Significant non-existence of sequences in genomes and proteomes.
Ontology highlight
ABSTRACT:
SUBMITTER: Koulouras G
PROVIDER: S-EPMC8034619 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Neurodevelopmental disorders such as intellectual disability, autism spectrum disorder and schizophrenia lack precise boundaries in their clinical definitions, epidemiology, genetics and protein-protein interactomes. This calls into question the appropriateness of current categorical disease concepts. Recently, there has been a rising tide to reformulate neurodevelopmental nosological entities from biology upward. To facilitate this developing trend, we propose that identification of unique proteomic signatures that can be strongly associated with patient's risk alleles and proteome-interactome-guided exploration of patient genomes could define biological mechanisms necessary to reformulate disorder definitions.
| S-EPMC4030327 | biostudies-other
Project description:Dramatic examples of repeated sequences occur in the genomes of some naturally competent bacteria, which contain hundreds or thousands of copies of short motifs called DNA uptake signal sequences. Here, we analyze the evolutionary interactions between coding-region uptake sequences and the proteomes of Haemophilus influenzae, Actinobacillus pleuropneumoniae, and Neisseria meningitidis. In all three genomes, uptake sequence accumulation in coding sequences has approximately doubled the frequencies of those tripeptides specified by each species' uptake sequence. The presence of uptake sequences in particular reading frames correlated most strongly with the use of preferred codons at degenerately coded positions, but the density of uptake sequences correlated only poorly with protein functional category. Genes lacking homologs in related genomes also lacked uptake sequences, strengthening the evidence that uptake sequences do not drive lateral gene transfer between distant relatives but instead accumulate after genes have been transferred. Comparison of the uptake sequence-encoded peptides of H. influenzae and N. meningitidis proteins with their homologs from related bacteria without uptake sequences indicated that uptake sequences were also preferentially located in poorly conserved genes and at poorly conserved amino acids. With few exceptions, amino acids at positions encoded by uptake sequences were as well conserved as other amino acids, suggesting that extant uptake sequences impose little or no constraint on coding for protein function. However, this state is likely to be achieved at a substantial cost because of the selective deaths required to eliminate maladaptive mutations that improve uptake sequences.
| S-EPMC2817400 | biostudies-literature
Project description:More than a dozen large DNA viruses exceeding 240-kb genome size were recently discovered, including the "giant" mimivirus with a 1.2-Mb genome size. The detection of mimivirus and other large viruses has stimulated new analysis and discussion concerning the early evolution of life and the complexity and mechanisms of evolutionary transitions. This paper presents analysis in three contexts. (i) Genome signatures of large viruses tend to deviate from the genome signatures of their hosts, perhaps indicating that the large viruses are lytic in the hosts. (ii) Proteome composition within these viral genomes contrast with cellular organisms; for example, most eukaryotic genomes, with respect to acidic residue usages, select Glu over Asp, but the opposite generally prevails for the large viral genomes preferring Asp more than Glu. In comparing Phe vs. Tyr usage, the viral genomes select mostly Tyr over Phe, whereas in almost all bacterial and eukaryotic genomes, Phe is used more than Tyr. Interpretations of these contrasts are proffered with respect to protein structure and function. (iii) Frequent oligonucleotides and peptides are characterized in the large viral genomes. The frequent words may provide structural flexibility to interact with host proteins.
| S-EPMC1829274 | biostudies-literature
Project description:There is growing recognition that the elemental composition of genomes and proteins can be related to resource limitation. We examine the possibility that the elemental composition of nucleic acids and the amino acids (and proteins) they encode are correlated. We report a positive association between the stoichiometric ratio of N/C content of individual amino acids and their codons. Potentially, this is an outcome of chemical interactions between amino acids and anticodons that influenced the evolution of the genetic code. We also find a strong, positive relationship between N/C values of whole genomes and proteomes, across 94 prokaryotic species. This relationship is part of a spectrum in nitrogen versus carbon use across genomes and proteomes, which is correlated with genomic GC content. GC content is correlated positively with average nitrogen use, and negatively with average carbon use, across both genomes and proteomes.
