Genomic analyses of Paenibacillus polymyxa CR1, a bacterium with potential applications in biomass degradation and biofuel production

Lignin is a polyphenolic heteropolymer constituting between 18 to 35% of lignocellulose and is recognized as preventative of cellulosic biofuel commercialization. Paenibacillus polymyxa CR1 was isolated from naturally degrading corn stover and shown to produce alcohols using lignin as a sole carbon source. Genome sequencing and comparative genomics of P. polymyxa CR1 identified two homologs, a Dyp-type peroxidase and a laccase, which have previously been implicated in lignin metabolism in other bacteria. Knockout mutants of the identified genes displayed no growth deficiency and P. polymyxa CR1 is incapable of metabolizing common aromatic intermediates of lignin, suggesting the bacterium employs a novel catabolic pathway. To identify genes involved in lignin metabolism, a transposon library was generated and screened for abnormal lignin growth phenotypes. The results contained within will help elucidate the genetic basis of known functions helping delineate regulatory pathways and metabolic versatility in P. polymyxa relevant to lignin metabolism

Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats

Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection. Comparative genomic analysis showed that many of them had conserved backbones. Plasmid coding sequences corresponding to plasmid specific functions were bioinformatically and functionally analyzed. Replication initiation protein analysis revealed the predominance of the Rep_3 superfamily. The phylogenetic tree constructed from all Acinetobacter Rep_3 superfamily plasmids showed 16 intermingled clades originating from nosocomial and environmental habitats. Phylogenetic analysis of relaxase proteins revealed the presence of a new sub-clade named MOBQAci, composed exclusively of Acinetobacter relaxases. Functional analysis of proteins belonging to this group showed that they behaved differently when mobilized using helper plasmids belonging to different incompatibility groups.Fil: Salto, Ileana Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Torres Tejerizo, Gonzalo Arturo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Wibberg, Daniel. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Pühler, Alfred. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Schlüter, Andreas. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Pistorio, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentin

VIBRIO VULNIFICUS VIRULENCE AND SURVIVAL MECHANISMS REVEALED THROUGH COMPARATIVE MICROBIAL GENOMIC ANALYSIS

A sound genome assembly and robust annotations are essential to the differential analysis of bacterial genomes. Using a case study data set of newly sequenced Vibrio vulnificus genomes, both the biology of these bacteria, and the bioinformatics processes that support identification of the similarities and differences found within the different isolates of V. vulnificus, were examined. The two main themes of this research are 1) identification of the virulence and survival mechanisms of clinical and environmental biotypes of Vibrio vulnificus and 2) quantification of the impact of different analysis choices on the overall biological conclusions of the study. Whole genome sequencing, in conjunction with comparative genomics, are current techniques used to capture the genetic and functional repertoire of organisms. It is important to consider and track analytic provenance in bacterial genomics because the impact of making alternate workflow choices can involve changing the biological interpretation of hundreds of genes, even in relatively simple bacterial genomes. Chapter 1 describes the bioinformatics analyses used to determine the draft genome sequences of three environmental genotype Vibrio vulnificus reference genomes and to identify genotype-specific genomic regions. Chapter 1 also highlights the functional systems including the virulence and survival genes that differentiate between clinical and environmental Vibrio vulnificus genotypes. Chapter 2 explores the direct impact of the parameter and methods selected during the assembly and annotation stage of a genome project. Despite decades of advances in ab initio gene prediction, method and parameter choices still strongly influence the identification of genes, and therefore the biologically significant results in a comparative genomics analysis. Using a benchmarking approach based on simulation studies with a related genome, it is possible to identify an optimal assembly-to-annotation pipeline for the collection of V. vulnificus strains. A software framework for comparing the outcomes of different assembly-to-annotation workflows was constructed in the Taverna workflow management system and used to carry out the bioinformatics experiments described in Chapter 3. Chapter 3 expands on the analysis performed in Chapter 1 by performing an extensive comparative genomics analysis of newly sequenced Vibrio vulnificus genomes, each ones represents the different biological classifications found within this species. The analysis of these genomes reveals genes that are specific to each of the biotypes. Comparative analysis of representative strains from each of the established Vibrio vulnificus biotypes is used to identify differentiating genes, which may relate to the apparent host-specificity of the different biotypes

The Chlamydomonas genome project: A decade on

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes