Giardia lamblia: haploid genome size determined by pulsed field gel electrophoresis is less than 12 Mb

Chromosome sequence maps of the Giardia lamblia assemblage A isolate WB

Two genotypes, assemblages A and B, of the pathogenic gut protozoan parasite Giardia lamblia infect humans. Symptoms of infection range from asymptomatic to chronic diarrhea. Giardia chromosomes have long been characterized but not until the publication of the first Giardia genome sequence was chromosome mapping work, commenced nearly two decades ago, completed. Initial mapping studies identified and ordered Not I chromosome segments (summating to 1.8 Mb) of the estimated 2 Mb chromosome 3. The resulting map was confirmed with the release of the Giardia genome sequence and this revitalized mapping. The result is that 93% of the WB isolate genome sequence has now been assigned to one of five major chromosomes, and community access to these data has been made available through GiardiaDB, the database for Giardia genomes.

Large genomic differences between the morphologically indistinguishable diplomonads Spironucleus barkhanus and Spironucleus salmonicida

BACKGROUND

Microbial eukaryotes show large variations in genome structure and content between lineages, indicating extensive flexibility over evolutionary timescales. Here we address the tempo and mode of such changes within diplomonads, flagellated protists with two nuclei found in oxygen-poor environments. Approximately 5,000 expressed sequence tag (EST) sequences were generated from the fish commensal Spironucleus barkhanus and compared to sequences from the morphologically indistinguishable fish parasite Spironucleus salmonicida, and other diplomonads. The ESTs were complemented with sequence variation studies in selected genes and genome size determinations.

RESULTS

Many genes detected in S. barkhanus and S. salmonicida are absent in the human parasite Giardia intestinalis, the most intensively studied diplomonad. For example, these fish diplomonads show an extended metabolic repertoire and are able to incorporate selenocysteine into proteins. The codon usage is altered in S. barkhanus compared to S. salmonicida. Sequence variations were found between individual S. barkhanus ESTs for many, but not all, protein coding genes. Conversely, no allelic variation was found in a previous genome survey of S. salmonicida. This difference was confirmed by sequencing of genomic DNA. Up to five alleles were identified for the cloned S. barkhanus genes, and at least nineteen highly expressed S. barkhanus genes are represented by more than four alleles in the EST dataset. This could be explained by the presence of a non-clonal S. barkhanus population in the culture, by a ploidy above four, or by duplications of parts of the genome. Indeed, genome size estimations using flow cytometry indicated similar haploid genome sizes in S. salmonicida and G. intestinalis (approximately 12 Mb), whereas the S. barkhanus genome is larger (approximately 18 Mb).

CONCLUSIONS

This study indicates extensive divergent genome evolution within diplomonads. Genomic traits such as codon usage, frequency of allelic sequence variation, and genome size have changed considerably between S. barkhanus and S. salmonicida. These observations suggest that large genomic differences may accumulate in morphologically indistinguishable eukaryotic microbes.

Sequence map of the 3-Mb Giardia duodenalis assemblage A chromosome

The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromosome, a library of probes specific for this chromosome was constructed. The probes were hybridised to NotI-cleaved whole chromosomes, and the combined size of different NotI segments identified by the probes was 2,225 kb indicating the probes were well distributed along the 3-Mb chromosome. Six scaffolds (CH991814, CH991779, CH991793, CH991763, CH991764, and CH991761) were identified as belonging to the 3-Mb chromosome, and these scaffolds were ordered and oriented according to scaffold features including I-PpoI sites and hybridisation pattern. However, the combined size of scaffolds was more than 4 Mb. Approximately, 1 Mb of scaffold CH991763 carrying previously identified sequences specific for the 1.5-Mb chromosome(s) including subtelomeric sequence was reassigned, and several other anomalies were addressed such that the final size of the apparently 3-Mb chromosome is estimated to be 2,885 kb. This work addresses erroneous computer-based assignment of a number of contigs and emphasises the need for alternative and confirmatory methods of scaffold construction.

Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome

A prominent feature of transcription in Giardia lamblia is the abundant production of sterile antisense transcripts (Elmendorf et al. The abundance of sterile transcripts in Giardia lamblia. Nucleic Acids., 29, 4674-4683). Here, we use a computational biology analysis of SAGE data to assess the abundance and distribution of sense and antisense messages in the parasite genome. Sterile antisense transcripts are produced at approximately 50% of loci with detectable transcription, yet their abundance at a given locus does not correlate to the abundance of the complementary sense transcripts at that locus or to transcription levels at neighboring loci. These data suggest that sterile antisense transcripts are not simply a local effect of open chromatin structure. Using 5'RACE, we demonstrate that Giardia promoters are a source of antisense transcripts through bidirectional transcription, producing both downstream coding sense and upstream sterile antisense transcripts. We use a dual reporter system to explore roles of specific promoter elements in this bidirectional initiation of transcription and suggest that the degenerate AT-rich nature of TATA and Inr elements in Giardia permits them to function interchangeably. The phenomenon of bidirectional transcription in G. lamblia gives us insight into the interaction between transcriptional machinery and promoter elements, and may be the prominent source of the abundant antisense transcription in this parasite.

A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution

BACKGROUND

Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus).

RESULTS

The analyses revealed a compact genome with few, if any, introns and very short 3' untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes--mostly encoding metabolic proteins--that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals.

CONCLUSION

Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution.

Cytogenetic evidence for diversity of two nuclei within a single diplomonad cell of Giardia

Giardia intestinalis is an ancient protist that causes the most commonly reported human diarrheal disease of parasitic origin worldwide. An intriguing feature of the Giardia cell is the presence of two morphologically similar nuclei, generally considered equivalent, in spite of the fact that their karyotypes are unknown. We found that within a single cell, the two nuclei differ both in the number and the size of chromosomes and that representatives of two major genetic groups of G. intestinalis possess different karyotypes. Odd chromosome numbers indicate aneuploidy of Giardia nuclei, and their stable occurrence is suggestive of a long-term asexuality. A semi-open type of Giardia mitosis excludes a chromosome interfusion between the nuclei. Differences in karyotype and DNA content, and cell cycle-dependent asynchrony are indicative of diversity of the two Giardia nuclei.

Biology of Giardia lamblia

Giardia lamblia is a common cause of diarrhea in humans and other mammals throughout the world. It can be distinguished from other Giardia species by light or electron microscopy. The two major genotypes of G. lamblia that infect humans are so different genetically and biologically that they may warrant separate species or subspecies designations. Trophozoites have nuclei and a well-developed cytoskeleton but lack mitochondria, peroxisomes, and the components of oxidative phosphorylation. They have an endomembrane system with at least some characteristics of the Golgi complex and encoplasmic reticulum, which becomes more extensive in encysting organisms. The primitive nature of the organelles and metabolism, as well as small-subunit rRNA phylogeny, has led to the proposal that Giardia spp. are among the most primitive eukaryotes. G. lamblia probably has a ploidy of 4 and a genome size of approximately 10 to 12 Mb divided among five chromosomes. Most genes have short 5' and 3' untranslated regions and promoter regions that are near the initiation codon. Trophozoites exhibit antigenic variation of an extensive repertoire of cysteine-rich variant-specific surface proteins. Expression is allele specific, and changes in expression from one vsp gene to another have not been associated with sequence alterations or gene rearrangements. The Giardia genome project promises to greatly increase our understanding of this interesting and enigmatic organism.

Initiator and upstream elements in the alpha2-tubulin promoter of Giardia lamblia

Giardia lamblia, one of the earliest diverging eukaryotes and a major cause of diarrhea world-wide, has unusually short intergenic regions, raising questions concerning its regulation of gene expression. We have approached this issue through examination of the alpha2-tubulin promoter and in particular investigated the function of an AT-rich element surrounding the transcription start site. Its placement and the ability of this sequence to direct transcription initiation in the absence of any other promoter elements is similar to the initiator element in higher eukaryotes. However, the sequence diversity of extremely short (8-10 bp) initiator elements is surprising, as is their ability to independently direct substantial levels of transcription. We also identified a large AT-rich element located between -64 and -29 bp upstream of the transcriptional start site and show using both deletions and site-specific mutations of this region that sequences between -60 and the start of transcription are important for promoter strength; interestingly this AT-rich sequence is not highly conserved among different Giardia promoters. These data suggest that while the overall structure of the core promoter has been conserved throughout eukaryotic evolution, significant variation and flexibility is allowed in element consensus sequences and roles in transcription. In particular, the short and diverse sequences that function in transcription initiation in Giardia suggest the potential for relaxed transcriptional regulation.

