Thesis (Ph. D.)--Oregon State University, 2008. / Printout. Includes bibliographical references (leaves 104-124). Also available on the World Wide Web.

Thesis (Ph. D.)--Rutgers University, 2008. / "Graduate Program in Ecology and Evolution." Includes bibliographical references (p. 69-81).

Thesis (M.S.)--Bioengineering, Georgia Institute of Technology, 2007. / Zhu, Cheng, Committee Chair ; Selvaraj, Periasamy, Committee Member ; Orville, Allen, Committee Member ; Butera, Robert, Committee Member.

<p>  </p> <p>Cyanobacteria are among the simplest organisms to display circadian rhythms that synchronize endogenous physiological activities with a ~12-hour-light:12-hour-dark (12L:12D) cycle of the external environment. Detected by the input pathway composed of CikA and LdpA proteins, light is transduced to the central circadian oscillator encoded by the gene cluster <em>kaiABC. </em>While KaiC phosphorylation is primarily regulated by KaiA and KaiB proteins, two key components of the output pathway, RpaA and SasA proteins, mediate between KaiC phosphorylation, genome-wide expression, and control of cell division. In this study, <em>Synechococcus elongatus </em>UTEX 2973 showed similar growth patterns when subjected to white light only and white light supplemented with ultraviolet A (UV-A) radiation under 12L:12D intervals, although UV-A radiation hindered growth during light periods. Under continuous illumination, growth rates of <em>S. elongatus </em>UTEX 2973 were reduced by UV-A radiation but reflected intrinsic circadian rhythmicity. To elucidate the critical role of the circadian clock, a mutant void of <em>kaiABC</em> was generated via the CRISPR/Cpf1 system. A dysfunctional clock severely disrupted inherent growth rhythmicity, which was exacerbated by UV-A radiation. To investigate the effects of UV-A radiation on transcription patterns in <em>S. elongatus </em>UTEX 2973, expression levels of circadian genes, specifically <em>kaiABC</em>, <em>cikA</em>, <em>lpdA</em>, <em>rpaA</em>, and <em>sasA</em>, were assessed by qPCR analysis. For the UV-A-treated wild-type strain, <em>kaiA</em> and <em>kaiB</em> expression was generally downregulated, <em>kaiC</em> expression was upregulated during the second dark period, and <em>rpaA</em> expression was either upregulated or downregulated depending on the period. For the UV-A-treated Δ<em>kaiABC </em>strain, <em>lpaA</em> expression was upregulated in darkness, whereas <em>rpaA</em> and <em>sasA</em> expression was downregulated during light periods. When Δ<em>kaiABC </em>and wild-type strains were examined in the presence and absence of UV-A radiation, expression of <em>lpaA</em>, <em>rpaA</em>, and <em>sasA</em> was universally downregulated, yet <em>cikA</em> expression was upregulated in the dark. This study was the first to evaluate the impact of UV-A radiation on cyanobacterial circadian rhythms, in which UV-A radiation negatively affected cyanobacterial growth and strongly altered gene expression patterns over time. Without the circadian clock, rhythmicity of growth and transcription was demolished, such that the consequences were aggravated for the output pathway that relayed signals downstream from the central oscillator. </p>

A systematic study of a collection of Lon⁻ mutants has been made in order to determine whether their pleiotropic phenotype is due to mutations affecting one or more genes. A fine structure map of the lon locus was constructed by Pl mediated generalized transduction. The lon⁻ mutations were found to map in two "clusters" within the region. Phenotypic characterization of a set of isogenic Lon⁻ strains derived from these experiments indicated that all Lon-associated phenotypes (e.g. sensitivity to UV irradiation, decreased ability to inherit plasmid and prophage, abnormal polypeptide degradation and regulation of capsular polysaccharide biosynthesis) are differentially expressed in Lon⁻ strains. A direct correlation exists between the intracistronic ordering of the lon⁻ alleles and the degree of expression the Lon⁻ phenotypes in each strain. All isogenic Lon⁻ strains exhibit conditional lethality upon a nutritional shift-up. However, some filamenting Lon⁻ mutants are not able to overcome this defect when exposed to growth conditions known to promote cell division in Lon⁻ strains. Evidence was obtained that suggest a role for nucleotide pools in the control of cell division and capsular polysaccharide production. Reversion studies indicated that all lon⁻ mutations studied are point mutations. The failure to generate deletions of the lon region in χ573, an F' strain carrying the lac to minE region on the plasmid, and the inability to cure F' strains carrying a lon⁻ mutation on the plasmid suggest that the lon gene product may be indispensable for the cell's survival. From transductional crosses, two intermediate phenotypic classes: UV-resistant, mucoid (UV^RMuc), (Class A) and UV-sensitive, nonmucoid (UV^SRou) (Class B), were obtained that did not segregate colonies of the opposite morphology. Genetic analysis of these strains by back-transduction into a proC⁻ lon⁺ background, indicated that complete genetic separation of all Lon-associated phenotypes tested was not achieved, although differences in the expression of some of these persisted. Data obtained from complementation analysis ruled out the presence of two genes at the lon locus. The patterns of complementation observed were compatible with the existence of one lon gene, having at least two distinct domains, and whose product is a multifunctional polypeptide. / Ph. D.

A Mata Atlântica brasileira é apontada como um dos mais importantes refúgios da biodiversidade em todo o planeta. Este bioma é extremamente importante sob o aspecto da riqueza de espécies vegetais e animais na sua composição e interações, porém ainda pouco conhecido e explorado sob o ponto de vista microbiológico. Um grama de solo pode conter cerca de 10 bilhões de micro-organismos de diferentes espécies. A maioria dos micro-organismos presentes nos solos não é de fácil cultivo em laboratório (somente 0.1-10% são recuperados), sendo necessária à utilização de novas técnicas para superar este problema. Muitos micro-organismos presentes no solo tem grande importância biotecnológica por produzirem compostos bioativos. O filo Actinobacteria é abundante em solos e de grande importância econômica, tendo em vista que a maioria dos antibióticos comercializados é produzido por membros deste grupo. Porém a biodiversidade microbiana da Mata Atlântica, bem como, o seu potencial biotecnológico não tem sido plenamente estudado. Poucos trabalhos mostram produtos do metabolismo microbiano com potencial em uso em indústrias e mostram menos ainda antimicrobianos produzidos por isolados bacterianos desta região. Dentro deste contexto, o presente trabalho buscou em duas alternativas metodológicas como a técnica independente de cultivo, o metagenoma, verificar a presença de genes de uma importante via biossintética os policetídeos sintases e com a técnica dependente de cultivo, selecionar prováveis bactérias produtoras de composto bioativos. O metagenoma propõe fazer uma análise do DNA total de amostras do solo, visando conhecer a informação gênica destes compostos na complexa diversidade microbiana. Desta forma, várias abordagens foram empregadas para conseguir um DNA de alto peso molecular e de qualidade suficiente para construir bibliotecas metagenômicas, e procurar nestas, genes das vias de sínteses dos policetídeos (PKS) tipo I e tipo II, que ficam agrupados em clusters que variam de tamanho entre 20 a 100 kb. Otimizamos um método de extração de DNA do solo e conseguimos obter um DNA de aproximadamente 50kb, que foi amplificado por PCR utilizando primers para regiões conservadas dos genes policetídeos sintases tipo I e II (acetosintase ) de Actinomicetos. Os fragmentos obtidos, PKS I e PKS II, com tamanho entre 600pb a 700pb, foram clonados, construído-se duas bibliotecas metagenômicas (KSI e KS II). Os clones foram sequênciados e analisados em uma árvore filogenética. A análise filogenética de genes policetídeos tipo I demonstrou similaridade com estes genes de diversas divisões de bactérias, revelando a presença de prováveis genes novos não apenas relacionados a via de PKSI, como também aos genes de PKSI híbridos com peptídeos não ribossomais. Em complemento a filogenia de policetídeos tipo II apresentou uma similaridade com genes de Actinobacteria, formando um grupo que também está relacionados a presença de prováveis genes novos de importantes famílias de antibióticos. Através do cultivo utilizando meio seletivo para o crescimento de bactérias não cultivadas, foi possível isolar sete bactérias que possuem atividade antibacteriana e/ou antifúngica. / The Brazilian Atlantic Forest is considered as one of the most important reservoir of biodiversity in the planet. This biome is extremely important for its richness of plant and animal species but although with their composition and interactions poorly known and unexplored from a microbiological perspective. One gram of soil can contain near 10 billion microorganisms of different species. The majority of the soil microorganisms is not cultivable in laboratory (only 0.1-10% are recovered), being necessary to use new techniques to overcome this problem. Many of the soil microorganisms are biotechnologically important for the production of bioactive compounds. The Actinobacteria phylum is abundant in soil and important economically due to the capacity of synthesize many antibiotics. Nevertheless, the Atlantic Forest microbial biodiversity has not been properly study. Few works show microbial metabolic products with potential use in industries and, still less, antimicrobials isolated from this biome. The present work searched two new methodological alternatives: one culture independent, the metagenome, to verify the presence of polyketide synthases biosynthetic genes; and the second, the culture dependent, to select potential bacteria producers of bioactive compounds. The metagenome intend the total DNA analysis of a sample, focusing in to know the genetic information of the complex microbial diversity. Several approaches were used in order to obtain DNA of high molecular weight and quality toconstruct metagenomic libraries and search for polyketide synthases (PKS) genes types I and II, that usually are organized in clusters of 30 to 100 kb. A DNA extraction method was optimized obtaining DNA of approximately 50 kb, and used for the detection of PKS gens by PCR approaches using primers based in polyketide synthases type I and II (ketosynthase ) conserved regions of Actinomycetes. The PKS I and PKSII amplicons (600-700 bp) were cloned and two metagenoic libraries were obtained (KS I and KS II). The clones were sequenced and analyzed in a phylogenetic tree. Phylogenetic analysis of PKS I genes reveled high similarities with genes of several divisions of bacterias pointing the presence of provable new genes related with the synthesis of polyketides produzrd by PKS I and hybrid PKS with non ribosomal peptides (NRPs). Polyketide type I genes showed similarity with Streptomyces and uncultered bacteria. The analysis of polyketide II genes showed high similarity with genes of Actinobacteria gruped in two main groups, one of them with possible new genes related with the production of important antibiotics. Using selective medium for uncultered bacteria, seven isolates were obtained being studied taxonomically and tested for the production of secondary metabolites with antibacterial and antifungal activities.

Caulobacter crescentus sobrevive em baixas temperaturas e mostrou ser um organismo psicrotolerante e de alta resistência ao congelamento, característica resultante de múltiplos fatores. C. crescentus possui quatro genes codificantes para CSPs, sendo cspA e cspB induzidos em baixas temperaturas e cspB, cspC e cspD em fase estacionária. A ausência de cspA e cspB ou cspA e cspC confere grande deficiência de crescimento em baixas temperaturas. cspA e cspB não são autorregulados e são regulados pós-transcricionalmente via estabilização de seu mRNA e traducionalmente após o choque-frio. A expressão de cspB é influênciada por CspC a 30 graus e durante o choque-frio, e por CspC, SpdR e SpoT durante a fase estacionária. A ausência de CspC ou CspC e CspD compromete a adaptação à fase estacionária promovendo alterações morfológicas. Nenhuma das CSPs de C. crescentus é capaz de reverter o fenótipo de E. coli BX04 por expressão heteróloga, embora todas possuam atividade antiterminadora que, nestas proteínas, não depende dos mesmos aminoácidos que CspE de E. coli. / Characterization of Caulobacter crescentus cold response was performed. This bacterium showed to be psicrotolerant and have remarkable freezing resistance, which may be a result of multiple traits. C. crescentus has four CSP encoding genes, being cspA and cspB cold-induced and cspB, cspC and cspD stationary phase-induced. The absence of cspA and cspB or cspA and cspC led to growth deficiency under low temperature incubation. cspA and cspB are not self-regulated and are post-transcriptionally and translationally regulated during cold-shock. The cspB gene expression is affected by CspC at exponential growth phase and by CspC, SpdR and SpoT at stationary phase. The absence of CspC, or CspC and CspD, affects stationary phase fitness of this organism, also promoting morphological alterations. None of the C. crescentus CSPs were able to restore the phenotype of E. coli BX04 strain by heterologous expression. Although all of them have shown to be transcription antiterminators, this ability is not dependent on the same critical aminoacids displayed by CspE from E. coli.

Alper e colaboradores demonstraram que a linhagem BY4741 recombinante portadora de cópias adicionais de um alelo SPT15 mutagenizado em três diferentes posições (spt15-300) utiliza mais rapidamente a glicose e aumenta a produção de etanol. Neste trabalho, foi realizada a clonagem deste alelo, aqui chamado spt15*. Inicialmente o DNA genômico da linhagem S. cerevisiae S288C foi utilizado como molde para amplificação por SOEing-PCR. O alelo spt15* foi clonado no plasmídeo pGEMT-Easy e, em seguida, introduzido no plasmídeo epissomal pMA91. Após construções moleculares, foi obtido o fragmento de DNA dpPGKspt15*tPGKd, empregado na transformação genética, da linhagem S. cerevisiae YPH252, por d-integração. Os clones recombinantes YHP252/pMA91spt15* e YHP252/dpPGKspt15*tPGKd consomem mais eficientemente a glicose e aumentam a produção de etanol. O seqüenciamento do alelo SPT15 da levedura industrial PE-2 revelou 100% de identidade com o alelo das linhagens BY4741 e S288C, criando ótimas perspectivas para trabalhos futuros. / Alper and colleagues demonstrated that the yeast S. cerevisiae BY4741 recombinant strain carrying additional copies of a SPT15 allele mutagenized in three different positions (spt15-300) uses glucose more speedily and produces more ethanol. In this work, this allele, here called spt15*, was cloned. The genomic DNA of the S. cerevisiae S288C strain was used for amplification through SOEing-PCR. The spt15* allele was cloned in the plasmid pGEMT-Easy and introduced in the episomal plasmid pMA91. After molecular constructions the DNA dpPGKspt15*tPGKd fragment was obtained to be employed in the genetic transformation of laboratory S. cerevisiae strains using d-integration. Both recombinant clones YHP252/pMA91spt15* and YHP252/dpPGKspt15*tPGKd consume glucose more speedily and produce more ethanol. The sequencing of the SPT15 allele of the industrial yeast PE-2 revealed 100% identity with BY4741 and S288C alleles, creating huge perspectives for future works.

A major factor in the ability of Pseudomonas fluorescens Pf-5 to act as a biological control agent is its production of antibiotics, including pyoluteorin (PLT), 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin (PRN). The data provided in this thesis demonstrate that the presence of any of these antibiotics in the extracellular milieu affects production of that same antibiotic, as well as others, by Pf-5. Amending the growth medium with antibiotics had multiple effects on secondary metabolism in Pf-5. i) PLT positively regulated its own production, ii) 2,4-DAPG positively regulated its own production. iii) PLT suppressed 2,4-DAPG production. iv) 2,4- DAPG inhibited PLT production. v) PLT suppressed transcription of a heterologous ferric-pyoverdine uptake gene. vi) PRN exerted a slight inhibitory effect on PLT gene transcription and production. PLT autoinduction by Pf-5 was extensively characterized, and was shown to require concentrations of exogenous PLT in the nanomolar range. These low concentrations are comparable to those of many molecules proposed to function in signaling roles. PLT served as a signal between distinct populations of cells within the rhizosphere, where it prompted autoinduction by those cells. Aside from effects of Pf- 5 antibiotics on one another, I also described the positive effect of exogenous PLT on expression of a set of transport genes flanking the PLT biosynthetic gene cluster. Sequence data and experimental evidence suggests that these genes encode a transport apparatus for PLT. The deduced amino acid sequences for four adjacent open reading frames together resemble Type I secretion apparatuses, which typically function in transport of proteins rather than secondary metabolites. The intact transporter genes are necessary for optimal PLT production. Taken together, the data from the studies described herein demonstrate that i) the production of PLT by Pf-5 can affect the production of PLT by neighboring cells, and ii) PLT and other exogenous secondary metabolites have both autoregulatory and cross-regulatory effects in culture. Because Pf-5 derivatives engaged in PLT crossfeeding in the rhizosphere, it is likely that cross-feeding occurs for other secondary metabolites as well. Thus, production of an antibiotic by one cell can profoundly affect secondary metabolism in neighboring cells occupying natural habitats. / Graduation date: 2004

CD16 is a physiologically essential Fc and #947; receptor III as either a single- pass transmembrane protein (CD16A) or as a glycosylated phosphatidylinositol (GPI) anchored protein (CD16B) on the surface of immune cells that have been implicated in many autoimmune and immune complex-mediated diseases. Its functions include binding and clearing antibody (IgG) coated foreign pathogens, receptor-mediated phagocytosis, and triggering antibody dependent cellular cytotoxicity. It is well established that these functions depend on protein-protein interaction between CD16 and the Fc domain of IgG. However, the molecular details of CD16-IgG interactions are less well defined, but are essential to developing therapeutic compounds to treat many autoimmune and IC diseases. Stable mammalian cell lines expressing wild-type CD16 isoforms and site-specific mutants, including extracellular soluble fragments of CD16 have been established. Soluble forms of wild type CD16A and these CD16 mutants were expressed in a bacterial pathway in order to amass sufficient quantities for x-ray crystallographic studies. The soluble portions of wild-type CD16A and several site-specific CD16A and CD16B mutants were constructed by PCR amplification and ligation with a pET vector. The proteins were expressed in a prokaryotic pathway, BL21 AI, for 8-10 hours and lysed to obtain inclusion bodies. A hand-held sonicator was used to wash the inclusion bodies, while a Urea solution separated and dissolved the proteins. The target proteins were then refolded by rapid dilution, concentrated with a stir cell, and purified. Wild type sCD16A and four site specific mutants were constructed with good sequencing, while wild type sCD16A, sCD16A F176V, and sCD16A G147D were expressed and refolded to optimal levels. X-ray crystallographic data has been collected from sCD16A F176V as a result of these studies and crystals are currently being grown from wild type sCD16A and sCD16A G147D.