Long non-coding RNAs in the human genome acquired by horizontal gene transfer

BACKGROUND : Horizontal gene transfer of mobile genetic elements is an essential component of prokaryotic evolution. These insertion events in eukaryotes and particularly in the human genome have been investigated by various methodologies with varying results. OBJECTIVE : In this paper, we implement a sequence composition approach to investigate insertions of genomic islands in the human genome. METHODS : A modified version of a prokaryotic GI identifier, SeqWord Gene Island Sniffer v.2.0, was used to predict genomic islands in the hg38 version of the human genome. RESULTS : Predicted genomic islands were enriched with long non-coding RNAs and also contributed to the acquisition and modification of proteins associated with the immune system and gonad development, albeit to a lesser extent. The estimated rate of acquisition of these genomic islands in vertebrate genomes was non-linear with regards to species divergence times with an acceleration at the time of vertebrate land invasion and during the transition of prosimians to monkeys soon after the Cretaceous-Paleogene extinction. CONCLUSION : The rapid acquisition of non-conserved long non-coding RNAs in the human genome and probably in vertebrata genomes was facilitated by horizontal gene transfer. All predicted human genomic islands and supporting information are freely accessible from http://hislands.bi.up.ac.za.The National Research Foundation (NRF) grant 105996am2019BiochemistryGeneticsMicrobiology and Plant Patholog

Whole genome sequence data of Stenotrophomonas maltophilia SCAID WND1-2022 (370)

The whole genome sequence of a hospital infection agent, Stenotrophomonas maltophilia SCAID WND1-2022 (370), is reported. Raw PacBio generated reads and the genome sequence were deposited at NCBI under BioPro- ject PRJNA754843. The genome comprises two replicons: 4,880,425 bp long chromosome comprising 4524 proteins and functional RNA coding genes and 38,606 bp long plasmid containing 40 CDS. Both replicons were methylated at third cytosine residues of AC C TC motifs. The taxonomic provenance of SCAID WND1-2022 (370) was determined by calculating sequence similarity to the reference genomes at NCBI that showed the highest 97.35% identity to S. maltophilia ISMMS4. Many antibiotic resistance and virulence genes were identi- fied on the chromosome of S. maltophilia SCAID WND1-2022 (370), which include multiple efflux pumps, beta-lactamases, and genes involved in biofilm formation. The plasmid se- quence was dissimilar to any known plasmid and seemingly was acquired from a distant microorganism. Plasmid-born genes possibly contributed to the virulence of the pathogens, but not to its drug resistance.The Ministry of Healthcare of the Republic of Kazakhstan.http://www.elsevier.com/locate/dibam2023BiochemistryGeneticsMicrobiology and Plant Patholog

Developing the MAR databases – Augmenting Genomic Versatility of Sequenced Marine Microbiota

This thesis introduces the MAR databases as marine-specific resources in the genomic landscape. Paper 1 describes the curation effort and development leading to the MAR databases being created. It results in the highly valued reference database MarRef, the broader MarDB, and the marine gene catalog MarCat. Definition of a marine environment, the curation process, and the Marine Metagenomics Portal as a public web-service are described. It facilitates scientists to find marine sequence data for prokaryotes and to explore rich contextual information, secondary metabolites, updated taxonomy, and helps in evaluating genome quality. Many of these database advancements are covered in Paper 2. This includes new entries and development of specific databases on marine fungi (MarFun) and salmon related prokaryotes (SalDB). With the implementation of metagenome assembled and single amplified genomes it leads up to the database quality evaluation discussed in Paper 3. The lack of quality control in primary databases is here discussed based on estimated completeness and contamination in the genomes of the MAR databases. Paper 4 explores the microbiota of skin and gut mucosa of Atlantic salmon. By using a database dependent amplicon analysis, the full-length 16 rRNA gene proved accurate, but not a game-changer in taxonomic classification for this environmental niche. The proportion of dataset sequences lacking clear taxonomic classification suggests lack of diversity in current-day databases and inadequate phylogenetic resolution. Advancing phylogenetic resolution was the subject of Paper 5. Here the highly similar species of genus Aliivibrio became delineated using six genes in a multilocus sequence analysis. Five potentially novel species could in this way be delineated, which coincided with recent genome-wide taxonomy listings. Thus, Paper 4 and 5 parallel those of the MAR databases by providing insight into the inter-relational framework of bioinformatic analysis and marine database sources

Prospects of a new antistaphylococcal drug batumin revealed by molecular docking and analysis of the complete genome sequence of the batumin-producer Pseudomonas batumici UCM B-321

