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Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes  [PDF]
Yubo Hou, Senjie Lin
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0006978
Abstract: The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log10-transformed protein-coding gene number (Y′) versus log10-transformed genome size (X′, genome size in kbp) were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y′ = ln(-46.200+22.678X′, whereas non-eukaryotes a linear model, Y′ = 0.045+0.977X′, both with high significance (p<0.001, R2>0.91). Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%–1%) compared to higher and relatively stable percentages in prokaryotes and viruses (97%–47%). The eukaryotic regression models project that the smallest dinoflagellate genome (3×106 kbp) contains 38,188 protein-coding (40,086 total) genes and the largest (245×106 kbp) 87,688 protein-coding (92,013 total) genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.
Massive expansion of the calpain gene family in unicellular eukaryotes  [cached]
Zhao Sen,Liang Zhe,Demko Viktor,Wilson Robert
BMC Evolutionary Biology , 2012, DOI: 10.1186/1471-2148-12-193
Abstract: Background Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex determination in nematodes and embryo lethality in plants. Although the calpain family is well characterized in animal and plant model organisms, there is a great lack of knowledge about these genes in unicellular eukaryote species (i.e. protists). Here, we study the distribution and evolution of calpain genes in a wide range of eukaryote genomes from major branches in the tree of life. Results Our investigations reveal 24 types of protein domains that are combined with the calpain-specific catalytic domain CysPc. In total we identify 41 different calpain domain architectures, 28 of these domain combinations have not been previously described. Based on our phylogenetic inferences, we propose that at least four calpain variants were established in the early evolution of eukaryotes, most likely before the radiation of all the major supergroups of eukaryotes. Many domains associated with eukaryotic calpain genes can be found among eubacteria or archaebacteria but never in combination with the CysPc domain. Conclusions The analyses presented here show that ancient modules present in prokaryotes, and a few de novo eukaryote domains, have been assembled into many novel domain combinations along the evolutionary history of eukaryotes. Some of the new calpain genes show a narrow distribution in a few branches in the tree of life, likely representing lineage-specific innovations. Hence, the functionally important classical calpain genes found among humans and vertebrates make up only a tiny fraction of the calpain family. In fact, a massive expansion of the calpain family occurred by domain shuffling among unicellular eukaryotes and contributed to a wealth of functionally different genes.
Analysis of Gene Order Conservation in Eukaryotes Identifies Transcriptionally and Functionally Linked Genes  [PDF]
Marcela Dávila López,Juan José Martínez Guerra,Tore Samuelsson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010654
Abstract: The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control.
Gene flow and biological conflict systems in the origin and evolution of eukaryotes  [PDF]
L. Aravind
Frontiers in Cellular and Infection Microbiology , 2012, DOI: 10.3389/fcimb.2012.00089
Abstract: The endosymbiotic origin of eukaryotes brought together two disparate genomes in the cell. Additionally, eukaryotic natural history has included other endosymbiotic events, phagotrophic consumption of organisms, and intimate interactions with viruses and endoparasites. These phenomena facilitated large-scale lateral gene transfer and biological conflicts. We synthesize information from nearly two decades of genomics to illustrate how the interplay between lateral gene transfer and biological conflicts has impacted the emergence of new adaptations in eukaryotes. Using apicomplexans as example, we illustrate how lateral transfer from animals has contributed to unique parasite-host interfaces comprised of adhesion- and O-linked glycosylation-related domains. Adaptations, emerging due to intense selection for diversity in the molecular participants in organismal and genomic conflicts, being dispersed by lateral transfer, were subsequently exapted for eukaryote-specific innovations. We illustrate this using examples relating to eukaryotic chromatin, RNAi and RNA-processing systems, signaling pathways, apoptosis and immunity. We highlight the major contributions from catalytic domains of bacterial toxin systems to the origin of signaling enzymes (e.g., ADP-ribosylation and small molecule messenger synthesis), mutagenic enzymes for immune receptor diversification and RNA-processing. Similarly, we discuss contributions of bacterial antibiotic/siderophore synthesis systems and intra-genomic and intra-cellular selfish elements (e.g., restriction-modification, mobile elements and lysogenic phages) in the emergence of chromatin remodeling/modifying enzymes and RNA-based regulation. We develop the concept that biological conflict systems served as evolutionary “nurseries” for innovations in the protein world, which were delivered to eukaryotes via lateral gene flow to spur key evolutionary innovations all the way from nucleogenesis to lineage-specific adaptations.
Lateral gene transfer between prokaryotes and multicellular eukaryotes: ongoing and significant?
Vera ID Ros, Gregory DD Hurst
BMC Biology , 2009, DOI: 10.1186/1741-7007-7-20
Abstract: Although lateral gene transfer (LGT) is known to play an important role in the evolution of prokaryotes and unicellular eukaryotes [1-3], lateral transfer between prokaryotes and multicellular eukaryotes has been more controversial. In recent years, evidence has accumulated for genes of prokaryotic origin – particularly bacterial symbiotic origin – within eukaryotic genomes. The examples have come from fractions (and even nearly complete copies) of the genome of the bacterial symbiont Wolbachia in the host nuclear genome [4-7]. However, there has been little evidence that the transferred copies of the genes are functional in the eukaryotic genome. For example, only very low expression levels have been found for some transferred genes, and this may represent no more than background noise [5,8]. Their dynamics seem to be similar to that of mitochondrial genes that have recently transferred to the nucleus (numts) – a balance of new copies appearing and their subsequent degradation associated with lack of function. However, recent studies have shown cases in which transferred prokaryotic genes are actively expressed in the eukaryotic recipient, a first step in demonstrating the full functionality of horizontally acquired genes in eukaryotes.Nikoh and Nakabachi [9] show that the pea aphid Acyrthosiphon pisum seems to have acquired two genes from bacteria. These have probably been acquired independently from facultative secondary symbionts: one from Wolbachia or a close relative, the other from an undescribed bacterium. The authors further demonstrate that these genes are both highly expressed in the bacteriocytes, specialized cells that harbor the aphid's obligate primary symbiont Buchnera aphidicola. Buchnera, which has a strongly reduced genome, lacks both genes, whereas most other bacteria, including Buchnera's close free-living relatives, possess these genes. Both genes may be functionally essential to maintain Buchnera – making the nuclear inserted copy a strong can
Elucidation of Gene Structure and Function of Prokaryotes and Eukaryotes Through DNA Information Technology  [PDF]
Abdul Sattar Larik,Zahoor Ahmed Soomro
Asian Journal of Plant Sciences , 2003,
Abstract: Significant and far reaching developments are constantly taking place in the new emerging field of genomics, the study of gene structure and function. Part of the need for genomics capabilities involves the rapidly emerging field of bioinformatics, which involves obtaining, storing and analysing information derived from studying biological systems. Crucial to bioinformatic analysis are computer algorithms that can compare newly isolated genes with databases containing genetic sequence of known function. A gene product is the key to the understanding of the intricate biological phenomenon from simple unicellular organisms to the incredibly complex multicellular organisms. This review places in contemporary context the new information on gene structure such as the role of DNA in information storage, coding of genetic information, flow of information from DNA to protein, the satellite DNA`s, information from RNA. Gene function is critically traced through the flow of information from DNA to RNA; the expression of functional products in prokaryotic and eukaryotic genomes, new proteomic approaches to gene expression/function, genetrap database, feed forward loop (FFL) system, extensive information through cDNA libraries. Informational implications of gene function in eukaryotes include: the nuclear DNA reversion, feedback from nucleus to cytoplasm, gene activity in coupling and repulsion phases, branching enzymes and the ectopic expression of gene and aberrant transcripts. In addition to the academic goals of perceiving gene structure and functions, there is great potential for agricultural and medicinal applications of functional data in the perceiving of plant and human diseases for pragmatic remedies.
A Metastate HMM with Application to Gene Structure Identification in Eukaryotes  [cached]
Winters-Hilt Stephen,Baribault Carl
EURASIP Journal on Advances in Signal Processing , 2010,
Abstract: We introduce a generalized-clique hidden Markov model (HMM) and apply it to gene finding in eukaryotes (C. elegans). We demonstrate a HMM structure identification platform that is novel and robustly-performing in a number of ways. The generalized clique HMM begins by enlarging the primitive hidden states associated with the individual base labels (as exon, intron, or junk) to substrings of primitive hidden states, or footprint states, having a minimal length greater than the footprint state length. The emissions are likewise expanded to higher order in the fundamental joint probability that is the basis of the generalized-clique, or "metastate", HMM. We then consider application to eukaryotic gene finding and show how such a metastate HMM improves the strength of coding/noncoding-transition contributions to gene-structure identification. We will describe situations where the coding/noncoding-transition modeling can effectively recapture the exon and intron heavy tail distribution modeling capability as well as manage the exon-start needle-in-the-haystack problem. In analysis of the C. elegans genome we show that the sensitivity and specificity (SN,SP) results for both the individual-state and full-exon predictions are greatly enhanced over the standard HMM when using the generalized-clique HMM.
Group II Intron-Based Gene Targeting Reactions in Eukaryotes  [PDF]
Marta Mastroianni, Kazuo Watanabe, Travis B. White, Fanglei Zhuang, Jamie Vernon, Manabu Matsuura, John Wallingford, Alan M. Lambowitz
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003121
Abstract: Background Mobile group II introns insert site-specifically into DNA target sites by a mechanism termed retrohoming in which the excised intron RNA reverse splices into a DNA strand and is reverse transcribed by the intron-encoded protein. Retrohoming is mediated by a ribonucleoprotein particle that contains the intron-encoded protein and excised intron RNA, with target specificity determined largely by base pairing of the intron RNA to the DNA target sequence. This feature enabled the development of mobile group II introns into bacterial gene targeting vectors (“targetrons”) with programmable target specificity. Thus far, however, efficient group II intron-based gene targeting reactions have not been demonstrated in eukaryotes. Methodology/Principal Findings By using a plasmid-based Xenopus laevis oocyte microinjection assay, we show that group II intron RNPs can integrate efficiently into target DNAs in a eukaryotic nucleus, but the reaction is limited by low Mg2+ concentrations. By supplying additional Mg2+, site-specific integration occurs in up to 38% of plasmid target sites. The integration products isolated from X. laevis nuclei are sensitive to restriction enzymes specific for double-stranded DNA, indicating second-strand synthesis via host enzymes. We also show that group II intron RNPs containing either lariat or linear intron RNA can introduce a double-strand break into a plasmid target site, thereby stimulating homologous recombination with a co-transformed DNA fragment at frequencies up to 4.8% of target sites. Chromatinization of the target DNA inhibits both types of targeting reactions, presumably by impeding RNP access. However, by using similar RNP microinjection methods, we show efficient Mg2+-dependent group II intron integration into plasmid target sites in zebrafish (Danio rerio) embryos and into plasmid and chromosomal target sites in Drosophila melanogster embryos, indicating that DNA replication can mitigate effects of chromatinization. Conclusions/Significance Our results provide an experimental foundation for the development of group II intron-based gene targeting methods for higher organisms.
Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes
Matteo Citarelli, Sachin Teotia, Rebecca S Lamb
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-308
Abstract: We identified in silico 236 PARP proteins from 77 species across five of the six eukaryotic supergroups. We performed extensive phylogenetic analyses of the identified PARPs. They are found in all eukaryotic supergroups for which sequence is available, but some individual lineages within supergroups have independently lost these genes. The PARP superfamily can be subdivided into six clades. Two of these clades were likely found in the last common eukaryotic ancestor. In addition, we have identified PARPs in organisms in which they have not previously been described.Three main conclusions can be drawn from our study. First, the broad distribution and pattern of representation of PARP genes indicates that the ancestor of all extant eukaryotes encoded proteins of this type. Second, the ancestral PARP proteins had different functions and activities. One of these proteins was similar to human PARP1 and likely functioned in DNA damage response. The second of the ancestral PARPs had already evolved differences in its catalytic domain that suggest that these proteins may not have possessed poly(ADP-ribosyl)ation activity. Third, the diversity of the PARP superfamily is larger than previously documented, suggesting as more eukaryotic genomes become available, this gene family will grow in both number and type.Poly(ADP-ribosyl)ation activity was originally identified in the 1960s [1-5]; it is the rapid and reversible posttranslational covalent attachment of ADP-ribose subunits onto glutamate, aspartate, and lysine residues of target proteins. The ADP-ribose polymer is formed by sequential attachment of ADP-ribosyl moieties from NAD+; the polymers can reach a length of over 200 units and can have multiple branching points. Overall, the ADP-ribose polymer is highly negatively charged and has large physiological consequences on functional and biochemical properties of the proteins modified.Poly(ADP-ribosyl)ation is done by enzymes called poly(ADP-ribose)polymerases (PARPs). The
Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes
Jan O Andersson, Andrew J Roger
BMC Evolutionary Biology , 2003, DOI: 10.1186/1471-2148-3-14
Abstract: We extend the taxon sampling of gdh genes with nine new eukaryotic sequences and examine the phylogenetic distribution pattern of the various GDH classes in combination with maximum likelihood phylogenetic analyses. The distribution pattern analyses indicate that LGT has played a significant role in the evolution of the four gdh gene families. Indeed, a number of gene transfer events are identified by phylogenetic analyses, including numerous prokaryotic intra-domain transfers, some prokaryotic inter-domain transfers and several inter-domain transfers between prokaryotes and microbial eukaryotes (protists).LGT has apparently affected eukaryotes and prokaryotes to a similar extent within the gdh gene families. In the absence of indications that the evolution of the gdh gene families is radically different from other families, these results suggest that gene transfer might be an important evolutionary mechanism in microbial eukaryote genome evolution.Lateral gene transfer (LGT) is a significant evolutionary mechanism in prokaryotic genome evolution. Indeed, it may be the most important mechanism for evolutionary innovation in Eubacteria and Archaea [1,2]. However, gene transfer events do not necessarily produce novel functions in recipient lineages; many documented gene transfers are replacements of genes by homologs or analogs with the same function [3,4]. The occurrence of LGT has been far less studied in eukaryotes than prokaryotes, partly because of the lack of complete genome sequences available from diverse eukaryotes. Nevertheless, several individual cases of gene transfer between prokaryotes and eukaryotes have been published [for example: [5-8]]. We recently presented an analysis which showed a number of transfers involving eukaryotes, mostly in the prokaryote-to-eukaryote direction, but also between different eukaryotic lineages [9]. Collectively, these examples indicate that LGT does affect protists, although the quantitative importance of the process in eu
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