Análise genética e mutagenese sítio dirigida do gene glnE de Herbaspirillum seropedicae

Orientadores: Maria Berenice Reynaud Steffens, Fábio de Oliveira Pedrosa, Liu Un Rigo, Roseli WasserriMonografia (Bacharelado) - Universidade Federal do Paraná.Setor de Ciencias Biologicas. Curso de Graduaçao em Ciencias BiologicasResumo : GlnE é uma enzima efetora bifuncional que atua regulando a cascata do metabolismo de nitrogênio controlando a atividade da enzima Glutamina Sintetase (GS). GS é uma das enzimas centrais envolvidas na assimilação de nitrogênio catalisando a conversão de glutamato e amônio em glutamina. A proteína GlnE regula a atividade enzimática de GS através da adenililação/desadenilidação de suas subunidades. Em H. seropedicae, uma bactéria diazotrófica endofitica, o gene glnE foi identificado durante o programa de sequenciamento genômico (GENOP AR). Nesse organismo, o gene glnE codifica para uma proteína de 927 aminoácidos que apresenta alta similaridade com o gene glnE de outros organismos. O gene glnE é, aparentemente, monocistrônico e constitutivamente expresso. Dois domínios homólogos conservados foram identificados na proteína GlnE: um na região Cterminal que possui o sítio de desadenililação e outro na região C-terminal que possui o sítio de adenililação. Um cassete de canamicina foi clnserido no gene glnE clonado no vetor pUC18. O plasmídeo resultante (PHF16), foi eletroporado na estirpe selvagem SMRl de H seropedicae gerando duas estirpes mutantes por inserção cromossomal (HEL 1 e HEL2). O mutante HEL 1 apresentou atividade nitrogenase reduzida em relação à estirpe selvagem SMRl

Prospecção metagenômica de biocatalisadores da microbiota de solos da Floresta Atlântica paranaense

Resumo: A diversidade bacteriana do solo e seu potencial biotecnologico sao pouco explorados. Dados indicam que 1 g de solo contem mais de 10 bilhoes de micro-organismos distribuidos em milhares de especies. Entretanto, a grande maioria dessas especies sao desconhecidas devido a sua inabilidade de se multiplicar nos meios de cultivo tradicionalmente usados em laboratorio. A Metagenomica tornou possivel o acesso a essa vasta diversidade genetica permitindo a analise direta do DNA de uma comunidade bacteriana e levando a descoberta de novos biocatalisadores. Nesse trabalho sao descritas a construcao de tres bibliotecas metagenomicas, a prospeccao por novos biocatalisadores e a caracterizacao de uma nova lipase identificada nessas bibliotecas. As bibliotecas foram construidas a partir de amostras de solo da Floresta Atlantica Paranaense coletadas em diferentes altitudes. O DNA das amostras de solo foi purificado, reparado e clonado no vetor pCC2FOS. Os fosmideos recombinantes foram transformados na estirpe EPI300 de Escherichia coli gerando as bibliotecas metagenomicas MAF1, MAF2 e MAF3 com 34.560, 29.280 e 36.288 clones, respectivamente. Todos os clones foram analisados quanto a atividade triacil-hidrolasica em tributirina (315 clones positivos), tricaprilina (10 clones positivos) e trioleina (3 clones positivos). Os clones da biblioteca MAF1 tambem foram analisados quanto a atividade de protease (460 clones positivos) e atividade de amilase (4 clones positivos). O DNA inserto dos clones com atividade lipolitica MAF1LP001, MAF1LP018 e MAF1LP090 foram sequenciados, o que permitiu identificar 80 ORFs/genes. A lipase LP001ORF27 foi identificada como membro da familia I das lipases e similaridade proxima a subfamilia termofilica I.5. A enzima purificada apresenta atividade contra diferentes para-nitrofenil-monoacilesteres (pNP monoacilesteres) com atividade maxima (7 U/mg) contra pNP decanoato. LP001ORF27 apresentou atividade do pH 5,0 ao 11,0, com atividade otima em pH 7,0 e nao apresentou dependencia de metais. A temperatura otima de atividade ocorreu na faixa de 50-60oC e a enzima apresentou ativacao termica de 80% apos incubacao por 1 hora a 50oC. A lipase LP018ORF16 nao apresentou similaridade com sequencias de lipases conhecidas e a analise filogenetica sugeriu que ela constitui uma nova familia. Essa enzima tambem demonstrou dependencia da proteina LP018ORF15, provavelmente uma chaperona, para atividade. LP090ORF24 foi identificada como membro da familia I das lipases, proxima a subfamilia I.2, e tambem apresenta similaridade com uma poli-hidroxialcanoato (PHA) depolimerase. Proximo a LP090ORF24 foi identificado um gene que codifica uma Ą-amilase. Finalmente, a analise da sequencia dessa proteina sugeriu que ela contem um dominio de ciclodextrina glicosiltansferase (CGTase). Os resultados obtidos nesse trabalho confirmam o potencial da Metagenomica para a descoberta de novas enzimas de importancia biotecnologica