Genome ploidy in different stages of the Giardia lamblia life cycle

The early diverging eukaryotic parasite Giardia lamblia is unusual in that it contains two apparently identical nuclei in the vegetative trophozoite stage. We have determined the nuclear and cellular genome ploidy of G. lamblia cells during all stages of the life cycle. During vegetative growth, the nuclei cycle between a diploid (2N) and tetraploid (4N) genome content and the cell, consequently, cycles between 4N and 8N. Stationary phase trophozoites arrest in the G2 phase with a ploidy of 8N (two nuclei, each with a 4N ploidy). On its way to cyst formation, a G1 trophozoite goes through two successive rounds of chromosome replication without an intervening cell division event. Fully differentiated cysts contain four nuclei, each with a ploidy of 4N, resulting in a cyst ploidy of 16N. The newly excysted cell, for which we suggest the term 'excyzoite', contains four nuclei (cellular ploidy 16N). In a reversal of the events occurring during encystation, the excyzoite divides twice to form four trophozoites containing two diploid nuclei each. The formation of multiple cells from a single cyst is likely to be one of the main reasons for the low infectious doses of G. lamblia.

The cell cycle in protozoan parasites

Research into cell cycle control in protozoan parasites, which are responsible for major public health problems in the developing world, has been hampered by the difficulties in performing classical genetic analysis with these organisms. Nevertheless, in a large part thanks to the data gathered in other eukaryotic systems and to the acquisition of the sequences of parasite genes homologous to cell cycle regulators, many molecular tools required for an in-depth study of the cell cycle in protozoan parasites have been collected over the past few years. Despite the considerable phylogenetic divergence between these organisms and other eukaryotes, and notwithstanding important specificities such as the apparent lack of checkpoints during cell cycle progression, available data indicate that the major families of cell cycle regulators appear to operate in protozoan parasites. Functional studies are now needed to define the precise role of these regulators in the life cycle of the parasites, and to possibly validate cell cycle control elements as potential targets for chemotherapy.

Encephalitozoon cuniculi (Microspora) genome: physical map and evidence for telomere-associated rDNA units on all chromosomes

A restriction map of the 2.8-Mb genome of the unicellular eukaryote Encephalitozoon cuniculi (phylum Microspora), a mammal-infecting intracellular parasite, has been constructed using two restriction enzymes with 6 bp recognition sites (Bss HII and Mlu I). The fragments resulting from either single digestions of the whole molecular karyotype or double digestions of 11 individual chromosomes have been separated by two-dimensional pulsed field gel electrophoresis (2D-PFGE) procedures. The average distance between successive restriction sites is approximately 19 kb. The terminal regions of the chromosomes show a common pattern covering approximately 15 kb and including one 16S-23S rDNA unit. Results of hybridisation and molecular combing experiments indicate a palindromic-like orientation of the two subtelomeric rDNA copies on each chromosome. We have also located 67 DNA markers (clones from a partial E. cuniculi genomic library) by hybridisation to restriction fragments. Partial or complete sequencing has revealed homologies with known protein-coding genes for 32 of these clones. Evidence for two homologous chromosomes III, with a size difference (3 kb) related to a subtelomeric deletion/insertion event, argues for diploidy of E.cuniculi. The physical map should be useful for both the whole genome sequencing project and studies on genome plasticity of this widespread parasite.

The Giardia lamblia genome

Giardia lamblia is a protozoan parasite of humans and other mammals that is thought to be one of the most primitive extant eukaryotic organisms. Although distinctly eukaryotic, it is notable for its lack of mitochondria, nucleoli, and perixosomes. It has been suggested that Giardia spp. are pre-mitochondriate organisms, but the identification of genes in G. lamblia thought to be of mitochondrial origin has generated controversy regarding that designation. Giardi lamblia trophozoites have two nuclei that are identical in all ways that have been studied. They are polyploid with at least four, and perhaps eight or more, copies of each of five chromosomes per organism and have an estimated genome complexity of 1.2x10(7)bp of DNA, and GC content of 46%. There is evidence for recombination at the telomeres of some of the chromosomes, and multiple size variants of single chromosomes have been identified within cloned isolates. However, the internal regions of the chromosomes demonstrate no evidence of recombination. For example, there is no evidence for control of vsp gene expression by DNA recombination, and no evidence for rapid mutation in the vsp genes. Single pass sequences of approximately 9% of the G. lamblia genome have already been obtained. An ongoing genome project plans to obtain approximately 95% of the genome by a random approach, as well as a complete physical map using a bacterial artificial chromosome library. The results will facilitate a better understanding of the biology of Giardia spp. as well as their phylogenetic relationship to other primitive organisms.

Reconstructing Early Events in Eukaryotic Evolution

Resolving the order of events that occurred during the transition from prokaryotic to eukaryotic cells remains one of the greatest problems in cell evolution. One view, the Archezoa hypothesis, proposes that the endosymbiotic origin of mitochondria occurred relatively late in eukaryotic evolution and that several mitochondrion-lacking protist groups diverged before the establishment of the organelle. Phylogenies based on small subunit ribosomal RNA and several protein-coding genes supported this proposal, placing amitochondriate protists such as diplomonads, parabasalids, and Microsporidia as the earliest diverging eukaryotic lineages. However, trees of other molecules, such as tubulins, heat shock protein 70, TATA box-binding protein, and the largest subunit of RNA polymerase II, indicate that Microsporidia are not deeply branching eukaryotes but instead are close relatives of the Fungi. Furthermore, recent discoveries of mitochondrion-derived genes in the nuclear genomes of entamoebae, Microsporidia, parabasalids, and diplomonads suggest that these organisms likely descend from mitochondrion-bearing ancestors. Although several protist lineages formally remain as candidates for Archezoa, most evidence suggests that the mitochondrial endosymbiosis took place prior to the divergence of all extant eukaryotes. In addition, discoveries of proteobacterial-like nuclear genes coding for cytoplasmic proteins indicate that the mitochondrial symbiont may have contributed more to the eukaryotic lineage than previously thought. As genome sequence data from parabasalids and diplomonads accumulate, it is becoming clear that the last common ancestor of these protist taxa and other extant eukaryotic groups already possessed many of the complex features found in most eukaryotes but lacking in prokaryotes. However, our confidence in the deeply branching position of diplomonads and parabasalids among eukaryotes is weakened by conflicting phylogenies and potential sources of artifact. Our current picture of early eukaryotic evolution is in a state of flux.

Structural basis of karyotype heterogeneity in Giardia lamblia

The molecular karyotype of a series of Giardia lamblia isolates representing the two major genotypes (Groups 1 and 3) was generated by assigning 13 genetic markers to chromosomes separated by pulsed-field gel electrophoresis. The co-localization identified five linked groups of genetic markers in Group 1 isolates. For each of the five linkage groups, there were up to four size variants that hybridized with the same genetic markers. Long range physical maps of the regions flanking the low copy number genetic markers indicated that these size variants were homologous chromosomes. The linkage groups were similar in Group 1 and 3 isolates. The core of each chromosome was stable while the subtelomeres were variable. The location of the ribosomal DNA repeats was variable among the different isolates and they were found in the subtelomeric regions of any of the five linkage groups. The data suggest a functional ploidy of at least four. Hypervariable subtelomeric regions of homologous chromosomes provide the structural basis of the chromosome size heterogeneity that is characteristic of G. lamblia.

Biodiversity, genomes, and DNA sequence databases

There are approximately 1.4 million organisms on this planet that have been described morphologically but there is no comparable coverage of biodiversity at the molecular level. Little more than 1% of the known species have been subject to any molecular scrutiny and eukaryotic genome projects have focused on a group of closely related model organisms. The past year, however, has seen an approximately 80% increase in the number of species represented in sequence databases and the completion of the sequencing of three prokaryotic genomes. Large-scale sequencing projects seem set to begin coverage of a wider range of the eukaryotic diversity, including green plants, microsporidians and diplomonads.

