RESUMO
BACKGROUND: Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil. RESULTS: Here we describe the genome sequencing and assessment of plant growth-promoting abilities of S. marcescens UENF-22GI, a strain isolated from mature cattle manure vermicompost. In vitro, S. marcescens UENF-22GI is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with this strain remarkably increased seedling growth and biomass under greenhouse conditions. The S. marcescens UENF-22GI genome has 5 Mb, assembled in 17 scaffolds comprising 4662 genes (4528 are protein-coding). No plasmids were identified. S. marcescens UENF-22GI is phylogenetically placed within a clade comprised almost exclusively of non-clinical strains. We identified genes and operons that are likely responsible for the interesting plant-growth promoting features that were experimentally described. The S. marcescens UENF-22GI genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to its competitiveness against other bacteria. CONCLUSIONS: Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for agriculture.
Assuntos
Compostagem , Genoma Bacteriano/genética , Serratia marcescens/genética , Serratia marcescens/fisiologia , Zea mays/crescimento & desenvolvimento , Zea mays/microbiologia , Biofilmes , Transporte Biológico/genética , Biomassa , Fusarium/crescimento & desenvolvimento , Transferência Genética Horizontal , Esterco/microbiologia , Controle Biológico de Vetores , Fenóis/metabolismo , Fósforo/química , Fósforo/metabolismo , Serratia marcescens/isolamento & purificação , Serratia marcescens/metabolismo , Solubilidade , Espermidina/biossíntese , Zinco/química , Zinco/metabolismoRESUMO
Gene regulatory networks (GRNs) evolve as a result of the coevolutionary processes acting on transcription factors (TFs) and the cis-regulatory modules they bind. The zinc-finger TF zelda (zld) is essential for the maternal-to-zygotic transition (MZT) in Drosophila melanogaster, where it directly binds over thousand cis-regulatory modules to regulate chromatin accessibility. D. melanogaster displays a long germ type of embryonic development, where all segments are simultaneously generated along the whole egg. However, it remains unclear if zld is also involved in the MZT of short-germ insects (including those from basal lineages) or in other biological processes. Here we show that zld is an innovation of the Pancrustacea lineage, being absent in more distant arthropods (e.g. chelicerates) and other organisms. To better understand zld´s ancestral function, we thoroughly investigated its roles in a short-germ beetle, Tribolium castaneum, using molecular biology and computational approaches. Our results demonstrate roles for zld not only during the MZT, but also in posterior segmentation and patterning of imaginal disc derived structures. Further, we also demonstrate that zld is critical for posterior segmentation in the hemipteran Rhodnius prolixus, indicating this function predates the origin of holometabolous insects and was subsequently lost in long-germ insects. Our results unveil new roles of zld in different biological contexts and suggest that changes in expression of zld (and probably other major TFs) are critical in the evolution of insect GRNs.
Assuntos
Proteínas de Drosophila/genética , Desenvolvimento Embrionário/genética , Evolução Molecular , Redes Reguladoras de Genes/genética , Fatores de Transcrição/genética , Animais , Padronização Corporal/genética , Besouros/genética , Proteínas de Drosophila/biossíntese , Drosophila melanogaster/genética , Drosophila melanogaster/crescimento & desenvolvimento , Regulação da Expressão Gênica no Desenvolvimento , Proteínas Nucleares , Regiões Promotoras Genéticas , Interferência de RNA , Fatores de Transcrição/biossíntese , Ativação Transcricional/genética , Asas de Animais/crescimento & desenvolvimentoRESUMO
Large-scale chemical genetics screens (chemogenomics) in yeast have been widely used to find drug targets, understand the mechanism-of-action of compounds, and unravel the biochemistry of drug resistance. Chemogenomics is based on the comparison of growth of gene deletants in the presence and absence of a chemical substance. Such studies showed that more than 90% of the yeast genes are required for growth in the presence of at least one chemical. Analysis of these data, using computational approaches, has revealed non-trivial features of the natural chemical tolerance systems. As a result two non-overlapping sets of genes are seen to respectively impart robustness and evolvability in the context of natural chemical resistance. The former is composed of multidrug-resistance genes, whereas the latter comprises genes sharing chemical genetic profiles with many others. Recent publications showing the potential applications chemogenomics in studying the pharmacological basis of various drugs are discussed, as well as the expansion of chemogenomics to other organisms. Finally, integration of chemogenomics with sensitive sequence analysis and ubiquitination/phosphorylation data led to the discovery of a new conserved domain and important post-translational modification pathways involved in stress resistance.
RESUMO
We describe AMIN (Amidase N-terminal domain), a novel protein domain found specifically in bacterial periplasmic proteins. AMIN domains are widely distributed among peptidoglycan hydrolases and transporter protein families. Based on experimental data, contextual information and phyletic profiles, we suggest that AMIN domains mediate the targeting of periplasmic or extracellular proteins to specific regions of the bacterial envelope.