Identification and characterization of a new true lipase isolated through metagenomic approach

<p>Abstract</p> <p>Background</p> <p>Metagenomics, the application of molecular genomics to consortia of non-cultivated microbes, has the potential to have a substantial impact on the search for novel industrial enzymes such as esterases (carboxyl ester hydrolases, EC 3.1.1.1) and lipases (triacylglycerol lipases, EC 3.1.1.3). In the current work, a novel lipase gene was identified from a fosmid metagenomic library constructed with the "prokaryotic-enriched" DNA from a fat-contaminated soil collected from a wastewater treatment plant.</p> <p>Results</p> <p>In preliminary screening on agar containing 1% tributyrin, 2661 of the approximately 500,000 clones in the metagenomic library showed activity. Of these, 127 showed activity on agar containing 1% tricaprylin, while 32 were shown to be true lipase producers through screening on agar containing 1% triolein. The clone with the largest halo was further characterized. Its lipase gene showed 72% identity to a putative lipase of <it>Yersinia enterocolitica </it>subsp. <it>palearctica </it>Y11. The lipase, named LipC12, belongs to family I.1 of bacterial lipases, has a chaperone-independent folding, does not possess disulfide bridges and is calcium ion dependent. It is stable from pH 6 to 11 and has activity from pH 4.5 to 10, with higher activities at alkaline pH values. LipC12 is stable up to 3.7 M NaCl and from 20 to 50°C, with maximum activity at 30°C over a 1 h incubation. The pure enzyme has specific activities of 1722 U/mg and 1767 U/mg against olive oil and pig fat, respectively. Moreover, it is highly stable in organic solvents at 15% and 30% (v/v).</p> <p>Conclusions</p> <p>The combination of the use of a fat-contaminated soil, enrichment of prokaryotic DNA and a three-step screening strategy led to a high number of lipase-producing clones in the metagenomic library. The most notable properties of the new lipase that was isolated and characterized were a high specific activity against long chain triacylglycerols, activity and stability over a wide range of pH values, good thermal stability and stability in water-miscible organic solvents and at high salt concentrations. These characteristics suggest that this lipase has potential to perform well in biocatalytic processes, such as for hydrolysis and synthesis reactions involving long-chain triacylglycerols and fatty acid esters.</p

Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera

© 2021 by the authors.Among other attributes, the Betaproteobacterial genus Azoarcus has biotechnological importance for plant growth-promotion and remediation of petroleum waste-polluted water and soils. It comprises at least two phylogenetically distinct groups. The “plant-associated” group includes strains that are isolated from the rhizosphere or root interior of the C4 plant Kallar Grass, but also strains from soil and/or water; all are considered to be obligate aerobes and all are diazotrophic. The other group (now partly incorporated into the new genus Aromatoleum) comprises a diverse range of species and strains that live in water or soil that is contaminated with petroleum and/or aromatic compounds; all are facultative or obligate anaerobes. Some are diazotrophs. A comparative genome analysis of 32 genomes from 30 Azoarcus-Aromatoleum strains was performed in order to delineate generic boundaries more precisely than the single gene, 16S rRNA, that has been commonly used in bacterial taxonomy. The origin of diazotrophy in Azoarcus-Aromatoleum was also investigated by comparing full-length sequences of nif genes, and by physiological measurements of nitrogenase activity using the acetylene reduction assay. Based on average nucleotide identity (ANI) and whole genome analyses, three major groups could be discerned: (i) Azoarcus comprising Az. communis, Az. indigens and Az. olearius, and two unnamed species complexes, (ii) Aromatoleum Group 1 comprising Ar. anaerobium, Ar. aromaticum, Ar. bremense, and Ar. buckelii, and (iii) Aromatoleum Group 2 comprising Ar. diolicum, Ar. evansii, Ar. petrolei, Ar. toluclasticum, Ar. tolulyticum, Ar. toluolicum, and Ar. toluvorans. Single strain lineages such as Azoarcus sp. KH32C, Az. pumilus, and Az. taiwanensis were also revealed. Full length sequences of nif-cluster genes revealed two groups of diazotrophs in Azoarcus-Aromatoleum with nif being derived from Dechloromonas in Azoarcus sensu stricto (and two Thauera strains) and from Azospira in Aromatoleum Group 2. Diazotrophy was confirmed in several strains, and for the first time in Az. communis LMG5514, Azoarcus sp. TTM-91 and Ar. toluolicum TT. In terms of ecology, with the exception of a few plant-associated strains in Azoarcus (s.s.), across the group, most strains/species are found in soil and water (often contaminated with petroleum or related aromatic compounds), sewage sludge, and seawater. The possession of nar, nap, nir, nor, and nos genes by most Azoarcus-Aromatoleum strains suggests that they have the potential to derive energy through anaerobic nitrate respiration, so this ability cannot be usefully used as a phenotypic marker to distinguish genera. However, the possession of bzd genes indicating the ability to degrade benzoate anaerobically plus the type of diazotrophy (aerobic vs. anaerobic) could, after confirmation of their functionality, be considered as distinguishing phenotypes in any new generic delineations. The taxonomy of the Azoarcus-Aromatoleum group should be revisited; retaining the generic name Azoarcus for its entirety, or creating additional genera are both possible outcomes.This research was funded by the BBSRC-Newton Fund (grant numbers BB/N013476/1 and BB/N003608/1). MC was funded by grant BIO2016-79736-R from the Ministry of Economy and Competitiveness of Spain.Peer reviewe

Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts

Abstract Background Herbaspirillum seropedicae is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, strains of H. seropedicae have been isolated from immunocompromised patients and associated with human infections and deaths. In this work, we sequenced the genomes of two clinical strains of H. seropedicae, AU14040 and AU13965, and compared them with the genomes of strains described as having an environmental origin. Results Both genomes were closed, indicating a single circular chromosome; however, strain AU13965 also carried a plasmid of 42,977 bp, the first described in the genus Herbaspirillum. Genome comparison revealed that the clinical strains lost the gene sets related to biological nitrogen fixation (nif) and the type 3 secretion system (T3SS), which has been described to be essential for interactions with plants. Comparison of the pan-genomes of clinical and environmental strains revealed different sets of accessorial genes. However, antimicrobial resistance genes were found in the same proportion in all analyzed genomes. The clinical strains also acquired new genes and genomic islands that may be related to host interactions. Among the acquired islands was a cluster of genes related to lipopolysaccharide (LPS) biosynthesis. Although highly conserved in environmental strains, the LPS biosynthesis genes in the two clinical strains presented unique and non-orthologous genes within the genus Herbaspirillum. Furthermore, the AU14040 strain cluster contained the neuABC genes, which are responsible for sialic acid (Neu5Ac) biosynthesis, indicating that this bacterium could add it to its lipopolysaccharide. The Neu5Ac-linked LPS could increase the bacterial resilience in the host aiding in the evasion of the immune system. Conclusions Our findings suggest that the lifestyle transition from environment to opportunist led to the loss and acquisition of specific genes allowing adaptations to colonize and survive in new hosts. It is possible that these substitutions may be the starting point for interactions with new hosts.https://deepblue.lib.umich.edu/bitstream/2027.42/152201/1/12864_2019_Article_5982.pd

Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species

Rare genetic variants involved in multisystem inflammatory syndrome in children: a multicenter Brazilian cohort study