Structure of a frequently rearranged rRNA-encoding chromosome in Giardia lamblia

It has been shown previously that the rRNA encoding chromosomes in Giardia lamblia undergo frequent rearrangements with an estimated rate of approximately 1% per cell per division (Le Blancq et al., 1992, Nucleic Acids Res., 17, 4539-4545). Following these observations, we searched for highly recombinogenic regions in one of the frequently rearranged rRNA encoding chromosomes, that is chromosome 1, a small, 1.1 Mb chromosome. Chromosome 1 undergoes frequent rearrangements that result in size variation of 5-20%. We analyzed the structure of chromosome 1 in clonal lineages from the WB strain. The two ends of chromosome 1 comprise telomere repeat [TAGGG] arrays joined to a truncated rRNA gene and a sequence referred to as '4e', respectively. Comparison of the structure of four polymorphic versions of chromosome 1, resulting from independent rearrangement events in four cloned lines, located a single polymorphic region to the variable rDNA-telomere domain. Chromosome 1 is organized into two domains: a core region spanning approximately 850 kb that does not exhibit size heterogeneity among different chromosome 1 and a variable region that spans 185-450 kb and includes the telomeric rRNA genes, referred to as the variable rDNA-telomere domain. The core region contains a conserved region, spanning approximately 550 kb adjacent to the telomeric 4e sequence, which is only present in the 4e containing chromosomes and a 300 kb region of repetitive sequences that are also components of other chromosomes as well. Changes in the number of rDNA repeats accounted for some, but not all, of the size variation. Since there are four chromosomes that share the core region of chromosome 1, we suggest that the genome is tetraploid for this chromosome.

Analysis of consensus sequence patterns in Giardia cytoskeleton gene promoters

Protein-coding genes in the ancient eukaryote Giardia lamblia lack typical promoter consensus elements. We have analysed the immediate 5' flanking sequences of seven genes of related function (structural cytoskeleton proteins) to identify shared DNA motifs that might have a role in transcription initiation. Transcription start sites for five genes have been determined previously. Genomic mapping and mRNA primer extension experiments demonstrate additionally that the genes for beta-giardin and median body protein are (i) present as single copies in the genome, (ii) transcribed with very short 5' leader sequences. Two search algorithms designed to extract conserved motifs from either aligned or non-aligned sequences independently discovered three sites constituting a common pattern in all seven promoters. Sites were optimally aligned using weight matrix building trials to achieve the maximum 'information content'. Profiling the information content of best alignments defines the extent of the homologies as: a 9 bp box (initiator) at the start site and upstream 18 and 6 bp boxes. The initiator is the most highly conserved element and contains a universal Py-A-Pu motif at which transcription starts. We show that the best matrices can be combined in a search pattern that correctly locates transcription start sites in genomic DNA sequences.

Parasitism and chromosome dynamics in protozoan parasites: is there a connection?

Genomic plasticity is a hallmark of many protozoan parasites, including Plasmodium spp, Trypanosoma spp, Leishmania ssp and Giardia lamblia. Strikingly, there is a common theme regarding the structural basis of this karyotype variability. Chromosomes are compartmentalized into conserved central domains and polymorphic chromosome ends. Since antigen-encoding genes frequently reside in telomere-proximal domains, it is tempting to speculate that the genetic flexibility of chromosome ends has been recruited as a tool in immune evasion strategies by some parasitic protozoa.

The asexual ploidy cycle and the origin of sex

Sex involves syngamy (gamete fusion), which doubles the amount of DNA in a cell, and meiosis, which halves it. The result is a 'ploidy cycle' of alternating diploid and haploid phases. Asexual reproduction does not require changes of ploidy, and yet asexual forms may have ploidy cycles. Here I show that such cycles lessen the mutation load, compared with permanent diploidy or polyploidy, and are thus likely to evolve in cases where it is always advantageous to have more than one copy of the genome per cell. The asexual ploidy cycle could have facilitated the origin of sex, by providing a means of orderly genetic reduction available immediately after the origin of syngamy.

Physical map of a 2 Mb chromosome of the intestinal protozoan parasite Giardia duodenalis

The protozoan parasite, Giardia duodenalis, is regarded as the most primitive eukaryote. The two apparently identical nuclei presumably carry the same chromosomes but the number of different chromosomes in the organism is unknown. A genome map of G. duodenalis is required to resolve this issue and mapping studies were initiated using chromosome 5. This chromosome was estimated to be approximately 2 Mb when Giardia chromosomes were separated by contour-clamped homogeneous electric field gel electrophoresis. A plasmid library of chromosome 5-specific DNA sequences was constructed from gel-extracted chromosome 5 and selected probes were used as markers to identify NotI DNA segments derived from chromosome 5. Fifty-nine unique copy markers were used to identify thirteen NotI segments which ranged in size from 47 kb to 400 kb. The sum of the NotI segments was 1.78 Mb which indicated that most, if not all, of the chromosome was accounted for and that chromosome band 5 of the cloned line WB-1B, used in this study comprised only one chromosome type. The NotI segments were ordered on the map by comparison of hybridization patterns of the markers with partial NotI cleavages of whole chromosomes. Chromosome rearrangements occur readily in Giardia, and in two drug-resistant lines selected for resistance to different drugs, partial conservative duplications of chromosome 5 were observed in addition to the original, full length chromosome 5. Both duplications retained the central region of chromosome 5 but were deleted at different termini resulting in one duplication of 1.5 Mb and the other of 1.3 Mb.(ABSTRACT TRUNCATED AT 250 WORDS)

