How Many Initiator tRNA Genes Does Escherichia coli Need?

Multiple copies of a gene require enhanced investment on the part of the cell and, as such, call for an explanation. The observation that Escherichia coli has four copies of initiator tRNA (tRNA(i)) genes, encoding a special tRNA (tRNA(fMet)) required to start protein synthesis, is puzzling particularly because the cell appears to be unaffected by the removal of one copy. However, the fitness of an organism has both absolute and relative connotations. Thus, we carried out growth competition experiments between E. coli strains that differ in the number of tRNA(i) genes they contain. This has enabled us to uncover an unexpected link between the number of tRNA(i) genes and protein synthesis, nutritional status, and fitness. Wild-type strains with the canonical four tRNA(i) genes are favored in nutrient-rich environments, and those carrying fewer are favored in nutrient-poor environments. Auxotrophs behave as if they have a nutritionally poor internal environment. A heuristic model that links tRNA(i) gene copy number, genetic stress, and growth rate accounts for the findings. Our observations provide strong evidence that natural selection can work through seemingly minor quantitative variations in gene copy number and thereby impact organismal fitness.

CINCINNATA in Antirrhinum majus directly modulates genes involved in cytokinin and auxin signaling

Mutations in the CINCINNATA (CIN) gene in Antirrhinum majus and its orthologs in Arabidopsis result in crinkly leaves as a result of excess growth towards the leaf margin. CIN homologs code for TCP (TEOSINTE-BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 AND 2) transcription factors and are expressed in a broad zone in a growing leaf distal to the proliferation zone where they accelerate cell maturation. Although a few TCP targets are known, the functional basis of CIN-mediated leaf morphogenesis remains unclear. We compared the global transcription profiles of wild-type and the cin mutant of A. majus to identify the targets of CIN. We cloned and studied the direct targets using RNA in situ hybridization, DNA-protein interaction, chromatin immunoprecipitation and reporter gene analysis. Many of the genes involved in the auxin and cytokinin signaling pathways showed altered expression in the cin mutant. Further, we showed that CIN binds to genomic regions and directly promotes the transcription of a cytokinin receptor homolog HISTIDINE KINASE 4 (AmHK4) and an IAA3/SHY2 (INDOLE-3-ACETIC ACID INDUCIBLE 3/SHORT HYPOCOTYL 2) homolog in A. majus. Our results suggest that CIN limits excess cell proliferation and maintains the flatness of the leaf surface by directly modulating the hormone pathways involved in patterning cell proliferation and differentiation during leaf growth. 10.1111/(ISSN)1469-8137

Characterization of type I interferon pathway during hepatic differentiation of human pluripotent stem cells and hepatitis C virus infection

Pluripotent stem cells are being actively studied as a cell source for regenerating damaged liver. For long-term survival of engrafting cells in the body, not only do the cells have to execute liver-specific function but also withstand the physical strains and invading pathogens. The cellular innate immune system orchestrated by the interferon (IFN) pathway provides the first line of defense against pathogens. The objective of this study is to assess the innate immune function as well as to systematically profile the IFN-induced genes during hepatic differentiation of pluripotent stem cells. To address this objective, we derived endodermal cells (day 5 post-differentiation), hepatoblast (day 15) and hepatocyte-like cells (day 21) from human embryonic stem cells (hESCs). Day 5, 15 and 21 cells were stimulated with IFN-alpha and subjected to IFN pathway analysis. Transcriptome analysis was carried out by RNA sequencing. The results showed that the IFN-alpha treatment activated STAT-JAK pathway in differentiating cells. Transcriptome analysis indicated stage specific expression of classical and non-classical IFN-stimulated genes (ISGs). Subsequent validation confirmed the expression of novel ISGs including RASGRP3, CLMP and TRANK1 by differentiated hepatic cells upon IFN treatment. Hepatitis C virus replication in hESC-derived hepatic cells induced the expression of ISGs - LAMP3, ETV7, RASGRP3, and TRANK1. The hESC-derived hepatic cells contain intact innate system and can recognize invading pathogens. Besides assessing the tissue-specific functions for cell therapy applications, it may also be important to test the innate immune function of engrafting cells to ensure adequate defense against infections and improve graft survival. (C) 2015 The Authors. Published by Elsevier B.V.