Meticillin-resistant Staphylococcus aureus (MRSA) is a serious public health threat causing outbreaksof clinical infection around the world. Mupirocin is a promising anti-MRSA drug, however mupirocin-resistant strains of S. aureus are emerging at an increasing rate. The newly discovered antibiotic batuminmay contribute to anti-MRSA therapy. The objective of this work was to identify possible molecular targetsfor batumin as well as mechanisms of its antistaphylococcal activity using computational moleculardocking and by analysing the complete genome sequence of the batumin-producer Pseudomonas batumiciUCM B-321. It was found that batumin acted very similarly to mupirocin by inhibiting aminoacyl tRNAsynthetases. A previous hypothesis considering the trans-enoyl-CoA reductase FabI as a prime moleculartarget of batumin was rejected. However, indirect inhibition of fatty acid biosynthesis in sensitive bacteriadoes take place as a part of stringent response repression triggered by accumulation of uncharged tRNAmolecules. Paralogues of diverse leucine-tRNA synthetases in the genome of P. batumici indicated that thisprotein might be the prime target of batumin. A batumin biosynthesis operon comprising 28 genes wasfound to be acquired through horizontal gene transfer. It was hypothesised that, in contrast to mupirocin,batumin could inhibit a broader range of aminoacyl tRNA synthetases and that acquired resistance tomupirocin might not endow S. aureus strains with resistance against batumin.The grant #86941 provided by the National Research Foundation (NRF) of South Africa.http://www.elsevier.com/locate/ijantimicag2017-01-30hb201

The Geobacillus pan-genome : implications for the evolution of the genus

The genus Geobacillus is comprised of a diverse group of spore-forming Gram-positive thermophilic bacterial species and is well known for both its ecological diversity and as a source of novel thermostable enzymes. Although the mechanisms underlying the thermophilicity of the organism and the thermostability of its macromolecules are reasonably well understood, relatively little is known of the evolutionary mechanisms, which underlie the structural and functional properties of members of this genus. In this study, we have compared 29 Geobacillus genomes, with a specific focus on the elements, which comprise the conserved core and flexible genomes. Based on comparisons of conserved core and flexible genomes, we present evidence of habitat delineation with specific Geobacillus genomes linked to specific niches. Our analysis revealed that Geobacillus and Anoxybacillus share a high proportion of genes. Moreover, the results strongly suggest that horizontal gene transfer is a major factor deriving the evolution of Geobacillus from Bacillus, with genetic contributions from other phylogenetically distant taxa.FIGURE S1 : Barplot of pan-genome matrix determined from the Geobacillus genomes.FIGURE S2 : Clusters of Orthologous Groups (COG) analysis of the Geobacillus pan-genome.FIGURE S3 : Heatmap comparison of the Geobacillus core genes against Anoxybacillus and Bacillus genomes.FIGURE S4 : Heatmap comparison of the Geobacillus soft-coregenes against Anoxybacillus and Bacillus genomes.FIGURE S5 : Heatmap comparison of the Geobacillus shell genes against Anoxybacillus and Bacillus genomes.FIGURE S6 : Heatmap comparison of the Geobacillus cloud genes against Anoxybacillus and Bacillus genomes.The National Research Foundation of South Africa, the University of Pretoria Genomics Research Institute and the Department of Research and Innovation’s Research Development Program (University of Pretoria).http://www.frontiersin.orgam2016BiochemistryGenetic

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Lactobacillus crispatus and Propionibacterium freudenreichii : A Genomic and Transcriptomic View

