protein glycosylation that may be exploited in developing new antiparasite drugs.     

Analysis on Frequency and Density of Microsatellites in Coding Seauences of Several Eukarvotic Genomes

Microsatellites or simple sequence repeats (SSRs) have been found in most organisms during the last decade. Since large-scale sequences are being generated, especially those that can be used to search for microsatellites, the development of these markers is getting more convenient. Keeping SSRs in viewing the importance of the application, available CDS (coding sequences) or ESTs (expressed sequence tags) of some eukaryotic species were used to study the frequency and density of various types of microsatellites. On the basis of surveying CDS or EST sequences amounting to 66.6 Mb in silkworm, 37.2 Mb in fly, 20.8 Mb in mosquito, 60.0 Mb in mouse, 34.9 Mb in zebrafish and 33.5 Mb in Caenorhabditis elegans, the frequency of SSRs was 1/1.00 Kb in silkworm, 1/0.77 Kb in fly, 1/1.03 Kb in mosquito, 1/1.21 Kb in mouse, 1/1.25 Kb in zebrafish and 1/1.38 Kb in C. elegans. The overall average SSR frequency of these species is 1/1.07 Kb. Hexanucleotide repeats (64.5%-76.6%) are the most abundant class of SSR in th     

Teleost Fish Genomes Contain a Diverse Array of L1 RetrotransposonLineages That Exhibit a Low Copy Number and High Rate of Turnover

Retrotransposable elements exhibit a wide range of variation in population dynamics, abundance, and lineage diversity among host genomes across taxa. This range of diversity is illustrated by a single well-defined constituent monophyletic clade of L1 non-LTR retrotransposons that is shared between mammalian and teleost fish genomes. Despite the clear phylogenetic relationships that exist between mammalian and teleost L1 sequences, these elements exhibit markedly different dynamics within their respective taxa. While mammalian genomes typically contain a single, abundant lineage of L1 elements that traces millions of years of evolution, the zebraflsh genome was recently shown to exhibit a high diversity of ancient lineages coexisting at a very low copy number and apparently exhibiting a high rate of turnover. In the present study, a combination of degenerate PCR, lineage-specific PCR, and genomic Southern blot analysis is utilized to demonstrate high L1 lineage diversity, low copy number, and a high proportion of polymorphic inserts in the genomes of the killifish species, Fundulus heteroclitus. Additional species surveyed by degenerate PCR include Cyprinodon variegatus, Rivulus marmoratus, and Menidia beryllina. These results further support the generality of the differences that exist in host–element dynamics between teleost fish and mammalian genomes with regard to L1 retrotransposons.Reviewing Editor: Dr. Axel Meyer     

Trypanosomatid parasites of plants (phytomonas)

Trypanosomatids of the genus Phytomonas have been known as parasites of lactiferous plants since the beginning of the century and have been the subject of renewed attention in the past decade, as they are now recognized to be pathogenic in plants of economic interest. Nevertheless, information about these flagellates is still scanty. Until recently they had not been cultured, or studied biochemically or ultrastructurally. Phytophagous insects are their putative vectors but exactly which species are involved remains to be established. There are many unanswered questions about the taxonomic identification, pathogenecity and transmission of Phytomonas spp as well as about their natural hosts and reservoirs; this article by Erney Camargo, Pieter Kastelein and Isaac Roitman highlights some of them.     

Evolutionary History of B1 Retroposons in the Genus Mus

Short interspersed DNA elements (SINEs) amplify by retroposition either by (i) successive waves of amplification from one or a few evolving master genes or by (ii) the generation of new master genes that coexist with their progenitors. Individual, highly conserved, elements of the B1 SINE family were identified from the GenBank nucleotide database using various B1 subfamily consensus query sequences to determine their integration times into the mouse genome. A comparison of orthologous loci in various species of the genus Mus demonstrated that four subfamilies of B1 elements have been amplifying within the last 1–3 million years. Therefore, B1 sequences are generated by coexisting source genes. Additionally, three B1 subfamilies have been concurrently propagated during subspecies divergence and strain formation in Mus, indicating very recent activity of this retroposon family. The patterns of intra- and interspecies variations of orthologous loci demonstrate the usefulness of B1 integrations as a phylogenetic tool. A single inconsistency in the phylogenetic trends was depicted by the presence of a B1 insert in an orthologous locus exclusively in M. musculus and M. pahari. However, DNA sequence analysis revealed that these were independent integrations at the same genomic site. One highly conserved B1 element that integrated at least 4–6 million years ago suggests the possibility of occasional function for B1 integrations. Received: 25 February 2000 / Accepted: 5 June 2000     

Isolation of Ergosterol from the Trypanosomatid Leptomonas culicidarum

SYNOPSIS. The chief sterol of the trypanosomatid, Leptomonas culicidarum , was isolated and identified as ergosterol. Its isolation was aided by devising a better method for mass cultivation of Trypanosomatidae. This consisted of growing the parasites in suspension with shaking instead of the usual stationary condition. The implications of these findings are discussed.     

Identification of Sequences Encoding the Detoxification Metalloisomerase Glyoxalase I in Microbial Genomes from Several Pathogenic Organisms

The ubiquitous glyoxalase system, which is composed of two enzymes, removes cellular cytotoxic methylglyoxal (MG). In an effort to identify critical residues conserved in the evolution of the first enzyme in this system, glyoxalase I (GlxI), as well as the structural implications of sequence alterations in this enzyme, a search of the National Center for Biotechnology Information (NCBI) database of unfinished genomes was undertaken. Eleven putative GlxI sequences from pathogenic organisms were identified and analyses of these sequences in relation to the known and previously identified GlxI enzymes were performed. Several of these sequences show a very high similarity to the Escherichia coli GlxI sequence, most notably the 79% identity of the sequence identified from Yersinia pestis, the causative agent of bubonic plague. In addition to the conservation of residues critical to binding the catalytic metal in all of the proposed GlxI enzymes, four regions in the Homo sapiens GlxI enzyme are absent in all of the bacterial GlxI sequences, with the exception of Pseudomonas putida. Removal of these regions may alter the active-site conformation of the bacterial enzymes in relation to that of the H. sapiens. These differences may be targeted for the development of inhibitors selective to the bacterial enzymes. Received: 13 October 1999 / Accepted: 17 January 2000     

Trypanosomatid protozoa: survey of acetylornithinase and ornithine acetyltransferase

Trypanosomatid protozoa (Crithidia deanei, C. deanei aposymbiotic, C. oncopelti, C. fasciculata, C. acanthocephali, Leptomonas seymouri, L. collosoma, L. samueli, Herpetomonas samuelpessoai, H. sp., H. megaseliae, H. muscarum muscarum, Leishmania donovani, L. braziliensis, Trypanosoma cruzi, T. conorhini and T. mega) were examined for the presence of acetylornithinase (EC 3.5.1.16) and ornithine acetyltransferase (EC 2.3.1.35). As a rule, species of the genus Crithidia presented one of the two enzymes for the conversion of acetylornithine into ornithine. Crithidia fasciculata and C. acanthocephali presented acetylornithinase, while C. deanei and C. oncopelti, species harboring symbionts, presented ornithine acetyltransferase. The enzyme was absent in the aposymbiotic strain of C. deanei, which suggests that the enzyme belongs to the symbiont. Among the other trypanosomatids examined only Herpetomonas samuelpessoai presented acetylomithinase. The participation of acetylornithinase and ornithine acetyltransferase in the metabolism of trypanosomatids is discussed in the light of their nutritional requirements and possession of enzymes of the arginineornithine metabolism.     

Comparative Genomics of Trypanosomatid Pathogens using Codon Usage Bias

It is well known that an amino acid can be encoded by more than one codon, called synonymous codons. The preferential use of one particular codon for coding an amino acid is referred to as codon usage bias (CUB). A quantitative analytical method, CUB and a related tool, Codon Adaptative Index have been applied to comparatively study whole genomes of a few pathogenic Trypanosomatid species. This quantitative attempt is of direct help in the comparison of qualitative features like mutational and translational selection. Pathogens of the Leishmania and Trypanosoma genus cause debilitating disease and suffering in human beings and animals. Of these, whole genome sequences are available for only five species. The complete coding sequences (CDS), highly expressed, essential and low expressed genes have all been studied for their CUB signature. The codon usage bias of essential genes and highly expressed genes show distribution similar to codon usage bias of all CDSs in Trypanosomatids. Translational selection is the dominant force selecting the preferred codon, and selection due to mutation is negligible. In contrast to an earlier study done on these pathogens, it is found in this work that CUB and CAI may be used to distinguish the Trypanosomatid genomes at the sub-genus level. Further, CUB may effectively be used as a signature of the species differentiation by using Principal Component Analysis (PCA).

Abbreviations

CUB - Codon Usage Bias, CAI - Codon Adaptative Index, CDS - Coding sequences, t-RNA - Transfer RNA, PCA - Principal Component Analysis.     

Trypanosomatid protozoa in fruit of Solanaceae in southeastern Brazil

Fruits of cultivated and indigenous Solanaceae from Southeastern Brazil have been examined for the presence of trypanosomatid flagellates. The 14 species found infected were: Capsicum annuum, C. praetermissum, Lycopersicon esculentum, Nicandra physaloides, Physalis angulata, Solanum sp., S. americanum, S. concinnum, S. diflorum, S. erianthum, S. gilo, S. robustum, S. variable and S. viarum. The pentatomid hemipteran Arvelius albopunctatus experimentally transmitted flagellates to fruits of some species. Cultures of flagellates were obtained from fruits of eight species of Solanaceae and from A. albopunctatus.