Engineering thermostable fungal cellobiohydrolases

Meeting the world's growing energy demands while protecting our fragile environment is a challenging issue. Second generation biofuels are liquid fuels like long-chain alcohols produced from lignocellulosic biomass. To reduce the cost of biofuel production, we engineered fungal family 6 cellobiohydrolases (Cel6A) for enhanced thermostability using random mutagenesis and recombination of beneficial mutations. During long-time hydrolysis, engineered thermostable cellulases hydrolyze more sugars than wild-type Cel6A as single enzymes and binary mixtures at their respective optimum temperatures. Engineered thermostable cellulases exhibit synergy in binary mixtures similar to wild-type cellulases, demonstrating the utility of engineering individual cellulases to produce novel thermostable mixtures. Crystal structures of the engineered thermostable cellulases indicate that the stabilization comes from improved hydrophobic interactions and restricted loop conformations by proline substitutions. At high temperature, free cysteines contribute to irreversible thermal inactivation in engineered thermostable Cel6A and wild-type Cel6A. The mechanism of thermal inactivation in this cellulase family is consistent with disulfide bond degradation and thiol-disulfide exchange. Enhancing the thermostability of Cel6A also increases tolerance to pretreatment chemicals, demonstrated by the strong correlation between thermostability and tolerance to 1-ethyl-3-methylimidazolium acetate. Several semi-rational protein engineering approaches – on the basis of consensus sequence analysis, proline stabilization, FoldX energy calculation, and high B-factors – were evaluated to further enhance the thermostability of Cel6A.

Análise do perfil de genes relacionados ao SST5 e SST6, formação de biofilme e invasão em cepas de Escherichia coli enteroagregativa

A Escherichia coli enteroagregativa (EAEC) é um patotipo emergente e heterogêneo que causa a diarréia aguda ou persistente em indivíduos de diferentes faixas etárias e em pacientes imunocomprometidos. Além disso, EAEC é um dos principais agentes etiológicos da diarréia dos viajantes. O padrão de aderência agregativa de EAEC está associado ao plasmídeo de aderência agregativa (pAA). Genes presentes no plasmídeo e no cromossomo codificam proteínas envolvidas na secreção extracelular de fatores de virulência na superfície ou diretamente na célula hospedeira. A capacidade de produção de muco e biofilme, elaboração de toxinas, aderência e indução de inflamação intensa na mucosa intestinal são importantes características da patogenicidade de EAEC. Nesse estudo, determinamos o perfil genotípico de genes do sistema de secreção Tipo V (SST5) e sistema de secreção Tipo VI (SST6) em cepas de EAEC. Os genes do SST5 ocorreram com mais frequência que os genes do SST6. A presença de pelo menos um gene do SST5 foi detectada em 79% das cepas, enquanto que os genes relacionados ao SST6 foram detectados em apenas 42% das cepas analisadas. A produção de biofilme foi observada em teste quantitativo e verificamos que 67% das cepas produziram biofilme. No teste qualitativo, o tipo de biofilme que predomina é o biofilme moderado (11 cepas), seguido do biofilme forte (9 cepas) e do biofilme discreto (4 cepas). A presença ou ausência de genes do SST5 e SST6 não parece interferir com a capacidade de produção de biofilme, nem com o tipo de biofilme formado. Em ensaios de citotoxicidade, apenas 25% das cepas EAEC (sobrenadante) causaram redução significativa na viabilidade de células T84 avaliada pelo teste de redução com MTT. Nossos resultados mostram que as cepas EAEC isoladas de crianças com diarréia aguda ou de grupo controle são invasoras para células T84. Ao compararmos a capacidade invasora das cepas clinicas e controle, observamos que a média do índice de internalização obtido nas 15 cepas do grupo clinico foi de 5,7% 1,7 e para as 9 cepas do grupo controle foi de 2.4 % 0,7; entretanto essa diferença observada não foi estatisticamente significativa. Não foi possível correlacionar o perfil genotípico dos genes do SST5 e SST6 com o perfil fenotípico analisado (formação de biofilme, citotoxicidade e invasão).O que pode ser atribuído a heterogeneidade genotípica e fenotípica, uma característica relevante de cepas EAEC.

Characterisation of patients with brachydactyly type E associated or not with hormonal resistance: clinical, genetic and radiological approach

334 p.

Distribuição e conservação dos genes que codificam as proteínas VgrG e Hcp em espécies de Aeromonas

Aeromonas spp. são bastonetes Gram negativos amplamente distribuídos nos ambientes aquáticos, com relatos de isolamento em água de abastecimento público e alimentos. Este micro-organismo possui potencial de causar doenças intestinais e extraintestinais cuja patogenicidade está associada a sua virulência multifatorial. Diversos determinantes de virulência de Aeromonas já foram identificados, incluindo sistemas de secreção de proteínas. O sistema de secreção tipo VI (SST6) é o mais recente sistema de secreção de proteínas identificado em bactérias cuja presença em estirpes no gênero Aeromonas pode implicar atividades de citotoxicidade para o hospedeiro, pois esse sistema é capaz de injetar moléculas efetoras dentro da célula, interferindo diretamente nos processos celulares. A fim de determinar a presença e analisar a distribuição dos genes hcp e vgrG codificadores das proteínas efetoras do SST6 em Aeromonas spp. o presente estudo examinou 119 cepas isoladas de diversas origens pela técnica da PCR após o desenho de oligonucleotídeos iniciadores específicos. Objetivamos ainda analisar a variabilidade genética interespecífica dos genes hcp e vgrG a partir de dados de sequenciamento. Os resultados obtidos indicaram a distribuição dos genes vgrG e hcp em 46% das cepas de Aeromonas hydrophila e Aeromonas caviae de diferentes origens. Entre as cepas de A. hydrophila a maior frequência foi observada nas cepas isoladas de humanos, onde todas foram positivas para os iniciadores que amplificaram um produto de 541 pb do gene vgrG e 418 pb do gene hcp. Entre as cepas de A. caviae, a incidência de genes vgrG e hcp foi mais elevada nas cepas isoladas de alface (60%) e peixes (50%). As cepas analisadas de origem ambiental apresentaram índice total de 36% de positividade, apresentando frequência de 60% e 22% em A. hydrophila e A. caviae, respectivamente. Os dados obtidos da análise de cepas de origem alimentar mostraram a presença dos genes vgrG e hcp em 67% (A. hydrophila) e 60% (A. caviae) das cepas isoladas de folhas de alface. Nas cepas isoladas de queijo os genes foram encontrados em 67% e 12,5% das cepas de A. hydrophila e de A. caviae, respectivamente. O alinhamento múltiplo entre as sequências dos segmentos dos genes hcp e vgrG obtidas no sequenciamento indicou grau de identidade nucleotídica de 75 a 100% entre as sequências de hcp e 80 a 100% entre as sequências de vgrG. Em conclusão, nossos resultados indicaram que os iniciadores desenhados foram capazes de detectar suas sequências alvo em cepas de A. caviae e outras espécies de Aeromonas, sugerindo a existência de homologia entre os genes nas diferentes espécies, confirmada após sequenciamento de DNA. Os dados indicaram que esses genes estão distribuídos em várias espécies de Aeromonas e em cepas isoladas de diversas fontes. Ressaltamos a prevalência de cepas de A. hydrophila PCR-positivas em isolados clínicos, sugerindo a participação do SST6 no complexo universo da virulência multifatorial que permeia esse micro-organismo

Current Approaches for Predicting a Lack of Response to Anti-EGFR Therapy in KRAS Wild-Type Patients

Targeting epidermal growth factor receptor (EGFR) has been one of the most effective colorectal cancer strategies. Anti-EGFR antibodies function by binding to the extracellular domain of EGFR, preventing its activation, and ultimately providing clinical benefit. KRAS mutations in codons 12 and 13 are recognized prognostic and predictive biomarkers that should be analyzed at the clinic prior to the administration of anti-EGFR therapy. However, still an important fraction of KRAS wild-type patients do not respond to the treatment. The identification of additional genetic determinants of primary or secondary resistance to EGFR targeted therapy for further improving the selection of patients is urgent. Herein, we review the latest published literature highlighting the most important genes that may predict resistance to anti-EGFR monoclonal antibodies in colorectal cancer patients. According to the available findings, the evaluation of BRAF, NRAS, PIK3CA, and PTEN status could be the right strategy to select patients who are likely to respond to anti-EGFR therapies. In the future, the combination of those biomarkers will help establish consensus that can be introduced into clinical practice.

Perfil de secreção de citocinas e de ativação de células endoteliais após interação com cepas selvagens e mutantes de Aspergillus fumigatus

Apesar do desenvolvimento de novas drogas antifúngicas e da sua utilização como terapia profilática visando à prevenção de infecções fúngicas invasivas, estas ainda constituem-se num problema emergente, com elevadas taxas de mortalidade. Neste contexto, destaca-se a aspergilose invasiva, uma infecção fúngica oportunista que acomete pacientes com neutropenia profunda e prolongada, principalmente os pacientes com leucemia aguda ou submetidos a transplante de medula óssea. Aspergillus fumigatus, um fungo filamentoso, é o principal agente etiológico da aspergilose invasiva, sendo um patógeno angioinvasivo. As hifas deste fungo são capazes de causar injúria e ativação endotelial, induzindo o endotélio a um fenótipo pró-trombótico, que por sua vez, é mediado pela secreção de citocinas pró-inflamatórias, em especial, o TNF-α. O presente trabalho teve como objetivo estudar a capacidade de cepas mutantes de A. fumigatus em ativar células endoteliais, avaliando o perfil de secreção de citocinas em meio condicionado e a expressão de fator tecidual. Resumidamente, monocamadas confluentes de células endoteliais isoladas da veia umbilical humana foram incubadas com conídios e tubos germinativos de cepas selvagens (Af293 e Ku80) e mutantes (Δugm1, ΔcalA, ΔcrzA, ΔprtT) de A. fumigatus. A taxa de adesão e endocitose destas cepas às monocamadas de HUVEC foi avaliada a partir de um ensaio quantitativo de imunofluorescência diferencial. O perfil cinético de secreção de citocinas foi determinado em meio condicionado das HUVECs, por ensaio de multiplex para IL-6, IL-8 e TNF-α. A ativação endotelial, por sua vez, foi determinada pela expressão de fator tecidual por RT-PCR em tempo real. Os resultados obtidos demonstraram que a mutante para o gene ugm1, responsável por codificar a enzima UDP-galactopiranose mutase, que converte resíduos de galactopiranose a galactofuranose, apresentou um fenótipo hiperaderente às células endoteliais e um estímulo 10 vezes maior à secreção de TNF-α e 2,5 vezes maior a secreção de IL-6, quando comparada a ativação observada para as cepas selvagens. A galactofuranose é um componente importante de glicoconjugados da parede celular de A. fumigatus. Dessa forma, a ausência desse monossacarídeo na célula fúngica leva a um mecanismo compensatório caracterizado por um aumento na expressão de moléculas de galactosaminogalactana na parede celular. De maneira contrária, mutantes para os genes calA e crzA, apresentaram um fenótipo hipoaderente às HUVECs e uma perda na capacidade de induzir a secreção de citocinas e ativar o endotélio. Essas mutantes apresentam deleções que interferem na via de cálcio/calcineurina, responsável por regular a morfogênese e virulência de A. fumigatus, além de apresentarem alterações no conteúdo de beta-1-3 glucana. Já a cepa ΔprtT, mutante para o fator de transcrição prtT que regula a secreção de múltiplas proteases, apresentou um fenótipo de adesão, estímulo e ativação endotelial semelhante ao observado para as cepas selvagens. A comparação entre a capacidade de conídios e tubos germinativos em ativar células endoteliais, corroborou achados anteriores da literatura que reportam que só hifas são capazes de ativar células endoteliais, independentemente da sua viabilidade. Os dados deste estudo permitiram concluir que dentre os componentes de superfície celular de A. fumigatus, os polímeros de galactose, em especial a galactosaminogalactana, parecem ser responsáveis, pelo menos em parte, pelos mecanismos de interação e ativação endotelial.

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

Recent transcription profiling studies have revealed an unexpectedly large proportion of antisense transcripts in eukaryotic genomes. These antisense genes seem to regulate gene expression by interacting with sense genes. Previous studies have focused on the non-coding antisense genes, but the possible regulatory role of the antisense protein is poorly understood. In this study, we found that a protein encoded by the antisense gene ADF1 acts as a transcription suppressor, regulating the expression of sense gene MDF1 in Saccharomyces cerevisiae. Based on the evolutionary, genetic, cytological and biochemical evidence, we show that the protein-coding sense gene MDF1 most likely originated de novo from a previously non-coding sequence and can significantly suppress the mating efficiency of baker's yeast in rich medium by binding MAT alpha 2 and thus promote vegetative growth. These results shed new light on several important issues, including a new sense-antisense interaction mechanism, the de novo origination of a functional gene, and the regulation of yeast mating pathway.

The bacterial cytoskeleton modulates motility, type 3 secretion, and colonization in Salmonella.

Although there have been great advances in our understanding of the bacterial cytoskeleton, major gaps remain in our knowledge of its importance to virulence. In this study we have explored the contribution of the bacterial cytoskeleton to the ability of Salmonella to express and assemble virulence factors and cause disease. The bacterial actin-like protein MreB polymerises into helical filaments and interacts with other cytoskeletal elements including MreC to control cell-shape. As mreB appears to be an essential gene, we have constructed a viable ΔmreC depletion mutant in Salmonella. Using a broad range of independent biochemical, fluorescence and phenotypic screens we provide evidence that the Salmonella pathogenicity island-1 type three secretion system (SPI1-T3SS) and flagella systems are down-regulated in the absence of MreC. In contrast the SPI-2 T3SS appears to remain functional. The phenotypes have been further validated using a chemical genetic approach to disrupt the functionality of MreB. Although the fitness of ΔmreC is reduced in vivo, we observed that this defect does not completely abrogate the ability of Salmonella to cause disease systemically. By forcing on expression of flagella and SPI-1 T3SS in trans with the master regulators FlhDC and HilA, it is clear that the cytoskeleton is dispensable for the assembly of these structures but essential for their expression. As two-component systems are involved in sensing and adapting to environmental and cell surface signals, we have constructed and screened a panel of such mutants and identified the sensor kinase RcsC as a key phenotypic regulator in ΔmreC. Further genetic analysis revealed the importance of the Rcs two-component system in modulating the expression of these virulence factors. Collectively, these results suggest that expression of virulence genes might be directly coordinated with cytoskeletal integrity, and this regulation is mediated by the two-component system sensor kinase RcsC.

Effects of cyanobacterial toxin microcystin-LR on the transcription levels of immune-related genes in grass carp Ctenopharyngodon idella

Recent studies in mammals have revealed that the cyanobacterial toxin MC-LR suppresses immune functions. Nevertheless, immunotoxic effects of microcystins have been little studied in fish. In this paper, we present the profiles of the immune modulation of MC-LR in grass carp, and quantitative real-time PCR methodology was developed for the measurement of relative transcription changes of six immune-related genes in the spleen and head kidney of the grass carp Ctenopharyngodon idella, which were intraperitoneally injected with 50 mu g MC-LR center dot kg(-1) body weight in a three-week period. This study was focused exclusively on gene transcription level changes at different time points after MC-LR exposure, so, only one dose was given. The investigated genes were interleukin-1 beta (IL-1 beta), tumor necrosis factor-alpha (TNF-alpha), type I interferon (Type I IFN), peptidoglycan recognition protein-L (PGRP-L), immunoglobulin M (IgM) and major histocompatibility complex class I (MHC-I) genes. The results demonstrated that the transcription levels of the TNF-alpha, type I IFN, and PGRP-L genes in the spleen and head kidney were significantly low at all time points, and those of IL-1 beta were significantly low in the head kidney at different time points. In addition, IgM and MHC-I transcription levels were only significantly low in the spleen and head kidney at 21 d postinjection. The changes in the transcription levels of immune-related genes induced by MC-LR confirmed its effect on inhibiting immune function at the transcription level.

Differential expression of three Paralichthys olivaceus Hsp40 genes in responses to virus infection and heat shock

Heat shock proteins (Hsps) are a family of highly conserved cellular proteins present in all organisms, mediating a range of essential housekeeping and cytoprotective functions as well-known molecular chaperons and recently as regulators of the immune response. By subtractive suppression hybridization, three Hsp40 homologues have been identified in the flounder (Paralichthys olivaceus) embryonic cells (FEC) after treatment with UV-inactivated turbot (Scophthalmus maximus L.) rhabdovirus (SMRV), termed PoHsp40A4, PoHsp40B6 and PoHsp40B11, whose encoded proteins all possess the conserved DnaJ domain, a signature motif of the Hsp40 family. Based on different protein structure and phylogenetic analysis, they can be categorized into two subfamilies, PoHsp40A4 for Type I Hsp40, PoHsp40B6 and PoHsp40B11 for Type 11 Hsp40. Further expression analysis revealed two very different types of kinetics in response either to heat shock or to virus infection, with a marked induction for PoHsp4OA4 and a weak one for both PoHsp40B6 and PoHsp40B11. A very distinct tissue distribution of mRNA was also revealed among the three genes, even between PoHsp40B6 and PoHsp40B11. This is the first report on the transcriptional induction of Hsp40 in virally stimulated fish cells, and the differential expressions might reflect their different roles in unstressed and stressed cells. (c) 2005 Elsevier Ltd. All rights reserved.

Regulation by hetC of genes required for heterocyst differentiation and cell division in Anabaena sp strain PCC 7120

Unlike those of the wild-type strain, proheterocysts of the Anabaena sp. strain PCC 7120 hetC strain keep dividing. ftsZ, the most critical cell division gene, is up-regulated in hetC proheterocysts. Heterocyst differentiation genes hglD, hglE, patB, nijB, and xisA are no longer expressed in the hetC mutant. hetC also regulates the expression of patA, a pattern formation gene.

Research on the ultrafast fluorescence property of thylakoid membranes of the wild-type and mutant rice

A high yielding rice variety mutant (Oryza sativa L., Zhenhui 249) with low chlorophyll b (Chl b) has been discovered in natural fields. It has a quality character controlled by a pair of recessive genes (nuclear gene). The partial loss of Chl b in content affects the efficiency of light harvest in a light harvest complex (LHC), thus producing the difference of the exciting energy transfer and the efficiency of photochemistry conversion between the mutant and wild-type rice in photosynthetic unit. The efficiency of utilizing light energy is higher in the mutant than that in the wildtype rice relatively. For further discussion of the above-mentioned difference and learning about the mechanism of the increase in the photochemical efficiency of the mutant, the pico-second resolution fluorescence spectrum measurement with delay-frame-scanning single photon counting technique is adopted. Thylakoid membranes of the mutant and the wild-type rice are excited by an Ar+ laser with a pulse width of 120 ps, repetition rate of 4 MHz and wavelength of 514 nm. Compared with the time and spectrum property of exciting fluorescence, conclusions of those ultrafast dynamic experiments are: 1) The speeds of the exciting energy transferred in photo-system I are faster than that in photo-system II in both samples. 2) The speeds of the exciting energy transfer of mutant sample are faster than those of the wildtype. This might be one of the major reasons why the efficiency of photosynthesis is higher in mutant than that in the wild-type rice.