Modern DNA sequencing technologies have opened up new possibilities to study bacteria. These methods have not only enabled the characterization of the genetic capacities of bacteria at previously unseen scale but have also provided a wealth of information about bacterial transcriptomes. In this thesis, sequencing and subsequent analysis approaches were applied to study Lactobacillus crispatus and Propionibacterium freudenreichii. Specifically, the aim was to uncover how these two Gram-positive species of human relevance can live in and interact with their environments. L. crispatus is a prominent member of the human vaginal flora and important for urogenital health. In this thesis, an annotated genome sequence was produced for L. crispatus ST1 and analyzed in conjunction with publicly available genome sequences of nine vaginal L. crispatus isolates. The common ortholog groups of the ten isolates captured approximately 57% of the ortholog groups of each isolate and provided a good estimation of the final set of core features of this central urogenital species. Notably, several of the detected L. crispatus core features were of putative relevance to vaginal health. Among these features was a previously characterized adhesin, which was in this thesis identified as a likely antagonist to the harmful vaginal bacterium Gardnerella vaginalis. Altogether, the study revealed a notable functional similarity between the L. crispatus strains and established the role of L. crispatus core proteins in maintaining vaginal health. P. freudenreichii, in turn, is an industrially important dairy culture. In this thesis, the cheese starter P. freudenreichii ssp. shermanii JS was subjected to transcriptome and genome sequencing to gain a deeper understanding of the role of this bacterium in industrial cheese ripening. The genome of strain JS encoded several enzymes and metabolic pathways involved in the formation of flavor compounds and was highly similar to those of the other P. freudenreichii strains. Transcriptome analysis of industrial cheese samples revealed nearly 15% of the 2,377 protein-coding genes of strain JS to be significantly differentially expressed between the warm and cold room ripening of cheese. Several of the flavor-associated genes exhibited higher expression levels in the warm compared to the cold room samples, corroborating the hypothesis that P. freudenreichii contributes more to the cheese flavor development during warm than cold room ripening. Automated function prediction of bacterial protein sequences greatly facilitated the genomics investigations of L. crispatus and P. freudenreichii in this thesis, providing functional descriptions for a majority of the predicted coding sequences of strains ST1 and JS. Moreover, re-annotation of the coding sequences of the nine publicly available vaginal L. crispatus isolates significantly increased the portion of the L. crispatus coding sequences with functional descriptions in the comparative genomics study of L. crispatus. The different methods varied in their prediction capabilities and were often complementary, supporting the use of more than one function prediction method in a bacterial genome project. Moreover, extremely strict thresholds in the homology searches were noted to unnecessarily restrict the pool of hits available for annotation transfer, hampering both the annotation quality and the fraction of coding sequences with a functional classification. Taken together, the utilized sequencing approaches coupled with suitable downstream analyses proved effective in deciphering the physiology of lactobacilli and propionibacteria and offered novel insights into the health-promoting properties of L. crispatus and flavor-forming capabilities of P. freudenreichii.Laktobasillit ja propionibakteerit ovat elintarvikkeiden hapattamisessa yleisesti käytettyjä ja luontaisesti ihmiselimistössä eläviä Gram-positiivisia bakteereja. Niitä on käytetty vuosisatoja esimerkiksi juustojen valmistuksessa ja niiden on viime aikoina huomattu vaikuttavan jopa ihmisterveyteen. Tämän väitöskirjatyön tavoitteena on ollut parantaa tietämystämme näistä kahdesta merkittävästä bakteeriryhmästä etenkin perimänluentamenetelmiä sekä laskennallisen biologian työkaluja hyödyntämällä. Erityisesti väitöskirjatyössä on keskitytty selvittämään emätinterveydelle merkittävän Lactobacillus crispatus -bakteerin perimän monimuotoisuutta sekä teollisuudessa käytetyn Propionibacterium freudenreichii -hapatebakteerin toimintaa juustokypsytyksen eri vaiheissa. L. crispatus -lajin perimän monimuotoisuutta selvitettiin kartoittamalla L. crispatus ST1 -kannan perimä ja analysoimalla se yhdessä yhdeksän muun julkisesti saatavilla olevan L. crispatus -lajiin kuuluvan kannan perimän kanssa. Kaikki analysoidut perimät olivat hyvin samankaltaisia ja keskimäärin noin 57% yksittäisen kannan geeniperheistä oli läsnä kaikissa muissa perimissä. Kaikille kymmenelle perimälle yhteisten geeniperheiden todettiin kuvaavan edustavasti tälle lajille ominaisia perimäjaksoja ja selittävän lajiin liitettyjä emätinterveyttä edistäviä vaikutuksia. Tutkimuksessa myös osoitettiin erästä tällaista yhteisen geenin ilmenemistuotetta vastaan tuotettujen vasta-aineiden pystyvän estämään emätinterveydelle haitallisena pidetyn Gardnerella vaginalis -bakteerin kiinnittymistä ihmissoluihin. Nämä löydökset viittaavat emätinterveyttä edistävien toimintamekanismien olevan tyypillisiä L. crispatus -lajille ja voivat luoda uusia mahdollisuuksia emättimen bakteeritasapainon häiriöiden hoitoon. Teollisesti merkittävää juustohapatebakteeria puolestaan tutkittiin kartoittamalla P. freudenreichii ssp. shermanii JS -kannan perimä ja selvittämällä löydettyjen 2377 geenin aktiivisuus teollisen juustokypsytyksen kahdessa eri vaiheessa. Tutkitun kannan perimä osoittautui hyvin samankaltaiseksi aiemmin julkaistujen P. freudenreichii -kantojen perimien kanssa ja siitä tunnistettiin useita juuston maun kehityksen kannalta olennaisia geenejä. Useaa näistä makugeeneistä ilmennettiin voimakkaammin juuston lämpöisessä tapahtuneen esikellaroinnin kuin sitä seuranneen viileässä tapahtuneen kellaroinnin aikana. Nämä tulokset valottavat P. freudenreichii -bakteerin roolia juustokypsytyksessä ja korostavat erityisesti sen esikellaroinnin aikaisten toimintojen merkitystä juuston maulle. Yllä kuvatuissa perimäanalyyseissä hyödynnettiin laskennallisia menetelmiä ennustettujen geenien toiminnan luokittelemisessa. Näiden menetelmien avulla oli mahdollista ennustaa valtaosalle ST1- ja JS-kantojen geeneistä toimintakuvaus. Tämän lisäksi laskennallisen biologian menetelmiä hyödyntämällä pystyttiin tuottamaan tutkimukseen sisällettyjen julkisten L. crispatus -bakteerien perimien sisältämille geeneille aiempaa korkealaatuisempia toimintakuvauksia. Koska käytetyt laskennalliset menetelmät tuottivat usein toisiaan täydentäviä toimintakuvauksia, parhaat tulokset saavutettiin hyödyntämällä useaa menetelmää ja yhdistelemällä menetelmien tuloksia. Lisäksi käyttämällä löyhempiä kynnysarvoja sekvenssivertailutuloksien käsittelyssä pystyttiin luokittelemaan suurempi joukko geenejä kuin tiukkoja kynnysarvoja käyttämällä ilman että kuvausten laatu merkittävästi heikkeni. Tässä väitöskirjatyössä käytetyt menetelmät osoittautuivat tehokkaiksi ja käytännöllisiksi työkaluiksi laktobasillien ja propionihappobakteerien tutkimuksessa. Lisäksi esitetyt tutkimustulokset edistävät huomattavasti tietämystämme L. crispatus -bakteerin emätinterveydelle merkittävistä ominaisuuksista ja P. freudenreichii -bakteerin toiminnasta juuston valmistuksessa