| S-EPMC1810051 | biostudies-literature
Project description:Bacteriophages are the most abundant life forms in the biosphere. They play important roles in bacterial ecology, evolution, adaptation to new environments, and pathogenesis of human bacterial infections. Here, we report the complete genomic sequences, and predicted proteins of 27 bacteriophages of the Gram-positive bacterium Staphylococcus aureus. Comparative nucleotide and protein sequence analysis indicates that these phages are a remarkable source of untapped genetic diversity, encoding 2,170 predicted protein-encoding ORFs, of which 1,402 cannot be annotated for structure or function, and 522 are proteins with no similarity to other phage or bacterial sequences. Based on their genome size, organization of their gene map and comparative nucleotide and protein sequence analysis, the S. aureus phages can be organized into three groups. Comparison of their gene maps reveals extensive genome mosaicism, hinting to a large reservoir of unidentified S. aureus phage genes. Among the phages in the largest size class (178-214 kbp) that we characterized is phage Twort, the first discovered bacteriophage (responsible for the Twort-D'Herelle effect). These phage genomes offer an exciting opportunity to discern molecular mechanisms of phage evolution and diversity.
| S-EPMC556006 | biostudies-literature
Project description:Cyanobacterial KnowledgeBase (CKB) is a free access database that contains the genomic and proteomic information of 74 fully sequenced cyanobacterial genomes belonging to seven orders. The database also contains tools for sequence analysis. The Species report and the gene report provide details about each species and gene (including sequence features and gene ontology annotations) respectively. The database also includes cyanoBLAST, an advanced tool that facilitates comparative analysis, among cyanobacterial genomes and genomes of E. coli (prokaryote) and Arabidopsis (eukaryote). The database is developed and maintained by the Sub-Distributed Informatics Centre (sponsored by the Department of Biotechnology, Govt. of India) of the National Facility for Marine Cyanobacteria, a facility dedicated to marine cyanobacterial research. CKB is freely available at http://nfmc.res.in/ckb/index.html.
| S-EPMC4549288 | biostudies-literature
Project description:Non-retroviral RNA virus sequences (NRVSs) have been found in the chromosomes of vertebrates and fungi, but not plants. Here we report similarly endogenized NRVSs derived from plus-, negative-, and double-stranded RNA viruses in plant chromosomes. These sequences were found by searching public genomic sequence databases, and, importantly, most NRVSs were subsequently detected by direct molecular analyses of plant DNAs. The most widespread NRVSs were related to the coat protein (CP) genes of the family Partitiviridae which have bisegmented dsRNA genomes, and included plant- and fungus-infecting members. The CP of a novel fungal virus (Rosellinia necatrix partitivirus 2, RnPV2) had the greatest sequence similarity to Arabidopsis thaliana ILR2, which is thought to regulate the activities of the phytohormone auxin, indole-3-acetic acid (IAA). Furthermore, partitivirus CP-like sequences much more closely related to plant partitiviruses than to RnPV2 were identified in a wide range of plant species. In addition, the nucleocapsid protein genes of cytorhabdoviruses and varicosaviruses were found in species of over 9 plant families, including Brassicaceae and Solanaceae. A replicase-like sequence of a betaflexivirus was identified in the cucumber genome. The pattern of occurrence of NRVSs and the phylogenetic analyses of NRVSs and related viruses indicate that multiple independent integrations into many plant lineages may have occurred. For example, one of the NRVSs was retained in Ar. thaliana but not in Ar. lyrata or other related Camelina species, whereas another NRVS displayed the reverse pattern. Our study has shown that single- and double-stranded RNA viral sequences are widespread in plant genomes, and shows the potential of genome integrated NRVSs to contribute to resolve unclear phylogenetic relationships of plant species.