Evidence for the existence of a single ubiquitin gene in Giardia lamblia

All eukaryotes investigated so far contain multiple copies of ubiquitin genes, most of which are arranged in fusions coding for either polyubiquitin or ubiquitin-ribosomal protein constructs; the former are normally under the control of a heat shock promoter. Giardia lamblia, an intestinal parasite, is the most primitive eukaryote known to date. We have investigated the arrangement and expression of ubiquitin genes in this organism by Southern and Northern blotting. Our data strongly suggest that G. lamblia contains just one ubiquitin gene, which consists of a single copy of the coding sequence and the expression of which is not enhanced by heat shock. By pulsed-field gel electrophoresis we localized this gene on the largest of the five giardial chromosomes. These data imply that the ubiquitin system in Giardia has probably been trapped at an original stage.

Genomic sequence sampling: a strategy for high resolution sequence-based physical mapping of complex genomes

We present a simple and efficient method for constructing high resolution physical maps of large regions of genomic DNA based upon sampled sequencing. The physical map is constructed by ordering high density cosmid contigs and determining a sequence fragment from each end of every clone. The resulting map, which contains 30-50% of the complete DNA sequence, allows the identification of many genes and makes possible PCR amplification of virtually any part of the genome. We apply this strategy to the automated analysis of the genome of the primitive eukaryote Giardia lamblia and evaluate its applicability to the physical mapping and DNA sequencing of the human genome.

Chromosome rearrangements in Giardia lamblia

Recent studies have shown that the genome of Giardia lamblia is plastic. Clinical isolates exhibit extensive karyotypic heterogeneity and chromosome rearrangements occur frequently, in vitro. In this review, Sylvie Le Blancq looks at genome organization and the impact of DNA rearrangement events.

Electrophoretic analysis of the nuclear and organellar genomes in the ultra-small alga Cyanidioschyzon merolae

Electrophoretic analysis reveals that the nucleus of the ultra-small eukaryotic alga Cyanidioschyzon merolae contains approximately 11.7 x 10(6) base pairs (11.7 Mb) of DNA. This compact genome is fragmented into 15 small chromosomes ranging in size from 410 to 1700 kb. The migratory behaviour of chloroplast DNA is consistent with the presence of a circular plastid genome of about 170 kb. The conformation of mitochondrial DNA resembles that in yeasts and fungi and is predominantly linear and heterogenous in size.

Codon usage in Giardia lamblia

A codon usage table for the intestinal parasite Giardia lamblia was generated by analysis of the nucleotide sequences of eight genes comprising 3,135 codons. Codon usage revealed a biased use of synonymous codons with a preference for NNC codons (42.1%). The codon usage of G. lamblia more closely resembles that of the prokaryote Halobacterium halobium (correlation coefficient r = 0.73) rather than that of other eukaryotic protozoans, i.e. Trypanosoma brucei (r = 0.434) and Plasmodium falciparum (r = -0.31). These observations are consistent with the view that G. lamblia represents the first line of descent from the ancestral cells that first took on eukaryotic features.

Chromosome-size variation in Giardia lamblia: the role of rDNA repeats

Giardia lamblia trophozoites contain at least five sets of chromosomes that have been categorized by chromosome-specific probes. Pulsed field separations of G. lamblia chromosomes also demonstrated minor bands in some isolates which stained less intensely with ethidium than the major chromosomal bands. Two of the minor bands of the E11 clone of the ISR isolate, MBa and MBb, were similar to each other and to chromosomal band I by hybridization to total chromosomal DNA and by hybridization of specific probes. In order to determine the extent of this similarity, I have developed a panel of probes for many of the Pacl restriction fragments and have shown that most of the Pacl and Notl fragments found in MBa are also present in MBb. The differences are found in both telomeric regions. At one end, MBb contains a 300 kb region not found in MBa. At the other end of MBb is a 160 kb region containing the rDNA repeats which is bounded on one end by the telomeric repeat and on the other by sites for multiple enzymes that do not digest the rDNA repeats. The corresponding region of MBa is 23 kb in size. The size difference is consistent with the eightfold greater number of rDNA repeats in MBb than MBa and suggests that 30% of the size difference is accounted for by different numbers of copies of the rDNA repeat. MBa of another ISR clone (ISR G5) is 150 kb larger in size than MBa of ISR E11. The data suggest that MBa and MBb are homologous chromosomes of different sizes and that a portion of the size difference is accounted for by different copy numbers of the rDNA repeat.

Localizing genes on the map of the genome of Haloferax volcanii, one of the Archaea

We have assigned genetic markers to locations on the physical map of the genome of the archaeon Haloferax volcanii, using both a physical method (hybridization) and a more specific genetic technique (transformation with cosmids). Hybridizations were against restriction digests of each of 151 cosmids making up a minimally overlapping set and covering 96% of the genome. Results with a cloned insertion sequence and a tRNA probe indicated that transposable elements are concentrated on two of the four plasmids of this species, whereas regions complementary to tRNA are largely chromosomal. For a genetic analysis of genes involved in the biosynthesis of amino acids, purines, and pyrimidines, we used cosmid transformation to assign 139 of 243 ethyl methanesulfonate-induced auxotrophic mutations, generated and characterized for this study, to single cosmids or pairs of cosmids from the minimal set. Mutations affecting the biosynthesis of uracil, adenine, guanine, and 14 amino acids have been mapped in this way. All mutations mapped to the 2920-kilobase-pair chromosome of Hf. volcanii and seemed uniformly distributed around this circular replicon. In some cases, many mutations affecting a single pathway map to the same or overlapping cosmids, as would be expected were genes for the pathway linked. For other biosynthetic pathways, several unlinked genetic loci can be identified.

The biology of Giardia spp

Gardia spp. are flagellated protozoans that parasitize the small intestines of mammals, birds, reptiles, and amphibians. The infectious cysts begin excysting in the acidic environment of the stomach and become trophozoites (the vegetative form). The trophozoites attach to the intestinal mucosa through the suction generated by a ventral disk and cause diarrhea and malabsorption by mechanisms that are not well understood. Giardia spp. have a number of unique features, including a predominantly anaerobic metabolism, complete dependence on salvage of exogenous nucleotides, a limited ability to synthesize and degrade carbohydrates and lipids, and two nuclei that are equal by all criteria that have been tested. The small size and unique sequence of G. lamblia rRNA molecules have led to the proposal that Giardia is the most primitive eukaryotic organism. Three Giardia spp. have been identified by light lamblia, G. muris, and G. agilis, but electron microscopy has allowed further species to be described within the G. lamblia group, some of which have been substantiated by differences in the rDNA. Animal models and human infections have led to the conclusion that intestinal infection is controlled primarily through the humoral immune system (T-cell dependent in the mouse model). A major immunogenic cysteine-rich surface antigen is able to vary in vitro and in vivo in the course of an infection and may provide a means of evading the host immune response or perhaps a means of adapting to different intestinal environments.

Electrophoretic karyotyping and chromosomal gene mapping of Chlorella

Molecular karyotypes for six strains of four Chlorella species were obtained by using an alternating-field gel electrophoresis system which employs contour-clamped homogenous electric fields (CHEF). The number and migration pattern of the chromosomal DNA molecules varied greatly from strain to strain: for example, nine separated chromosomes of C. ellipsoidea C87 ranged from 2.5 to 6.5 megabase pairs (mbp) in size, whereas 16 chromosomes of C. vulgaris C169 were from 980 kilobase pairs (kbp) to 4.0 mbp. Depending on the chromosome migration patterns, the six strains were classified into two major chromosome-length polymorphism groups. Using hybridization techniques, the genes for alpha-tublin, chlorophyll-a, b-binding proteins, ribosomal RNAs, and the small subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase (RuBisCO) were mapped on the separated chromosomes of C. vulgaris C169. Since Chlorella chromosomes are small enough to separate and isolate individually by CHEF gel electrophoresis under ordinary conditions, they should serve as excellent materials to study the fundamental molecular structure of plant-type chromosomes.