IntroductionDespite the existing data on the Multisystem Inflammatory Syndrome in Children (MIS-C), the factors that determine these patients evolution remain elusive. Answers may lie, at least in part, in genetics. It is currently under investigation that MIS-C patients may have an underlying innate error of immunity (IEI), whether of monogenic, digenic, or even oligogenic origin.MethodsTo further investigate this hypothesis, 30 patients with MIS-C were submitted to whole exome sequencing. ResultsAnalyses of genes associated with MIS-C, MIS-A, severe covid-19, and Kawasaki disease identified twenty-nine patients with rare potentially damaging variants (50 variants were identified in 38 different genes), including those previously described in IFNA21 and IFIH1 genes, new variants in genes previously described in MIS-C patients (KMT2D, CFB, and PRF1), and variants in genes newly associated to MIS-C such as APOL1, TNFRSF13B, and G6PD. In addition, gene ontology enrichment pointed to the involvement of thirteen major pathways, including complement system, hematopoiesis, immune system development, and type II interferon signaling, that were not yet reported in MIS-C.DiscussionThese data strongly indicate that different gene families may favor MIS- C development. Larger cohort studies with healthy controls and other omics approaches, such as proteomics and RNAseq, will be precious to better understanding the disease dynamics

Prospecção metagenômica de biocatalisadores da microbiota de solos da Floresta Atlântica paranaense

Resumo: A diversidade bacteriana do solo e seu potencial biotecnologico sao pouco explorados. Dados indicam que 1 g de solo contem mais de 10 bilhoes de micro-organismos distribuidos em milhares de especies. Entretanto, a grande maioria dessas especies sao desconhecidas devido a sua inabilidade de se multiplicar nos meios de cultivo tradicionalmente usados em laboratorio. A Metagenomica tornou possivel o acesso a essa vasta diversidade genetica permitindo a analise direta do DNA de uma comunidade bacteriana e levando a descoberta de novos biocatalisadores. Nesse trabalho sao descritas a construcao de tres bibliotecas metagenomicas, a prospeccao por novos biocatalisadores e a caracterizacao de uma nova lipase identificada nessas bibliotecas. As bibliotecas foram construidas a partir de amostras de solo da Floresta Atlantica Paranaense coletadas em diferentes altitudes. O DNA das amostras de solo foi purificado, reparado e clonado no vetor pCC2FOS. Os fosmideos recombinantes foram transformados na estirpe EPI300 de Escherichia coli gerando as bibliotecas metagenomicas MAF1, MAF2 e MAF3 com 34.560, 29.280 e 36.288 clones, respectivamente. Todos os clones foram analisados quanto a atividade triacil-hidrolasica em tributirina (315 clones positivos), tricaprilina (10 clones positivos) e trioleina (3 clones positivos). Os clones da biblioteca MAF1 tambem foram analisados quanto a atividade de protease (460 clones positivos) e atividade de amilase (4 clones positivos). O DNA inserto dos clones com atividade lipolitica MAF1LP001, MAF1LP018 e MAF1LP090 foram sequenciados, o que permitiu identificar 80 ORFs/genes. A lipase LP001ORF27 foi identificada como membro da familia I das lipases e similaridade proxima a subfamilia termofilica I.5. A enzima purificada apresenta atividade contra diferentes para-nitrofenil-monoacilesteres (pNP monoacilesteres) com atividade maxima (7 U/mg) contra pNP decanoato. LP001ORF27 apresentou atividade do pH 5,0 ao 11,0, com atividade otima em pH 7,0 e nao apresentou dependencia de metais. A temperatura otima de atividade ocorreu na faixa de 50-60oC e a enzima apresentou ativacao termica de 80% apos incubacao por 1 hora a 50oC. A lipase LP018ORF16 nao apresentou similaridade com sequencias de lipases conhecidas e a analise filogenetica sugeriu que ela constitui uma nova familia. Essa enzima tambem demonstrou dependencia da proteina LP018ORF15, provavelmente uma chaperona, para atividade. LP090ORF24 foi identificada como membro da familia I das lipases, proxima a subfamilia I.2, e tambem apresenta similaridade com uma poli-hidroxialcanoato (PHA) depolimerase. Proximo a LP090ORF24 foi identificado um gene que codifica uma Ą-amilase. Finalmente, a analise da sequencia dessa proteina sugeriu que ela contem um dominio de ciclodextrina glicosiltansferase (CGTase). Os resultados obtidos nesse trabalho confirmam o potencial da Metagenomica para a descoberta de novas enzimas de importancia biotecnologica