| S-EPMC3136472 | biostudies-literature
Project description:BACKGROUND:Genome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of effort, increased costs, and suboptimal annotation quality. One way to address these issues is to encourage the adoption of annotation standards and technological solutions that enable the sharing of biological knowledge and tools for genome and proteome annotation. RESULTS:Here we demonstrate one approach to generate portable genome and proteome annotation pipelines that users can run without recourse to custom software. This proof of concept uses our own rule-based annotation pipeline HAMAP, which provides functional annotation for protein sequences to the same depth and quality as UniProtKB/Swiss-Prot, and the World Wide Web Consortium (W3C) standards Resource Description Framework (RDF) and SPARQL (a recursive acronym for the SPARQL Protocol and RDF Query Language). We translate complex HAMAP rules into the W3C standard SPARQL 1.1 syntax, and then apply them to protein sequences in RDF format using freely available SPARQL engines. This approach supports the generation of annotation that is identical to that generated by our own in-house pipeline, using standard, off-the-shelf solutions, and is applicable to any genome or proteome annotation pipeline. CONCLUSIONS:HAMAP SPARQL rules are freely available for download from the HAMAP FTP site, ftp://ftp.expasy.org/databases/hamap/sparql/, under the CC-BY-ND 4.0 license. The annotations generated by the rules are under the CC-BY 4.0 license. A tutorial and supplementary code to use HAMAP as SPARQL are available on GitHub at https://github.com/sib-swiss/HAMAP-SPARQL, and general documentation about HAMAP can be found on the HAMAP website at https://hamap.expasy.org.
| S-EPMC7007698 | biostudies-literature
Project description:Plastids are actively involved in numerous plant processes critical to growth, development and adaptation. They play a primary role in photosynthesis, pigment and monoterpene synthesis, gravity sensing, starch and fatty acid synthesis, as well as oil, and protein storage. We applied two complementary methods to analyze the recently published apple genome (Malus × domestica) to identify putative plastid-targeted proteins, the first using TargetP and the second using a custom workflow utilizing a set of predictive programs. Apple shares roughly 40% of its 10,492 putative plastid-targeted proteins with that of the Arabidopsis (Arabidopsis thaliana) plastid-targeted proteome as identified by the Chloroplast 2010 project and ∼57% of its entire proteome with Arabidopsis. This suggests that the plastid-targeted proteomes between apple and Arabidopsis are different, and interestingly alludes to the presence of differential targeting of homologs between the two species. Co-expression analysis of 2,224 genes encoding putative plastid-targeted apple proteins suggests that they play a role in plant developmental and intermediary metabolism. Further, an inter-specific comparison of Arabidopsis, Prunus persica (Peach), Malus × domestica (Apple), Populus trichocarpa (Black cottonwood), Fragaria vesca (Woodland Strawberry), Solanum lycopersicum (Tomato) and Vitis vinifera (Grapevine) also identified a large number of novel species-specific plastid-targeted proteins. This analysis also revealed the presence of alternatively targeted homologs across species. Two separate analyses revealed that a small subset of proteins, one representing 289 protein clusters and the other 737 unique protein sequences, are conserved between seven plastid-targeted angiosperm proteomes. Majority of the novel proteins were annotated to play roles in stress response, transport, catabolic processes, and cellular component organization. Our results suggest that the current state of knowledge regarding plastid biology, preferentially based on model systems is deficient. New plant genomes are expected to enable the identification of potentially new plastid-targeted proteins that will aid in studying novel roles of plastids.
| S-EPMC4231079 | biostudies-literature
Project description:BackgroundMicrosatellites are short, tandemly-repeated DNA sequences which are widely distributed among genomes. Their structure, role and evolution can be analyzed based on exhaustive extraction from sequenced genomes. Several dedicated algorithms have been developed for this purpose. Here, we compared the detection efficiency of five of them (TRF, Mreps, Sputnik, STAR, and RepeatMasker).ResultsOur analysis was first conducted on the human X chromosome, and microsatellite distributions were characterized by microsatellite number, length, and divergence from a pure motif. The algorithms work with user-defined parameters, and we demonstrate that the parameter values chosen can strongly influence microsatellite distributions. The five algorithms were then compared by fixing parameters settings, and the analysis was extended to three other genomes (Saccharomyces cerevisiae, Neurospora crassa and Drosophila melanogaster) spanning a wide range of size and structure. Significant differences for all characteristics of microsatellites were observed among algorithms, but not among genomes, for both perfect and imperfect microsatellites. Striking differences were detected for short microsatellites (below 20 bp), regardless of motif.ConclusionSince the algorithm used strongly influences empirical distributions, studies analyzing microsatellite evolution based on a comparison between empirical and theoretical size distributions should therefore be considered with caution. We also discuss why a typological definition of microsatellites limits our capacity to capture their genomic distributions.
| S-EPMC1876248 | biostudies-literature