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

A genomic analysis using RNA-Seq to investigate the adaptation of the psychrophilic diatom Fragilariopsis cylindrus to the polar environment

Diatoms are unicellular photosynthetic eukaryotes with a silicate cell wall. They often dominate polar marine ecosystems, driving the major biogeochemical cycles in these areas. The obligate psychrophilic diatom Fragilariopsis cylindrus is a keystone species in the Southern Ocean. It thrives both in open waters and sea ice and has become a model for studying eukaryotic microalgal adaptations to polar marine conditions. The aim of this thesis was to identify how the genome of F. cylindrus has evolved to cope with marine environmental conditions of the Southern Ocean. To identify key genes, comparative genomics, high-throughput transcriptome sequencing and reverse genetics were applied. Comparative genomics with the sequenced mesophilic diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana was combined with genome-wide RNA-Seq transcriptome analysis, leading to the discovery a new bacteria-like rhodopsin not present in other sequenced diatoms. The characterisation of a bacteria-like rhodopsin in F. cylindrus was conducted by applying reverse genetics tools. The genome was characterised by a low G+C content, which affected codon usage. High sequence polymorphism resulted in pronounced unequal expression of putative heterozygous allelic gene copies in response to six different conditions. RNA-Seq detected transcriptional activity for 95% of the 27,137 predicted genes and > 4 fold expression changes between 55% of putative alleles. The most significant transcriptional changes were detected during prolonged darkness affecting 70% of genes and 30% of RNA-Seq reads mapped to unannotated regions of the genome. Two rhodopsin alleles showed unequal bi-allelic expression in response to iron starvation and heterologous expression in Xenopus laevis oocytes experimentally confirmed light-driven proton pumping for the iron-induced rhodopsin allele, suggesting significance for the adaptation of F. cylindrus to environmental conditions of the Southern Ocean. These data show how the polar environment can shape the genome of a eukaryotic phytoplankton in unprecedented detail. High numbers of species-specific genes resulting in expansion of gene and protein families, low G+C likely enabling efficient translation at low temperatures and a high degree of heterozygosity combined with unequal bi-allelic expression, may provide an adaptive strategy to polar conditions by conferring metabolic flexibility and capacity to adapt to a rapidly changing environment